- A_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- A_DIPLOID_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- AboutBox - Class in net.maizegenetics.tassel
-
- AboutBox(parent) - Constructor for class net.maizegenetics.tassel.AboutBox
-
- absoluteDistance(mat) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
compute absolute distance to second distance matrix
- ABSTOL - Variable in interface net.maizegenetics.taxa.tree.BranchLimits
-
maximum tolerated error when determining branch lengths
- AbstractAdditiveSite - Class in net.maizegenetics.analysis.modelfitter
-
This class holds data for a variant site to provide an object to hold data used and returned by a stepwise model fitter. That makes it convenient to use in a parallel stream for processing.
- AbstractAdditiveSite(site, chromosomeName, pos, id, selectionCriterion) - Constructor for class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- AbstractAvailableListModel - Class in net.maizegenetics.gui
-
- AbstractAvailableListModel(realSize) - Constructor for class net.maizegenetics.gui.AbstractAvailableListModel
-
- AbstractByte2D - Class in net.maizegenetics.dna.snp.byte2d
-
- AbstractByte2D(scoreType, numTaxa, numSites) - Constructor for class net.maizegenetics.dna.snp.byte2d.AbstractByte2D
-
- AbstractDisplayPlugin - Class in net.maizegenetics.analysis.chart
-
This plugin abstract plugin provides mechanisms for setting a savefile and for saving a variety of images. This would be useful to plugin that create images and may want to automatically send them to a file.
- AbstractDisplayPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- AbstractDisplayPlugin.Outformat - Enum in net.maizegenetics.analysis.chart
-
- AbstractFixedEffectLM - Class in net.maizegenetics.analysis.association
-
- AbstractFixedEffectLM(dataset, parentPlugin) - Constructor for class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- AbstractForwardRegression - Class in net.maizegenetics.analysis.modelfitter
-
- AbstractForwardRegression(data) - Constructor for class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- AbstractForwardRegression(serialFilename, pheno) - Constructor for class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- AbstractGenotypeTableMask - Class in net.maizegenetics.gui
-
- AbstractGenotypeTableMask(align, name, color, type) - Constructor for class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- AbstractMaskMatrix - Class in net.maizegenetics.dna.snp
-
- AbstractPETags - Class in net.maizegenetics.dna.tag
-
Basic methods for working with PE Tags, including sorting and search.
- AbstractPETagsOnPhysicalMap - Class in net.maizegenetics.dna.map
-
Basic method of working with alignment of PE tags
- AbstractPETagsOnPhysicalMap.PETagType - Enum in net.maizegenetics.dna.map
-
- AbstractPlugin - Class in net.maizegenetics.plugindef
-
- AbstractPlugin() - Constructor for class net.maizegenetics.plugindef.AbstractPlugin
-
Creates a new instance of AbstractPlugin
- AbstractPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.plugindef.AbstractPlugin
-
Creates a new instance of AbstractPlugin
- AbstractPluginAction - Class in net.maizegenetics.plugindef
-
- AbstractPluginAction(plugin, name, icon) - Constructor for class net.maizegenetics.plugindef.AbstractPluginAction
-
Creates a new instance of AbstractPluginAction
- AbstractTableReport - Class in net.maizegenetics.util
-
- AbstractTag - Class in net.maizegenetics.dna.tag
-
Created by edbuckler on 7/26/14.
- AbstractTag(length, reference, name) - Constructor for class net.maizegenetics.dna.tag.AbstractTag
-
- AbstractTags - Class in net.maizegenetics.dna.tag
-
Basic methods for working with Tags, including sorting and search.
- AbstractTagsByTaxa - Class in net.maizegenetics.dna.tag
-
Basic method implementation of Tags by Taxa, including methods for reading and writing files
- AbstractTagsHDF5 - Class in net.maizegenetics.dna.tag
-
Basic implementations of HDF5 tags. This is designed to annotate tags with a bunch of attributes, to solve the memory issues
- AbstractTagsOnPhysicalMap - Class in net.maizegenetics.dna.map
-
Abstract TagsOnPhysicalMap object. Abstract alignment is implemented by two types of TOPM classes
class TagsOnPhysicalMap and
class TagsOnPhysMapHDF5. TagsOnPhysicalMap is fully loaded into memory when read, and it can only support one mapping position (the files are either binary or text). TagsOnPhysMapHDF5 can support a large number of mapping position, and only a portion of the data is loaded into memory. In most cases, TagsOnPhysMapHDF5 should be preferred going forward.
- AbstractTagsOnPhysicalMap() - Constructor for class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- accept(f) - Method in class net.maizegenetics.util.BasicFileFilter
-
- acceptsValue(value) - Method in class net.maizegenetics.plugindef.PluginParameter
-
- acceptsValue(input) - Method in class net.maizegenetics.plugindef.PluginParameter
-
- accumulator() - Method in class net.maizegenetics.dna.map.PositionList.PositionListCollector
-
- accumulator() - Method in class net.maizegenetics.taxa.TaxaList.TaxaListCollector
-
- accumulator() - Method in class net.maizegenetics.util.BitSet.BitSetListCollector
-
- actionPerformed(e) - Method in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- actionPerformed(e) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataDialog
-
- actionPerformed(e) - Method in class net.maizegenetics.gui.PrintHeapAction
-
- actionPerformed(e) - Method in class net.maizegenetics.tassel.AboutBox
-
- actionPerformed(e) - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- add(e) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- add(index, element) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- add(e) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- add(index, element) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- add(hap) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- add(data, c) - Method in class net.maizegenetics.analysis.gbs.neobio.Trie
-
Adds a new child to this node. The new node will be implicitly instantiated with the data argument, and the edge from this node to the new node will be labelled by the character argument. If this node already have an edge labelled with this character, an exception is raised. Otherwise, the new node created and returned.
- add(element) - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
Adds element to the PositionList.
- add(e) - Method in class net.maizegenetics.dna.snp.FilterList
-
- add(index, element) - Method in class net.maizegenetics.dna.snp.FilterList
-
- add(index) - Method in class net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
-
- add(taxon) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- add(taxon) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- add(shortForm, longForm) - Method in class net.maizegenetics.util.ArgsEngine
-
Configures the engine by adding options.
- add(shortForm, longForm, valued) - Method in class net.maizegenetics.util.ArgsEngine
-
Configures the engine by adding options.
- add(row) - Method in class net.maizegenetics.util.TableReportBuilder
-
- add(e) - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- addAlignment(topm) - Method in class net.maizegenetics.dna.map.TagGWASMap
-
- addAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- addAll(index, c) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- addAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- addAll(index, c) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- addAll(cluster) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
This function does not prevent Haplotypes from being duplicated. To avoid duplicates use addAllUnique.
- addAll(collection) - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
Adds each element of elements to the PositionList.
- addAll(builder) - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
- addAll(c) - Method in class net.maizegenetics.dna.snp.FilterList
-
- addAll(index, c) - Method in class net.maizegenetics.dna.snp.FilterList
-
- addAll(taxa) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addAll(a) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addAll(taxa) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addAll(taxa) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addAll(taxa) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addAll(builder) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addAll(c) - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- addAllBarcodes(barcodes) - Method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
Add a collection of barcodes to the trie.
- addAllBarcodesNoOverhang(barcodes) - Method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
Add a collection of barcodes with OUT overhangs to the trie.
- addAlleleProbability(alleleProbabilityBuilder) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addAllUnique(cluster) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
Adds Haplotypes from cluster that are not already contained in this cluster
- addAnno(key, value) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Add non-standard annotation, boolean and String are converted to String with toString, Number are stored as Number
- addAnno(keyValue) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Add non-standard annotation with key-value separated by '='
- addAnno(key, value) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Add non-standard annotation
- addAnno(key, value) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Add non-standard annotation
- addAnnotation(key, value) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- addAnnotation(key, value) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addAnnotation(key, value) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addAnnotation(key, value) - Method in class net.maizegenetics.util.GeneralAnnotationStorage.Builder
-
- addAnnotation(key, value) - Method in class net.maizegenetics.util.GeneralAnnotationStorage.Builder
-
- addAnnotations(existing) - Method in class net.maizegenetics.util.GeneralAnnotationStorage.Builder
-
- addBarcode(barcode) - Method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
Adds a Barcode to the trie
- addBarcodeNoOverhang(barcode) - Method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
Adds a Barcode to the trie
- addByteDepths(depth1, depth2) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
Returns the depth combined depths in byte format. Converts both to integers, adds, and reconverts back.
- addChild(c) - Method in interface net.maizegenetics.taxa.tree.Node
-
add new child node
- addChild(n) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
add new child node
- addDataSet(theDataSet, defaultNode) - Method in class net.maizegenetics.tassel.DataTreePanel
-
- addDataSet(theDataSet, defaultNode) - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- addDatum(dataParent, theDatum) - Method in class net.maizegenetics.tassel.DataTreePanel
-
- addDatum(theDatum) - Method in class net.maizegenetics.tassel.DataTreePanel
-
- AddDistanceMatrixPlugin - Class in net.maizegenetics.analysis.distance
-
- AddDistanceMatrixPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
-
- addDistribution(label, theSP, poolMinor) - Method in class net.maizegenetics.analysis.popgen.PolymorphismDistribution
-
- AddDomPermutationTestSpliterator - Class in net.maizegenetics.analysis.modelfitter
-
This class calculates p-values for a test of a single SNP with a list of permuted data sets. myPermutedData is a list of double[] arrays, each of which is a data set to be tested. This class extends a parent class which tests an additive only model to test an additive + dominance model instead.
- AddDomPermutationTestSpliterator(permutedData, siteList, baseModel) - Constructor for class net.maizegenetics.analysis.modelfitter.AddDomPermutationTestSpliterator
-
- addDosage(dosageBuilder) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addEdge(u, v) - Method in class net.maizegenetics.util.GraphBuilder
-
Adds an edge to the graph with weight 1.
- addEdge(u, v, wt) - Method in class net.maizegenetics.util.GraphBuilder
-
Adds an edge to the graph
- addEffect(me) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- addElements(rowElements) - Method in class net.maizegenetics.util.TableReportBuilder
-
- addEndelmanDistance(matrices, listener) - Static method in class net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
-
- addFactors(factors) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- addFactors(names) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- addFactors(factors) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- addFactors(names) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- addFeature(feature) - Method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Adds a GenomeFeature to the map. If the feature's unique ID has already been loaded, it throws an UnsupportedOperationException
- addFeatureToRangemap(masterMap, feature) - Static method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Add a GenomeFeature to a RangeMap, stacking it on top of any existing features instead of overwriting them (how RangeMap behaves natively)
- addForkFlagsIfNeeded(args) - Static method in class net.maizegenetics.pipeline.TasselPipeline
-
- addFromFlatFile(filename) - Method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Load in data from a flat, tab-delimited text file. The first row should be a header identifying what attribute is in each column, and each subsequent row should correspond to a single feature. Columns that don't apply to a given feature should use "NA" or left empty. Common attributes (columns) are listed below. Although only the "id" attribute is required, a feature is pretty useless without some sort of positional information (chromosome, start/stop, etc.). "id": Unique identifier for this feature. Repeated identifiers throw an error (Also accepts "name".) Required. "chrom": Which chromosome it occurs on (Also accepts "chr" or "chromosome") "start": Start position on the chromosome "stop": Stop position on the chromosome (Also accepts "end") "position": Postion on chromosome (in place of "start" and "stop" for features that are a single nucleotide) "parent_id": What other named feature this descends from (eg, Gene -> Transcript -> Exon). If none given, this will default to the chromosome (or the genome if chromosome isn't supplied) This method does not build the map, so you can string multiple calls together (if, for example, you have different annotations in different files).
- addFromGffFile(filename) - Method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Load in data from a GFF (Gene Feature Format) file. Since GFF files have only a loose standard for the 9th column, this involves several ad-hoc heuristics about what things to look for. As such, it is not the preferred way to read in annotations. (That is JSON or tab-delimited format.) This method does not build the map, so you can string multiple calls together (if, for example, you have different annotations in different files)
- addFromJsonFile(filename) - Method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Load in data from a JSON-formatted file. JSON format is defined at http://www.json.org/, and consists of structured key-value pairs. For genome features, the key is the name of an attribute and the value is (obviously) its value. (For example: "chromosome":1). Note that if you have more than one feature per file (the normal case), all but the last closing brace ('}') should be followed by a comma, and the whole group should be within square braces ('[...]' That is, the first character of the file should be '[' and the last should be ']'). This makes it a properly-formatted JSON array. Common attributes (keys) are listed below. Although only the "id" attribute is required, a feature is pretty useless without some sort of positional information (chromosome, start/stop, etc.). "id": Unique identifier for this feature. Repeated identifiers throw an error. (Also accepts "name".) Required. "chrom": Which chromosome it occurs on (Also accepts "chr" or "chromosome") "start": Start position on the chromosome "stop": Stop position on the chromosome (Also accepts "end") "position": Postion on chromosome (in place of "start" and "stop" for features that are a single nucleotide) "parent_id": What other named feature this descends from (eg, Gene -> Transcript -> Exon). If none given, this will default to the chromosome (or the genome if chromosome isn't supplied) This method does not build the map, so you can string multiple calls together (if, for example, you have different annotations in different files).
- addGCTADistance(matrices, listener) - Static method in class net.maizegenetics.analysis.distance.GCTADistanceMatrix
-
- addGzSuffixIfNeeded(filename, suffix) - Static method in class net.maizegenetics.util.Utils
-
- addHaplotypesToReport(clusters, pos) - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- addIncludedTraits(traitsToInclude) - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- additionTaxaFile() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- additionTaxaFile(value) - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- AdditiveModelForwardRegression - Class in net.maizegenetics.analysis.modelfitter
-
- AdditiveModelForwardRegression(data, maxThreads) - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveModelForwardRegression
-
- AdditiveModelForwardRegression(serialFilename, pheno, maxThreads) - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveModelForwardRegression
-
- AdditiveModelForwardRegression(data) - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveModelForwardRegression
-
- AdditiveModelForwardRegression(serialFilename, pheno) - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveModelForwardRegression
-
- additiveOnlyModel() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
Should an additive only model be fit? If true, an additive model will be fit. If false, an additive + dominance model will be fit. Default = false.
- additiveOnlyModel(value) - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
Set Additive Only Model. Should an additive only model be fit? If true, an additive model will be fit. If false, an additive + dominance model will be fit. Default = false.
- AdditiveResidualForwardRegression - Class in net.maizegenetics.analysis.modelfitter
-
- AdditiveResidualForwardRegression(data) - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveResidualForwardRegression
-
- AdditiveSite - Interface in net.maizegenetics.analysis.modelfitter
-
- AdditiveSite.CRITERION - Enum in net.maizegenetics.analysis.modelfitter
-
- AdditiveSiteStorePlugin - Class in net.maizegenetics.analysis.modelfitter
-
- AdditiveSiteStorePlugin() - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- AdditiveSiteStorePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- addListener(listener) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
Adds listener to this plugin.
- addListener(listener) - Method in interface net.maizegenetics.plugindef.Plugin
-
Adds listener to this plugin.
- addMappingApproach(name) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Adds a mapping approach strategy to the mappingApproach table
- addMappingApproach(name) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- addMonetdbVariantData(ref, altsOrig, mline, isVCF, tabPos) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- addNode(n) - Method in class net.maizegenetics.util.GraphBuilder
-
Adds a single node
- addOrMerge(taxon) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- addOrReplaceFeature(feature) - Method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Adds a GenomeFeature to the map, regardless of whether or not it's already been added. This method throws no warnings if you'll overwrite existing data, so use it with caution.
- addPipelineSegment(plugins) - Method in class net.maizegenetics.progress.ProgressPanel
-
- addPlugin(plugin, description) - Method in class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- addPlugin(plugin) - Method in class net.maizegenetics.progress.ProgressPanel
-
- addPlugin(plugin, cancelButton, cancelPlugin) - Method in class net.maizegenetics.progress.ProgressPanel
-
- AddPlusDomModelEffect - Class in net.maizegenetics.analysis.modelfitter
-
A ModelEffect that takes an AdditiveSite as an argument and uses the additiveCovariate from that object to compute a covariate representing dominance. In general, the AdditiveSite will be supplied as the id, although that is not a requirement. The dominance values are calculated as 1 - abs(x - 1) where x is the addivitive value. The values of x are expected to be 0, 1, 2, where 0 and 1 are homozygous genotypes and 1 is the het.
- AddPlusDomModelEffect(id, addSite) - Constructor for class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- AddPlusDomModelEffect(id, additiveCovariate) - Constructor for class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- addPosToTagMapPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- addReadCount(tag, length, count) - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- addReadCount(tag, length, count) - Method in class net.maizegenetics.dna.tag.UTagCountMutable
-
- addReadCounts(tagCountsToAdd) - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
This adds a series of TagCounts to the list, preserving the count that each read has. Designed to make it easy to combine TagCounts from multiple barcodes, lanes or flowcells.
- addReadCounts(tagsToAdd, defaultCount) - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- addReadsToTagTaxon(tagIndex, taxaIndex, addValue) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- addReadsToTagTaxon(tagIndex, taxaIndex, addValue) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Method for incrementing the read depth for the specified tag and taxon.
- AddReferenceAlleleToHDF5Plugin - Class in net.maizegenetics.analysis.data
-
- AddReferenceAlleleToHDF5Plugin() - Constructor for class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- AddReferenceAlleleToHDF5Plugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- addReferenceGenome(refGenome) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Adds a mapping approach strategy to the mappingApproach table
- addReferenceGenome(name) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- addReferenceProbability(referenceProbabilityBuilder) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- AddReferenceToGenotypePlugin - Class in net.maizegenetics.analysis.data
-
- AddReferenceToGenotypePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
- addRefTag(refTag, nLongsPerTag, nullTag) - Method in class net.maizegenetics.dna.map.TagLocus
-
- addSibling(data, c) - Method in class net.maizegenetics.analysis.gbs.neobio.Trie
-
Adds a sibling to this node. The new node will be implicitly instantiated with the data argument, and the edge from this node to the new node will be labelled by the character argument. If this node already have a sibling with this character, an exception is raised. Otherwise, the new node is created and returned.
- addSite(pos, genos) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addSiteBlock(startSite, blkPositionList, blockGenotypes, blockDepths) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Add TasselHDF5 Block of positions (generally 1<<16 positions). @note This is synchronized, which certainly slows things down but it is needed to prevent the same taxa dataset from being accessed at once. This can probably be rethought with parallelization at this stage across datasets
- addSmallValue() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
Add Small Value
- addSmallValue(value) - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
Set Add Small Value. Add Small Value
- addSmallValue() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Add Small Value
- addSmallValue(value) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Set Add Small Value. Add Small Value
- addSuffixIfNeeded(filename, suffix) - Static method in class net.maizegenetics.util.Utils
-
Adds suffix (i.e. .txt) to end of filename if it's not already there.
- addSuffixIfNeeded(filename, defaultSuffix, possible) - Static method in class net.maizegenetics.util.Utils
-
Adds default suffix if not already one of the possible suffixes.
- addTag(tagTOPMIndex, theTOPM, theTBT, includeRefGenome, fuzzyStartPositions) - Method in class net.maizegenetics.dna.map.TagLocus
-
- addTaxa(addTaxaNames) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Add taxa to the TagsByTaxa matrix, they will all be set to distribution value of zero.
- addTaxa(addTaxaNames) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- addTaxa(addTaxaNames) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- addTaxa(addTaxaNames) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- addTaxa(addTaxaNames) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- addTaxa(addTaxaNames) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- addTaxa(addTaxaNames) - Method in class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- addTaxon(taxon, values) - Method in class net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
-
Add taxon and set values for all sites for that taxon.
- addTaxon(taxon, genos) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addTaxon(taxon, genos, depth) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addTaxon(taxon, depths, genos) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- addTaxon(taxon, breakPoints) - Method in class net.maizegenetics.dna.snp.ProjectionBuilder
-
- addTaxon(taxon, breakPoints) - Method in class net.maizegenetics.dna.snp.ProjectionBuilder
-
- addTaxon(taxon, breakPoints) - Method in class net.maizegenetics.dna.snp.ProjectionBuilder
-
- addTaxon(taxon, values, type) - Method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
- addTaxon(taxon, values) - Method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
- addTaxon(taxon, values, type) - Method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- addTaxon(taxon, values, type) - Method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- addTaxon(taxon, values) - Method in class net.maizegenetics.dna.snp.score.DosageBuilder
-
- addTaxon(taxon, depths) - Method in class net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder
-
Add taxon and set values for all sites and alleles for that taxon. First dimension of depths is number of alleles (6 for Nucleotide) and second dimension is sites.
- addTaxon(taxon, depths) - Method in class net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder
-
Add taxon and set values for all sites and alleles for that taxon. First dimension of depths is number of alleles (6 for Nucleotide) and second dimension is sites.
- addTaxon(taxon, values) - Method in class net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
-
- addTaxon(taxonName, values) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- addTaxon(taxonName) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- addTaxon(taxon) - Method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- addTaxon(h5w, taxon) - Static method in class net.maizegenetics.util.HDF5Utils
-
Adds a taxon to the taxon module
- addToAnovaReport(intervalList) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- addToMarkerEffectReport(CI) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
-
- addToMarkerEffectReport(CI) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- addToReadCountForTaxa(readIndex, taxaIndex, addValue) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- addToStepsReport(siteNumber, theModel, action, siteSSdf, errorSSdf, F, p) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- addTypeChangeMap(typeMap) - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- addVariant(site, p, iteration, step) - Method in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- addVariant(tagIndex, offset, base) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- addVariant(tagIndex, offset, base) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- addVariant(tagIndex, offset, base) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- addVariant(tagIndex, offset, base) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Adds Variant definition.
- adjustCoordinates(cigarString, startCoordinate) - Static method in class net.maizegenetics.dna.tag.SAMUtils
-
Uses a CIGAR code and the start coordinate of a BWA alignment to find the corresponding end coordinate. Adjusts start coordinate if beginning of alignment was soft clipped.
- adjustedProbability - Variable in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- adjustmentMatrix - Variable in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- AdjustPhasingPlugin - Class in net.maizegenetics.analysis.data
-
- AdjustPhasingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
- adjustPosition(position) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- adjustPositionToCenter() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- adjustPositionToSite(site) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- advanceToTagDist(tag) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- AGPMap - Class in net.maizegenetics.analysis.imputation
-
- AGPMap() - Constructor for class net.maizegenetics.analysis.imputation.AGPMap
-
- AGPMap(mapfile) - Constructor for class net.maizegenetics.analysis.imputation.AGPMap
-
- AGPMap(mapfile, useAgpV2) - Constructor for class net.maizegenetics.analysis.imputation.AGPMap
-
- aic(RSS, N, modelDf) - Static method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- AIC(l, k) - Static method in class net.maizegenetics.stats.statistics.PenalizedLikelihood
-
Akaike (AIC) correction (Akaike 1974)
- AICC(l, k, n) - Static method in class net.maizegenetics.stats.statistics.PenalizedLikelihood
-
Second-order Akaike (AICC) correction (Hurvich and Tsai 1989)
- algorithmVariation() - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
Algorithm Variation
- algorithmVariation(value) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
Set Algorithm Variation. Algorithm Variation
- alignment - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Stores the product of the last pairwise alignment performed. It contains a string representation of a highest scoring alignment between the two sequences and its score. It is set after a successful execution of the computePairwiseAlignment method that subclasses must implement. It is set to null if new sequences are loaded or a new scoring scheme is set.
- ALIGNMENT_RETAIN_RARE_ALLELES - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- ALIGNMENT_RETAIN_RARE_ALLELES_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- ALIGNMENT_TOP - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- AlignmentBlock - Class in net.maizegenetics.analysis.gbs.neobio
-
This class is used by the
class CrochemoreLandauZivUkelson algorithm to store the information of an alignment block. All fields are public (but final) in order to simplify the access to the data.
- AlignmentBlock(factor1, factor2) - Constructor for class net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
-
Creates a new root block. A root block does not have source_path and ancestor arrays. Moreover, its dist_column and output_border arrays are set to zero, and the direction array is set to contain an STOP_DIRECTION.
- AlignmentBlock(factor1, factor2, size) - Constructor for class net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
-
Creates a new alignment block, with all arrays created with the specified size.
- AlignmentInfo - Class in net.maizegenetics.analysis.gbs.repgen
-
This class is used by RepGenAlignerPlugin to store alignment info to db table tagAlignments. It is also used when pulling alignments from the DB. The tag2chrom and tag2pos fields are used to determine if the tag2 of this alignment class is a reference tag. If tag2chrom is null and tag2pos = -1, the tag alignment info is a non-ref tag. If these fields are populated with good values, the tag2 alignment info is for a reference tag. The "alignmentPos" field indicates the position within tag2 where the tag1 alignment starts. This position is adjusted for any clipping of tag1 that occurred during alignment.
- AlignmentInfo(tag2, chromosome, position, alignmentpos, ref_strand, ref_genome, score) - Constructor for class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- alignmentPos() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- AlignmentTableCellRenderer - Class in net.maizegenetics.gui
-
- AlignmentTableCellRenderer(model, alignment, masks) - Constructor for class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- AlignmentTableCellRenderer.RENDERING_TYPE - Enum in net.maizegenetics.gui
-
- AlignmentTableModel - Class in net.maizegenetics.gui
-
- AlignmentTableModel(alignment, horizontalPageSize) - Constructor for class net.maizegenetics.gui.AlignmentTableModel
-
- AlignmentTableModel(alignment) - Constructor for class net.maizegenetics.gui.AlignmentTableModel
-
- AlignmentTableModel.COLUMN_NAME_TYPE - Enum in net.maizegenetics.gui
-
- alignmentWithBowtie2() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- allAnnotationKeys(baseTaxaList) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Provides the set of all annotation key found in any of taxa
- allData - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- allele(aT, val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set allele annotation by Allele type (default=Alignment.UNKNOWN_ALLELE)
- allele(alleleType, site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return the (haploid) reference allele at given site.
- Allele - Interface in net.maizegenetics.dna.snp
-
Defines Allele present at a genomic Position
- allele() - Method in interface net.maizegenetics.dna.snp.Allele
-
- allele() - Method in class net.maizegenetics.dna.snp.SimpleAllele
-
- ALLELE_CNT - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- ALLELE_CNT - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- ALLELE_DEPTH_TYPES - Static variable in class net.maizegenetics.dna.snp.score.AlleleDepth
-
- ALLELE_FREQ_ORD - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- ALLELE_FREQ_ORD - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- ALLELE_PROBABILITY_TYPES - Static variable in class net.maizegenetics.dna.snp.score.AlleleProbability
-
- ALLELE_STATES - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- alleleA - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- alleleAsString() - Method in interface net.maizegenetics.dna.snp.Allele
-
- alleleAsString() - Method in class net.maizegenetics.dna.snp.SimpleAllele
-
- alleleC - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- alleleDefinitions() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- alleleDefinitions(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- alleleDefinitions() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- alleleDefinitions(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- alleleDefinitions() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns allele values as strings for all sites. The first dimension of the array indexes the sites. The second dimension indexes the allele values for given site. The indices for the allele values are used as the codes to store data. These codes (indices) are returned by the genotype() methods. If only one array of allele values is returned, that is the encoding for all sites.
- alleleDefinitions(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Same as getAlleleEncodings() for only one site.
- alleleDefinitions() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns allele values as strings for all sites. The first dimension of the array indexes the sites. The second dimension indexes the allele values for given site. The indices for the allele values are used as the codes to store data. These codes (indices) are returned by the genotype() methods. If only one array of allele values is returned, that is the encoding for all sites.
- alleleDefinitions(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Same as alleleDefinitions() for only one site.
- alleleDefinitions() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- alleleDefinitions(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- alleleDefinitions() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- alleleDefinitions(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- AlleleDepth - Class in net.maizegenetics.dna.snp.score
-
- AlleleDepthBuilder - Class in net.maizegenetics.dna.snp.score
-
- AlleleDepthBuilder(numSites) - Constructor for class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
- alleleDepths() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- AlleleDepthUtil - Class in net.maizegenetics.dna.snp.score
-
Depth compression utility. Depths are scored in byte (256 states). 0 to 127 are used for exact depth values. -128 to -1 are used for log approximations (1.0746^(-x)). This permits depths upto 10,482 to be stored with exact precision for low values, and <3% error for high depths.
- alleleEncodings(alleleEncodings) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- alleleForAllSites(alleleType) - Method in interface net.maizegenetics.dna.map.PositionList
-
Returns sequence alleles. One haploid allele for each site.
- AlleleFreqCache - Class in net.maizegenetics.dna.snp.genotypecall
-
Cache for allele frequency statistics. Allele frequency can be expensive to recalculate at large scale, so these class efficiently loops through blocks of sites and caches the statistics on them.
- AlleleFreqCache(genotype, maxNumAlleles) - Constructor for class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- alleleFrequencyFileter(rbt, minBorderMaf, maxBorderMaf) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- allelePresenceForAllSites(taxon) - Method in interface net.maizegenetics.dna.snp.bit.BitStorage
-
Returns sequence of true/false values indicating whether taxon at each site matches a specific allele.
- allelePresenceForAllSites(taxon) - Method in class net.maizegenetics.dna.snp.bit.DynamicBitStorage
-
- allelePresenceForAllSites(taxon, allele) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- allelePresenceForAllSites(taxon, allele) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- allelePresenceForAllSites(taxon, allele) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns sequence of true/false values indicating whether taxon at each site matches a specific allele (based on frequency). Allele number of value 0 would be the major allele. Allele number of value 1 would be the minor allele. Allele number of value 2 would be the third most frequent allele value and so on.
- allelePresenceForAllSites(taxon, allele) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- allelePresenceForAllSites(taxon, allele) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- allelePresenceForAllTaxa(site) - Method in interface net.maizegenetics.dna.snp.bit.BitStorage
-
Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.
- allelePresenceForAllTaxa(site) - Method in class net.maizegenetics.dna.snp.bit.DynamicBitStorage
-
- allelePresenceForAllTaxa(site, allele) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- allelePresenceForAllTaxa(site, allele) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- allelePresenceForAllTaxa(site, allele) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns sequence of true/false values indicating whether site at each taxon matches a specific allele.
- allelePresenceForAllTaxa(site, allele) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- allelePresenceForAllTaxa(site, allele) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- allelePresenceForSitesBlock(taxon, startBlock, endBlock) - Method in interface net.maizegenetics.dna.snp.bit.BitStorage
-
Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.
- allelePresenceForSitesBlock(taxon, startBlock, endBlock) - Method in class net.maizegenetics.dna.snp.bit.DynamicBitStorage
-
- allelePresenceForSitesBlock(taxon, allele, startBlock, endBlock) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- allelePresenceForSitesBlock(taxon, allele, startBlock, endBlock) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- allelePresenceForSitesBlock(taxon, allele, startBlock, endBlock) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns sequence of true/false values indicating whether taxon at sites (in given blocks, 64 sites per block including start block but excluding end block) matches a specific allele.
- allelePresenceForSitesBlock(taxon, allele, startBlock, endBlock) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- allelePresenceForSitesBlock(taxon, allele, startBlock, endBlock) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- alleleProbability() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- alleleProbability(taxon, site, type) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- alleleProbability() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- alleleProbability(taxon, site, type) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- alleleProbability() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns allele probability object (null if not present)
- alleleProbability(taxon, site, type) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
- alleleProbability() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- alleleProbability(taxon, site, type) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- AlleleProbability - Class in net.maizegenetics.dna.snp.score
-
- AlleleProbability(numTaxa, numSites) - Constructor for class net.maizegenetics.dna.snp.score.AlleleProbability
-
- alleleProbability() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- alleleProbability(taxon, site, type) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- AlleleProbabilityBuilder - Class in net.maizegenetics.dna.snp.score
-
- AlleleProbabilityFELM - Class in net.maizegenetics.analysis.association
-
- AlleleProbabilityFELM(data, parentPlugin) - Constructor for class net.maizegenetics.analysis.association.AlleleProbabilityFELM
-
- alleleProbsOfType(type, site) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- alleleReport() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- alleleReport() - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- alleleReportBuilder - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- alleleReportColumnNames() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- alleleReportColumnNames() - Method in class net.maizegenetics.analysis.association.ReferenceProbabilityFELM
-
- alleleReportFilename - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- alleleReportFilename() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
The name of the file to which these results will be saved.
- alleleReportFilename(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Genotype Effect File. The name of the file to which these results will be saved.
- alleleReportFilepath(savefile) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- alleleReportFilepath(savefile) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- alleles - Variable in class net.maizegenetics.analysis.modelfitter.SNP
-
- alleles(alleleType, startSite, endSite) - Method in interface net.maizegenetics.dna.map.PositionList
-
Returns reference sequence alleles in specified range. End site not included. One haploid allele for each site.
- alleles(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- alleles(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- alleles(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns all alleles at given site in order of frequency. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- alleles(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns all alleles at given site in order of frequency. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- ALLELES - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- alleles(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- alleles(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- allelesBySortType(scope, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- allelesBySortType(scope, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- allelesBySortType(scope, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns all alleles at given site in order defined by scope.
- allelesBySortType(scope, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- allelesBySortType(scope, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- allelesSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- allelesSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- allelesSortedByFrequency(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return sorted list of alleles from highest frequency to lowest at given site in alignment. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploids are not supported.
- allelesSortedByFrequency(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return sorted list of alleles from highest frequency to lowest at given site in genotype table. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploids are not supported.
- allelesSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- allelesSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- allelesSortedByFrequencyAndCountsNucleotide(index, data) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- allelesSortedByFrequencyNucleotide(data) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- allIntValues() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- allLabels() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- allOfTheResidualPhenotypes - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- allTaxa() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- allTaxaAsList() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- allValues() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- allValues() - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- allValues() - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
The return value will typically be a primitive array whose type depends on the sub class
- allValues() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- alpha() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- alpha() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- altAllele - Variable in class net.maizegenetics.plugindef.GenerateRCode.PositionVectors
-
- alternateAllele(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- alternateAllele(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- alternateAllele(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return (haploid) alternate allele value at given site.
- alternateAllele(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- alternateAllele(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- alternates() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- AltitudeKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for altitude the taxon was sampled
- aMatrix() - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
Pedigree Matrix
- aMatrix(value) - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
Set Pedigree Matrix. Pedigree Matrix
- AMatrixPlugin - Class in net.maizegenetics.analysis.distance
-
- AMatrixPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- analyzeByColumn - Variable in class net.maizegenetics.analysis.association.MLMPlugin
-
- analyzeByColumn - Variable in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- analyzeSite() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- analyzeSite() - Method in class net.maizegenetics.analysis.association.AlleleProbabilityFELM
-
- analyzeSite() - Method in class net.maizegenetics.analysis.association.DiscreteSitesFELM
-
- analyzeSite() - Method in class net.maizegenetics.analysis.association.ReferenceProbabilityFELM
-
- ANC_ALLELES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- ancestor - Variable in class net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
-
An array of pointers to prefix blocks of this block.
- ancestor - Variable in class net.maizegenetics.analysis.gbs.neobio.Factor
-
A pointer to this factor's ancestor, which represents a prefix of this factor's text.
- and(other) - Method in interface net.maizegenetics.util.BitSet
-
AND
- and(other) - Method in class net.maizegenetics.util.OpenBitSet
-
see intersect
- and(other) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- andNot(other) - Method in interface net.maizegenetics.util.BitSet
-
see andNot
- andNot(other) - Method in class net.maizegenetics.util.OpenBitSet
-
see andNot
- andNot(other) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- andNotCount(a, b) - Static method in class net.maizegenetics.util.OpenBitSet
-
Returns the popcount or cardinality of "a and not b" or "intersection(a, not(b))". Neither set is modified.
- annotateBestMappingImport(indexDirS, predictDirS, priorityAligner) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Import prediction result to TOPM, contain hard coding on map index
- annotateBestMappingPredict(modelFileS, tagCountFileS, inputDirS, indexDirS, outputDirS) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Command line version to predict if hypotheses are correct using weka RandomForest. Make sure weka is installed (in ClassPath) in local machine Contain hard coding
- annotateHDF5File(writer) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Annotates the HDF5 Genotype file with allele frequency information. Can only be called on unlocked HDF5 files. Currently, placed in the GenotypeTableBuilder as it still above genotypes, taxa, and sites.
- annotateHDF5FileWithRefAllele(writer, refAlleles) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Annotates the HDF5 Genotype file with the reference allele and reference genome version. Can only be called on unlocked HDF5 files.
- AnnotateTOPM - Class in net.maizegenetics.analysis.gbs
-
Methods to annotate TOPM file, including adding mapping info from aligners, adding PE tag position and genetic position, model prediction for the best position
- AnnotateTOPM(topm) - Constructor for class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Constructor from a TOPM file
- AnnotateTOPM.EvidenceType - Enum in net.maizegenetics.analysis.gbs
-
- AnnotateTOPMwSAMPlugin - Class in net.maizegenetics.analysis.gbs
-
This class reads in SAM mapping results tests them against an anchor map and creates a updated HDF5 TOPM file. TODO: Add mapping information from Bowtie2 Add mapping information from BWA Add mapping information from BLAST? Run genetic to compare hypotheses Call resort
- AnnotateTOPMwSAMPlugin() - Constructor for class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- AnnotateTOPMwSAMPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- annotateWithBLAST(blastM8FileS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM with BLAST
- annotateWithBlastFromDir(blastDirS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM with BLAST from a directory, where slices of blast result are stored
- annotateWithBowtie2(samFileS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM file using Bowtie2
- annotateWithBWA(samFileS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM with BWA
- annotateWithBWAMEM(samFileS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM file using bwa-mem
- annotateWithGMGW(TOGMFileS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM with whole genome genetic mapping
- annotateWithPE(PETOPMFileS, maxMappingNum) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Annotate the TOPM with PE, using bowtie2 sam file
- annotation - Variable in class net.maizegenetics.plugindef.GenerateRCode.TableReportVectors
-
- annotation(annotation) - Method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- ANNOTATION_DATA_SET_DESCRIPTION - Static variable in interface net.maizegenetics.dna.snp.GenotypeTable
-
- ANNOTATION_DATA_SET_NAME - Static variable in interface net.maizegenetics.dna.snp.GenotypeTable
-
Annotations
- ANNOTATION_SCHEMA - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- annotations() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
Returns a (shallow) copy of the Hashmap that keeps all annotations for this feature. Since the hashmap just stores Strings, a shallow copy is still safe to modify b/c it won't be reflected in the original.
- annotations - Variable in class net.maizegenetics.dna.pd.SiteAnnotation
-
- annotations() - Method in interface net.maizegenetics.dna.snp.Allele
-
- annotations() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- annotations() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- annotations() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Annotations of this Genotype Table. Null if there are none.
- annotations() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- annotations() - Method in class net.maizegenetics.dna.snp.SimpleAllele
-
- annotations() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- annotations() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- ANONYMOUS - Static variable in class net.maizegenetics.taxa.Taxon
-
- anovaReportFilename() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Name of file to which ANOVA report will be saved
- anovaReportFilename(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set ANOVA File. Name of file to which ANOVA report will be saved
- appendAddDom(append) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- appendAddDom(append) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- appendAddDom() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
If true, additive and dominance effect estimates will be added to the stats report for bi-allelic sites only. The effect will only be estimated when the data source is genotype (not a probability). The additive effect will always be non-negative.
- appendAddDom(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Append Effect Estimates to Stats. If true, additive and dominance effect estimates will be added to the stats report for bi-allelic sites only. The effect will only be estimated when the data source is genotype (not a probability). The additive effect will always be non-negative.
- appendAddDomEffects - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- appendAnovaResults(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- appendAnovaResultsWithCI(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- appendSiteEffectEstimates(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- appendSiteEffectEstimatesWithCI(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- applicationConfiguration - Static variable in class net.maizegenetics.analysis.gbs.ProductionPipelineMain
-
- applyBoxCox(pheno, addSmallVal, randomSeed, startLambda, endLambda, stepLambda) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformation
-
- ApproxFastChiSquareDistribution - Class in net.maizegenetics.stats.statistics
-
chi-square distribution (distribution of sum of squares of n uniform random variables) (Parameter: n; mean: n; variance: 2*n) The chi-square distribution is a special case of the Gamma distribution (shape parameter = n/2.0, scale = 2.0).
- ApproxFastChiSquareDistribution(maxX, maxN) - Constructor for class net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
-
- APPROXIMATE_MATCH_TAG - Static variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Tag character that signals an approximate match in the score tag line of an alignment.
- ArchaeopteryxPlugin - Class in net.maizegenetics.analysis.tree
-
- ArchaeopteryxPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
-
- archiveDirectory() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
Archive directory where to move processed files
- archiveDirectory(value) - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
Set Archive Directory. Archive directory where to move processed files
- areAttributeAndTypeListsCompatible(attributes, types) - Static method in class net.maizegenetics.phenotype.CorePhenotype
-
- areEncodingsEqual(encodings) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- areGenotypeValuesDiscrete() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- areReadsUnique() - Method in interface net.maizegenetics.dna.tag.Reads
-
Reports whether this list of reads includes duplicates True is there are no read duplicates, false otherwise. Collapses read files are likely to be unique While a virtual digest of a genome with contain some duplicates
- areReadsUnique() - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- areSameTag(site1, site2, a) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- areTagsEqual(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- areTagsUnique() - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- areTagsUnique() - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- areTagsUnique() - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- areTagsUnique() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- areTagsUnique() - Method in interface net.maizegenetics.dna.tag.Tags
-
Reports whether this list of reads includes duplicates True is there are no read duplicates, false otherwise. Collapses read files are likely to be unique While a virtual digest of a genome with contain some duplicates
- areTaxaReplicated - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- areTaxaReplicated() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- areTaxaReplicated() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- areTaxaReplicated() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- areTaxaReplicated() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- ArgsEngine - Class in net.maizegenetics.util
-
A reusable solution for Command Line Arguments Parsing in Java.
- arrangeMajorMinorBtwAlignments(unimpAlign, bt, donorOffset, donorLength, goodMask, swapMjMnMask, isSwapMajorMinor) - Static method in class net.maizegenetics.analysis.imputation.FILLINDonorGenotypeUtils
-
Major and minor allele get swapped between GenotypeTables. This method flips these, and sets the bad sites to missing
- arraycopy(row, src, startColumn) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Sets values at given row and starting column.
- arraycopy(row, src, startColumn) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- arraycopy(row, src, startColumn) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- arraycopy(row, src, startColumn) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- arraycopy(row, src, startColumn) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- asBigDecimal(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asBigDecimal(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asBigDecimal(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asBigDecimal(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asBoolean(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asBoolean(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asBoolean(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asBoolean(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asByte(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asByte(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asByte(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asByte(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asChar(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asChar(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asChar(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asChar(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asCorePhenotype() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- asCorePhenotype() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- asCorePhenotype() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- asDouble(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asDouble(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asDouble(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asDouble(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asFloat(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asFloat(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asFloat(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asFloat(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asInt(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asInt(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asInt(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asInt(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asLong(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asLong(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asLong(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asLong(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- assembleDistMatrix(block, dim, r, c, lc) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Assembles the DIST matrix of a block by retrieving the DIST columns of its prefix blocks. In fact, it also stores pointers to the owner block for each column retrieved. These pointers are later used during the trace back procedure that builds an optimal alignment from the information computed in the block table. This method is general enough to suit both global and local alignment versions of the algorithm.
- assembleInputBorder(dim, r, c, lr) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Assembles the input border of a block by retrieving the values at the output borders of the left and top blocks. This method is general enough to suit both global and local alignment versions of the algorithm. Note that it can be used to assemble the input border of any block but the root one (it will cause an ArrayIndexOutOfBoundsException.
- asShort(name) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asShort(index) - Method in interface net.maizegenetics.util.db.DBTuple
-
- asShort(name) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- asShort(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- assignHaplotyes() - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- assignHaplotypes() - Method in class net.maizegenetics.analysis.imputation.UseParentHaplotypes
-
- assignName(name) - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- association(kinship, genotype, phenotype, genoPheno, minClassSize, biallelicOnly, appendAddDom, saveToFile, outputFile, maxP) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- AssociationConstants - Class in net.maizegenetics.analysis.association
-
- AssociationUtils - Class in net.maizegenetics.analysis.association
-
- attribute(attrnum) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attribute(attrnum) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attribute(attrnum) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- attributeIndexForName(name) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeIndexForName(name) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeIndexForName(name) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- attributeIndicesOfType(type) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeIndicesOfType(type) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeIndicesOfType(type) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- attributeLabelForIndex(index) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- attributeListCopy() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeListCopy() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeListCopy() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- attributeListOfType(type) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeListOfType(type) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeListOfType(type) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- attributeName(attrnum) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeName(attrnum) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeName(attrnum) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- AttributeNode - Interface in net.maizegenetics.taxa.tree
-
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree. Unlike its superclass this node can have an arbitrary number of named attributes associated with it.
- attributes() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- attributes() - Method in class net.maizegenetics.dna.snp.FilterTaxa
-
- attributeStream() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeStream() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeStream() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- attributeType(attrnum) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- attributeType(attrnum) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- attributeType(attrnum) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- automaticMajorMAF() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Set to Major genotype if no imputation result and MAF is below threshold
- automaticMajorMAF(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Set Automatic MajorGenotype if MAF. Set to Major genotype if no imputation result and MAF is below threshold
- automaticMajorMAF() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Set to Major genotype if no imputation result and MAF is below threshold
- automaticMajorMAF(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Set Automatic MajorGenotype if MAF. Set to Major genotype if no imputation result and MAF is below threshold
- averagePheno(pheno, addSmallValue, randomSeed) - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotype
-
- aveSeqErrorRate() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Ave Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate(value) - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
Set Ave Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Set Ave Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- aveSeqErrorRate(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Set Ave Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls)
- AvgPhenotype - Class in net.maizegenetics.analysis.numericaltransform
-
- AvgPhenotypeByTaxaPlugin - Class in net.maizegenetics.analysis.numericaltransform
-
- AvgPhenotypeByTaxaPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- avgSegmentLength - Variable in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- avgSeqErrorRate() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls when merging taxa)
- avgSeqErrorRate(value) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Set Avg Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls when merging taxa)
- AvroConstants - Class in net.maizegenetics.analysis.avro
-
- AvroConstants.CHROMOSOME_INDICES - Enum in net.maizegenetics.analysis.avro
-
- AvroConstants.GENOTYPE_TABLE_COMPONENTS - Enum in net.maizegenetics.analysis.avro
-
- AvroConstants.POSITION_INDICES - Enum in net.maizegenetics.analysis.avro
-
- AvroConstants.TAXON_INDICES - Enum in net.maizegenetics.analysis.avro
-
- C - Variable in class net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
-
The value of the highest scoring path contained in this block, called C-path.
- c - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- C_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- C_DIPLOID_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- calcAccuracy(imputed, runtime) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
-
- calcAllelePresenceCountsBtwTargetAndDonors(modBitsOfTarget, donorAlign) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
Counts union and intersection of major and minor alleles between the target genotype and potential donor genotypes. The counts are done by 64 sites block. These counts can be quickly used to estimate distance for the set of blocks.
- calcBitPresenceFromGenotype(genotype, mjA, mnA) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Method for getting TBits rapidly from major and minor allele arrays
- calcBitPresenceFromGenotype(genotype, referenceValues) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- calcBitPresenceFromGenotype(genotype, mj, mn) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Method for getting Site Bits rapidly from major and minor alleles
- calcBitPresenceFromGenotype(genotype, referenceValue) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- calcBitPresenceFromGenotype15(genotype, mjA, mnA) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Method for getting TBits rapidly from major and minor allele arrays
- calcBitPresenceOfDiploidValueFromGenotype(genotype, diploidValue) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns BitSet indicating presence of given diploid value in genotype. This does unphased comparisons, so the order of the two allele values do not matter. If given diploid value is UNKNOWN, then it doesn't match anything. Bits set to 1 indicate match.
- calcBitUnknownPresenceFromGenotype(genotype) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- calcContigencyChiSquare(permutations) - Method in class net.maizegenetics.stats.statistics.ContigencyTable
-
This calculates the probability in the normal approach, using the Chi Square as the test statistic.
- calcIdentity(querySeq, refSeq) - Static method in class net.maizegenetics.analysis.rna.FindMatchByWordHash
-
- calcMonteCarloExactTest(permutations) - Method in class net.maizegenetics.stats.statistics.ContigencyTable
-
This calculates the probability in the normal permutation approach, using the method described by Weir, B. S. (1996) Genetic Data Analysis II (Sinauer, Sunderland, MA).
- calcRapidContigencyChiSquare(maxPermutations) - Method in class net.maizegenetics.stats.statistics.ContigencyTable
-
This calculates the probability in a rapid approach, using the Chi Square as the test statistic. It runs for maxPermutations permutations unless it find 10 values that beat the observed, and then it stops and calculates the p-value. This slighly biases the P-values but makes it much more rapid.
- calcRapidMonteCarloExactTest(maxPermutations) - Method in class net.maizegenetics.stats.statistics.ContigencyTable
-
This calculates the probability in the rapid permutational approach, using the method described by Weir, B. S. (1996) Genetic Data Analysis II (Sinauer, Sunderland, MA) It runs for 1000 permutations unless it find 10 values that beat the observed, and then it stops and calculates the p-value. This slighly biases the P-values but makes it much more rapid.
- calcTop2Depths(siteAlleleDepths) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- calculate() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithm
-
- calculate() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
-
- calculateAccuracy() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Masks input file before imputation and calculates accuracy based on masked genotypes
- calculateAccuracy(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Calculate accuracy. Masks input file before imputation and calculates accuracy based on masked genotypes
- calculateAccuracyWithinMAFCategories() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Calculate R2 accuracy within MAF categories based on donor file
- calculateAccuracyWithinMAFCategories(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Calculate accuracy within MAF categories. Calculate R2 accuracy within MAF categories based on donor file
- calculateAlpha() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- calculateAlpha() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- calculateBeta() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- calculateBeta() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- calculateBitLDForHaplotype(ignoreHets, minTaxaForEstimate, alignment, site1, site2) - Static method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- calculateBitLDForHaplotype(minTaxaForEstimate, minorCnt, alignment, site1, site2) - Static method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- calculateBLUP() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- calculateBlupsPredicted() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- calculateBlupsPredictedResiduals() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- calculateCladeProbabilities(tree, cladeSystems) - Static method in class net.maizegenetics.taxa.tree.CladeSystem
-
- calculateCorrelations(tagTagCorrelations, tagTaxaMap, tag1, tag2, ddepths1, depthsPrime1) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- calculateDistanceFromKin(kin) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- calculateDPrime(countAB, countAb, countaB, countab, minTaxaForEstimate) - Static method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- calculateFfromR2(r2, markerDf, errorDf) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- calculateP(F, markerDf, errorDf) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- calculatePCsAcrossNAMFounders(chr, theGenotypesForCalculatingPCs, chrVector, posVector, startPosVector, endPosVector, increment, selectedColumns) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- calculatePEV - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- calculateR2Fromp(alpha, modelDf, errorDf) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- calculateRSqr(countAB, countAb, countaB, countab, minTaxaForEstimate) - Static method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- calculateTagAveQS(tagCntQSMap, qualityScoreBase) - Static method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- calculateV(ZKZ, genvar, resvar) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- calculateV(ZKZ, W, genvar, resvar) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- call() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- callBasedOnDepth(genoDepths) - Method in class net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule
-
- callBasedOnDepth(genoDepths) - Method in class net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule
-
- callBasedOnDepth(genoDepths) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule
-
Makes a genotypic call based on allele depths
- callBasedOnDepth(genoDepths) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule
-
Makes a genotypic call based on allele depths
- callBasedOnDepth(genoDepths) - Method in class net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule
-
- callBasedOnDepth(genoDepths) - Method in class net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule
-
- callBasedOnDepth(genoDepths) - Method in class net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule
-
- callBasedOnDepth(genoDepths) - Method in class net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule
-
- callBiallelicSNPsWithGap() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Include sites where the third allele is a GAP (mutually exclusive with inclGaps)
- callBiallelicSNPsWithGap(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Call Biallelic SNPs with Gap. Include sites where the third allele is a GAP (mutually exclusive with inclGaps)
- callMergeSelection() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Selection for Call Merging
- callMergeSelection(value) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Set Call Merge Rule. Selection for Call Merging
- callParentAllelesByWindow(popdata, maxMissing, minMaf, windowSize, minR) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- callParentAllelesByWindowForBackcrosses(popdata, maxMissing, minMaf, windowSize, minR) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- callParentAllelesByWindowForMultipleBC(popdata, maxMissing, minMinorAlleleCount, windowSize) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- CallParentAllelesPlugin - Class in net.maizegenetics.analysis.imputation
-
- CallParentAllelesPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- callParentAllelesUsingClusters(popdata, maxMissing, minMaf, windowSize, checkSubpops) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- callParentAllelesUsingClustersOnly(popdata, maxMissing, minMaf, windowSize, checkSubpops) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- callParentAllelesUsingTaxaGroups(family, taxaGroups, snpList) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- cancel() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- cancel() - Method in interface net.maizegenetics.plugindef.Plugin
-
Attempt to cancel processing.
- capacity() - Method in interface net.maizegenetics.util.BitSet
-
Returns capacity.
- capacity() - Method in class net.maizegenetics.util.OpenBitSet
-
Returns the current capacity in bits (1 greater than the index of the last bit)
- capacity() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- cardinality() - Method in interface net.maizegenetics.util.BitSet
-
- cardinality(index) - Method in interface net.maizegenetics.util.BitSet
-
Return number of set bits up to and including bit at given index.
- cardinality() - Method in class net.maizegenetics.util.OpenBitSet
-
- cardinality(index) - Method in class net.maizegenetics.util.OpenBitSet
-
- cardinality() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- cardinality(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- case_sensitive - Variable in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Determines whether this scoring scheme ignores the case of characters when computing their score. It is set by the constructor and cannot be changed afterwards.
- CategoricalAttribute - Class in net.maizegenetics.phenotype
-
- CategoricalAttribute(name, stringValues) - Constructor for class net.maizegenetics.phenotype.CategoricalAttribute
-
- cdf(x, n) - Static method in class net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
-
cumulative density function of the chi-square distribution
- cdf(x, n) - Static method in class net.maizegenetics.stats.statistics.ChiSquareDistribution
-
cumulative density function of the chi-square distribution
- cdf(x, lambda) - Static method in class net.maizegenetics.stats.statistics.ExponentialDistribution
-
cumulative density function of the exponential distribution
- cdf(x, shape, scale) - Static method in class net.maizegenetics.stats.statistics.GammaDistribution
-
cumulative density function of the Gamma distribution
- cdf(x, m, sd) - Static method in class net.maizegenetics.stats.statistics.NormalDistribution
-
cumulative density function
- cdf(x, k, m) - Static method in class net.maizegenetics.stats.statistics.ParetoDistribution
-
cumulative density function of the Pareto distribution
- cdfFastApprox(x, n) - Method in class net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
-
cumulative density function of the chi-square distribution
- center(values) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- centerAndScale(values) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- CENTERED_IBS_SUMPK - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- changeAlignmentIdentifiers(alternateIdGroups) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- changeAttributeType(changeMap) - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- changeData(newdata) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- ChangeLog - Class in net.maizegenetics.util
-
This outputs the change logs messages in HTML for tassel-5-source since this last
"New Build Date" message. The results can be added to Tassel5ChangeHistory.html on
the website.
- changeName(newName) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- changeName(newName) - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- changeName(newName) - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- changeName(newName) - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- characteristics() - Method in class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- characteristics() - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
-
- characteristics() - Method in class net.maizegenetics.analysis.modelfitter.NestedCovariatePermutationTestSpliterator
-
- characteristics() - Method in class net.maizegenetics.dna.map.PositionList.PositionListCollector
-
- characteristics() - Method in class net.maizegenetics.taxa.TaxaList.TaxaListCollector
-
- characteristics() - Method in class net.maizegenetics.util.BitSet.BitSetListCollector
-
- charAt(pos) - Method in class net.maizegenetics.analysis.gbs.neobio.CharSequence
-
Returns the character at a given position. For the client, the first character is at position 1, while the last character is at position length(). This is convinient for sequence alignment algorithms based on a classic dynamic programming matrix since the sequences usually start at row/column 1. This method does not check boundaries, therefore an ArrayIndexOutOfBoundsException may be raised if pos is out of bounds.
- CharSequence - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implements a sequence of characters stored as an array that provides random access to any position in constant time.
- CharSequence(reader) - Constructor for class net.maizegenetics.analysis.gbs.neobio.CharSequence
-
Creates a new instance of a CharSequence, loading the sequence data from the Reader input stream.
- ChartDisplayPlugin - Class in net.maizegenetics.analysis.chart
-
- ChartDisplayPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
Creates a new instance of ChartDisplayPlugin
- ChartDisplayPlugin.ChartType - Enum in net.maizegenetics.analysis.chart
-
- checkAlignmentOrderIgnoringParents(alignments, family, r) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- checkParentage(popdata) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
Checks whether alleleA is parent1 and alleleC is parent2. If not, switches them.
- checkQuery(query) - Static method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
Checks that the query is safe and that the results will contain fields labeled "chr" & "position".
- checksubpops(popdata, halfWindowSize) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- CheckSum - Class in net.maizegenetics.util
-
- checkSynForDups() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- chiSquareDf1(ob1, ob2, ex1, ex2, chiValueCutoff) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- ChiSquareDistribution - Class in net.maizegenetics.stats.statistics
-
chi-square distribution (distribution of sum of squares of n uniform random variables) (Parameter: n; mean: n; variance: 2*n) The chi-square distribution is a special case of the Gamma distribution (shape parameter = n/2.0, scale = 2.0).
- chiSquareEvenDf1(ob1, ob2, chiValueCutoff) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- ChiSquareTest - Class in net.maizegenetics.stats.statistics
-
chi-square test
- chooseEnzyme(enzyme) - Static method in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
Determines which cut sites to look for, and sets them, based on the enzyme used to generate the GBS library. For two-enzyme GBS both enzymes MUST be specified and separated by a dash "-". e.g. PstI-MspI, SbfI-MspI
- chr() - Method in class net.maizegenetics.dna.snp.io.ReadBedfile.BedFileRange
-
Return chromosome
- chrB - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- chrContig - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- chrEndIndex - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
Last SNP index of gt chromosome in the whole SNP list, exclusive
- chrF - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- chrName - Variable in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- chrNum - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- chrom() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Chromosome as String
- chrom(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Set outputDir path. Directory file path where output files will be writen
- chromosomalPosition(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Returns the physical position at given site.
- chromosomalPosition(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosomalPosition(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosomalPosition(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns the physical position at given site.
- chromosomalPosition(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosomalPosition(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- chromosome() - Method in class net.maizegenetics.analysis.gbs.repgen.RefTagData
-
- chromosome - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- chromosome() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- Chromosome - Class in net.maizegenetics.dna.map
-
Defines the chromosome structure and length. The name and length recorded for each chromosome.
- Chromosome(name) - Constructor for class net.maizegenetics.dna.map.Chromosome
-
Deprecated.
- chromosome(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set Chromosome
- chromosome() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- chromosome(chr) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- chromosome(chr) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- chromosome(chr) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- chromosome(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return Chromosome for given site.
- chromosome(name) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return Chromosome with matching name. First to match will be returned.
- chromosome - Variable in class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
Chromosome of the most significant site
- chromosome - Variable in class net.maizegenetics.dna.map.TagMappingInfo
-
Chromosome as an integer
- chromosome - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Chromosome as an integer, unknown = Integer.MIN_VALUE
- chromosome(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosome(name) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosome(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosome(name) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosome(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return Chromosome for given site.
- chromosome(name) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return Chromosome with matching name. First to match will be returned.
- chromosome(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosome(name) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosome(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- chromosome(name) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- CHROMOSOME_INDICES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- CHROMOSOME_SCHEMA - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- chromosomeName() - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- chromosomeName() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- chromosomeName(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return Chromosome Name for given site.
- chromosomeName(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosomeName(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosomeName(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return Chromosome Name for given site.
- chromosomeName(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosomeName(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- chromosomeNumber - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- chromosomes() - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns a list of chromosomes whose sequences have been stored in the chromsomeSequence map of the class implementing this interface. Return empty set if empty.
- chromosomes() - Method in interface net.maizegenetics.dna.map.PositionList
-
Return all chromosomes.
- chromosomes() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosomes() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosomes() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return all chromosomes.
- chromosomes() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosomes() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- chromosomes - Variable in class net.maizegenetics.plugindef.GenerateRCode.PositionVectors
-
- CHROMOSOMES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- chromosomeSequence(chrom) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Takes a Chromosome object and returns the stored byte array representing the genomic sequence for the specified chromosome.
- chromosomeSequence(chrom, startSite, endSite) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the partial genomic sequence for a chromosome, from the specified start position to the specified end position. THe start/end positions are inclusive and the request is 1-based (though the alleles are stored in a 0-based byte array).
- chromosomeSequenceAndStats(chrom, startSite, lastSite) - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- chromosomeSiteCount(chromosome) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return number of sites for given Chromosome
- chromosomeSiteCount(locus) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosomeSiteCount(chromosome) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosomeSiteCount(chromosome) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return number of sites for given chromosome.
- chromosomeSiteCount(chromosome) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosomeSiteCount(chromosome) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- chromosomeSize(chromosome) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the length of the current chromsome
- chromosomesOffsets() - Method in interface net.maizegenetics.dna.map.PositionList
-
Returns starting site for each chromosome.
- chromosomesOffsets() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- chromosomesOffsets() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- chromosomesOffsets() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns starting site for each chromosome.
- chromosomesOffsets() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- chromosomesOffsets() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- chrPosFile() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Filter based on list of chromsome / position in file.
- chrPosFile(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Chr Pos File. Filter based on list of chromsome / position in file.
- chrPosFile() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- chrStartIndex - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
First SNP index of gt chromosome in the whole SNP list
- chunkSize - Static variable in class net.maizegenetics.dna.BaseEncoder
-
defines the number of bases fitting with a long
- chunkSizeForInt - Static variable in class net.maizegenetics.dna.BaseEncoder
-
- CLADE_PROBABILITY - Variable in interface net.maizegenetics.taxa.tree.AttributeNode
-
attribute name for the probability of the clade defined by an internal node.
- cladeCount(subtree, trees) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- CladeSystem - Class in net.maizegenetics.taxa.tree
-
data structure for a set of splits
- CladeSystem(idGroup, size) - Constructor for class net.maizegenetics.taxa.tree.CladeSystem
-
- ClassicMds - Class in net.maizegenetics.stats.PCA
-
- ClassicMds(dm) - Constructor for class net.maizegenetics.stats.PCA.ClassicMds
-
- cleanProgressUnit(plugin) - Method in class net.maizegenetics.progress.ProgressPanel
-
- clear() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- clear() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- clear() - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- clear() - Method in class net.maizegenetics.dna.snp.FilterList
-
- clear(index) - Method in interface net.maizegenetics.util.BitSet
-
Clears a bit, allowing access beyond the current set size without changing the size.
- clear(startIndex, endIndex) - Method in interface net.maizegenetics.util.BitSet
-
Clears a range of bits. Clearing past the end does not change the size of the set.
- clear(startIndex, endIndex) - Method in interface net.maizegenetics.util.BitSet
-
Clears a range of bits. Clearing past the end does not change the size of the set.
- clear(index) - Method in class net.maizegenetics.util.OpenBitSet
-
clears a bit, allowing access beyond the current set size without changing the size.
- clear(startIndex, endIndex) - Method in class net.maizegenetics.util.OpenBitSet
-
Clears a range of bits. Clearing past the end does not change the size of the set.
- clear(startIndex, endIndex) - Method in class net.maizegenetics.util.OpenBitSet
-
Clears a range of bits. Clearing past the end does not change the size of the set.
- clear() - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- clear(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- clear(startIndex, endIndex) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- clear(startIndex, endIndex) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- clearAlignmentData() - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Removes all data from the DB that was added from SAMToGBSDBPlugin call. The tables cleared are CutPosition and TagCutPosition
- clearAlignmentData() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- clearAlignmentData() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- clearAlignmentData() - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Removes all data from the DB that was added from SAMToGBSDBPlugin call. The tables cleared are CutPosition and TagCutPosition
- clearDiscoveryData() - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Removes all data from the DB that was added from the DiscoverySNPCallerPluginV2 The tables cleared are Allele, TagAllele and SNPPosition
- clearDiscoveryData() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- clearDiscoveryData() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- clearDiscoveryData() - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Removes all data from the DB that was added from the DiscoverySNPCallerPluginV2 The tables cleared are Allele, TagAllele and SNPPosition
- clearSNPQualityData() - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Removes all data from the snpQuality table
- clearSNPQualityData() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- clearSNPQualityData() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- clearSNPQualityData() - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Removes all data from the snpQuality table
- clearTagTaxaDistributionData() - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Removes all data from the tagtaxadistribution table. This should be called from GBSSeqToTagDBPlugin when a user requests an "append" option (ie, db exists, and user opted NOT to clear it). AFter we grab the existing data it is cleared. It will be re-entered when GBSSeqToTagDBPlugin completes.
- clearTagTaxaDistributionData() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- clearTagTaxaDistributionData() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- clearTagTaxaDistributionData() - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Removes all data from the tagtaxadistribution table. This should be called from GBSSeqToTagDBPlugin when a user requests an "append" option (ie, db exists, and user opted NOT to clear it). AFter we grab the existing data it is cleared. It will be re-entered when GBSSeqToTagDBPlugin completes.
- clearVariants() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
Sets the variant definition & offset arrays to null for each tag.
- clearVariants() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- clearVariants() - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- clearVariants() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Clears all variant definitions and position offsets.
- clone() - Method in class net.maizegenetics.util.OpenBitSet
-
- close() - Method in class net.maizegenetics.analysis.gbs.SNPLogging
-
- close() - Method in class net.maizegenetics.dna.tag.FastqReader
-
- close() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- close() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- closeInstance() - Static method in class net.maizegenetics.tassel.TasselLogging
-
- closeLogfile() - Static method in class net.maizegenetics.util.LoggingUtils
-
- closeUnfinished() - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Used to close an HDF5 GenotypeTableBuilder, when it will be reopened later and appended. This file cannot be used for other purposes in this unfinished state.
- cluster() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
use the cluster algorithm
- cluster(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Cluster. use the cluster algorithm
- clusterBySmallestDistance(orig) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
- clusterDistanceAveragePairDiff(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- clusterDistanceClusterDiffProportion(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- clusterDistanceClusterHaplotypeDiff(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- clusterDistanceDistinctHaplotypeProportion(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- clusterDistanceDistinctHaplotypes(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- clusterDistanceMaxPairDiff(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- clusterDistanceTotalPairDiff(cluster0, cluster1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- ClusterGenotypesPlugin - Class in net.maizegenetics.analysis.imputation
-
- ClusterGenotypesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
-
- clusteringMethod() - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Clustering Method
- clusteringMethod(value) - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Set Clustering Method. Clustering Method
- Clusters - Class in net.maizegenetics.analysis.gbs
-
- Clusters(rbt) - Constructor for class net.maizegenetics.analysis.gbs.Clusters
-
- Clusters(tbt) - Constructor for class net.maizegenetics.analysis.gbs.Clusters
-
- Clusters(infileS, binary) - Constructor for class net.maizegenetics.analysis.gbs.Clusters
-
- clusterWindow(a, start, length, maxdif, minNotMissingPerHaplotype) - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- clusterWindow(a, start, length, maxdif) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- clusterWindow(a, start, length, maxdif, minNotMissingPerHaplotype) - Method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- CMD_CANCEL - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_CHANGE_COV - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_CHANGE_DATA - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_EXCLUDE - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_EXCLUDE_ALL - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_INCLUDE - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_INCLUDE_ALL - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- CMD_OK - Static variable in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- cmdLineName() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- code(ifEvidence) - Static method in enum net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
-
- col - Variable in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
An array of column indexes reflecting the current state of the matrix. When columns are deleted, the corresponding indexes are simply moved to the end of the vector.
- col_codes - Variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Stores matrix column headers in the order they were found.
- colByte(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns keep as Byte. Comma separated list of column names to generate byte binaries for
- collapseCounts() - Method in class net.maizegenetics.dna.tag.PETagCounts
-
Collapse PETagCounts, the tag count of collapsed tags is set to 0
- collapseCounts() - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- collapseCounts() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- collect() - Static method in interface net.maizegenetics.taxa.TaxaList
-
Returns TaxaList Collector.
- collect(numBits) - Static method in interface net.maizegenetics.util.BitSet
-
Returns BitSet Collector.
- collectProportions(tree, trees) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- collectReorder() - Static method in interface net.maizegenetics.dna.map.PositionList
-
Returns PositionList Collector that reorders position if necessary.
- collectTaxa(root, table) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
Collects all of the names of the taxa in the tree into a hashtable.
- collectValidateOrder() - Static method in interface net.maizegenetics.dna.map.PositionList
-
Returns PositionList Collector that validates order of Positions.
- colsAllele() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate byte binaries for
- colsAllele(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns translate allele values to 0-5. Comma separated list of column names of single character alleles to be translated from A/C/G/T/+/- to 0-5.
- colsAllele() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate byte binaries for
- colsAllele(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns translate allele values to 0-5. Comma separated list of column names of single character alleles to be translated from A/C/G/T/+/- to 0-5.
- colsByte() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate byte binaries for
- colsByte() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate byte binaries for
- colsByte(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns keep as Byte. Comma separated list of column names to generate byte binaries for
- colsChar() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate char binaries for
- colsChar(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns keep as Char. Comma separated list of column names to generate char binaries for
- colsChar() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate char binaries for
- colsChar(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns keep as Char. Comma separated list of column names to generate char binaries for
- colsFloat() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate real binaries for
- colsFloat(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns keep as Real (Float). Comma separated list of column names to generate real binaries for
- colsFloat() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate real binaries for
- colsFloat(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns keep as Real (Float). Comma separated list of column names to generate real binaries for
- colsInt() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate int binaries for
- colsInt(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns keep as Int. Comma separated list of column names to generate int binaries for
- colsInt() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate int binaries for
- colsInt(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns keep as Int. Comma separated list of column names to generate int binaries for
- colsLog10() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to first transform using -log10 then generate binaries for
- colsLog10(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns to Keep and transform -log10. Comma separated list of column names to first transform using -log10 then generate binaries for
- colsLog10() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to first transform using -log10 then generate binaries for
- colsLog10(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns to Keep and transform -log10. Comma separated list of column names to first transform using -log10 then generate binaries for
- colsLong() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate long binaries for
- colsLong(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns keep as Long. Comma separated list of column names to generate long binaries for
- colsLong() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate long binaries for
- colsLong(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns keep as Long. Comma separated list of column names to generate long binaries for
- colsShort() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Comma separated list of column names to generate short binaries for
- colsShort(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Columns keep as Short. Comma separated list of column names to generate short binaries for
- colsShort() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Comma separated list of column names to generate short binaries for
- colsShort(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Columns keep as Short. Comma separated list of column names to generate short binaries for
- colStart - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
The beginning COLUMN of the matrix that was aligned. If seq1 is the same length or shorter then seq1, this correlates to the position on seq1 where alignment started. If seq2 is shorter than seq1, this correlates to the position on seq2 where alignment started.
- ColtDoubleMatrix - Class in net.maizegenetics.matrixalgebra.Matrix
-
- ColtDoubleMatrix(aMatrix) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(row, col) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(row, col, values) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(row, col, value) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(values) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(values) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(size) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtDoubleMatrix(diagonal) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- ColtEigenvalueDecomposition - Class in net.maizegenetics.matrixalgebra.decomposition
-
- ColtEigenvalueDecomposition(dm) - Constructor for class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- ColtEigenvalueDecomposition(dm) - Constructor for class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- ColtEigenvalueDecomposition(matrix) - Constructor for class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- ColtSingularValueDecomposition - Class in net.maizegenetics.matrixalgebra.decomposition
-
- ColtSingularValueDecomposition(dm) - Constructor for class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- ColtSingularValueDecomposition(matrix) - Constructor for class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- column(j) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- column(j) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- column(j) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- column(j) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- column(index) - Method in class net.maizegenetics.util.ColumnMatrix
-
- columnLabels() - Static method in interface net.maizegenetics.analysis.modelfitter.ForwardRegression
-
- ColumnMatrix - Class in net.maizegenetics.util
-
- ColumnMatrix.Builder - Class in net.maizegenetics.util
-
- columnMean(data, col) - Static method in class net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
-
- columnNames - Variable in class net.maizegenetics.plugindef.GenerateRCode.TableReportVectors
-
- columnRank() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- columnRank() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- columnRank() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- columnRank() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- ColumnsToBinaryFullGenomeTablePlugin - Class in net.maizegenetics.analysis.monetdb
-
This plugin is copied from the ColumnsToBinarySNPOnlyTablePlugin (which was copied Kelly's ColumnsToBinaryPlugin, which re-worked various lynn methods) to create binary files for loading into the hmp321_snp table in the maizeFullGEnomeDB of the Rare Alleles monetdb instance. THe difference between this plugin and the ColumnsToBinarySNPOnlyTablePlugin is the latter creates entries only for identified hmp321 SNPs This method (ColumnsToBinaryFullGenomePlugin) creates entries for all positions listed in in the reference genome. To be consistent with the existing columns in monetdb maize tables, the reference file must be a link to a copy of the Zea_mays.AGPv3.20.dna.genome.fa file stored on andersonii in Research/Zea/Genotypes/Annotations/monetDB/refGenomeFiles. The "inputFile" parameter can be either a single file containing data for all chromosomes or a directory of files split by chromosome. If all chroms are in a single file, that file must be sorted by chromosome and position, and must contain a header line that contains the columns "chr" and "pos" along with user specified data columns. If the "inputFile" parameter is a directory, the only *.txt files it holds must be files intended for this processing. These files must be split by chromosome and must be named such that they will sort lexicographically in chromosome order. For example: files named chr01.txt, chr02.txt ... chr09.txt, chr10.txt will sort from 1-10. But files named chr1.txt, chr2,txt ... chr9.txt, chr10.txt will not. In the latter case, chr10.txt will be processed before the other files. This plugin may also be used to create binaries for the maizeChrom10DB. In this case, we still use the full reference genome, but only chrom 10 is processed. The inputFile paramaeter shoudl be just 1 file containing chromosome 10 data.
- ColumnsToBinaryFullGenomeTablePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- ColumnsToBinaryFullGenomeTablePlugin() - Constructor for class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- ColumnsToBinarySNPOnlyTablePlugin - Class in net.maizegenetics.analysis.monetdb
-
This plugin is copied from Kelly's ColumnsToBinaryPlugin (which was re-worked from various lynn methods) to create binary files for loading into the hmp321_snp table in the maizeFullGenomeDB of the Rare ALleles monetdb instance. THe difference between this plugin and the ColumnsToBinaryFullGenomeTablePlugin is the latter creates entries for all positions listed in the reference genome. This method only creates entries positions identified as SNPs from hmp321. To be consistent with the existing columns in monetdb, the reference directory must be a link to a directory that contains copies of the SNPPos_chromX.txt files stored on andersonii in Research/Zea/Genotypes/Annotations/monetDB/refGenomeFiles. The "inputFile" parameter can be either a single file containing data for all chromosomes or a directory of files split by chromosome. If all chroms are in a single file, that file must be sorted by chromosome and position, and must contain a header line that contains the columns "chr" and "pos" along with user specified data columns. If the "inputFile" parameter is a directory, the only *.txt files it holds must be files intended for this processing. These files must be split by chromosome and must be named such that they will sort lexicographically in chromosome order. For example: files named chr01.txt, chr02.txt ... chr09.txt, chr10.txt will sort from 1-10. But files named chr1.txt, chr2,txt ... chr9.txt, chr10.txt will not. In the latter case, chr10.txt will be processed before the other files.
- ColumnsToBinarySNPOnlyTablePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- ColumnsToBinarySNPOnlyTablePlugin() - Constructor for class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- ColumnsToBinaryUtils - Class in net.maizegenetics.analysis.monetdb
-
This class contains utility functions to aid in creating monetdb binaries
- columnSum(column) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- columnSum(column) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- columnSum(column) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- columnSum(column) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- columnType - Variable in class net.maizegenetics.plugindef.GenerateRCode.TableReportVectors
-
- combine(taxaDist1, taxaDist2) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Combines a TaxaDistribution to an expandable TaxaDistribution. Can be used to convert a single TaxaDistribution to an expandable version
- combine(bases) - Static method in class net.maizegenetics.taxa.tree.Parameterized.Utils
-
Combine multiple parameterized objects into one
- combine(baseOne, baseTwo) - Static method in class net.maizegenetics.taxa.tree.Parameterized.Utils
-
Combine multiple parameterized objects into one
- CombineDataSetsPlugin - Class in net.maizegenetics.analysis.data
-
- CombineDataSetsPlugin() - Constructor for class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
Creates a new instance of CombineDataSetsPlugin
- combineDonorHypothArrays(maxDonorHypotheses, dhs) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
Combines arrays of donorHypoth, sorts them, and returns the best limited by maxDonorHypotheses
- CombineGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
-
- CombineGenotypeTable - Class in net.maizegenetics.dna.snp
-
Combines multiple GenotypeTables together.
- combiner() - Method in class net.maizegenetics.dna.map.PositionList.PositionListCollector
-
- combiner() - Method in class net.maizegenetics.taxa.TaxaList.TaxaListCollector
-
- combiner() - Method in class net.maizegenetics.util.BitSet.BitSetListCollector
-
- combineTwoHaplotypesAsHeterozygote() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
If true, uses combination mode in focus block, else does not impute
- combineTwoHaplotypesAsHeterozygote(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Combine two haplotypes as heterozygote. If true, uses combination mode in focus block, else does not impute
- COMMENT_CHAR - Static variable in class net.maizegenetics.analysis.gbs.neobio.CharSequence
-
The character used to start a comment line in a sequence file. When this character is found, the rest of the line is ignored.
- COMMENT_CHAR - Static variable in class net.maizegenetics.analysis.gbs.neobio.FactorSequence
-
The character used to start a comment line in a sequence file. When this character is found, the rest of the line is ignored.
- COMMENT_CHAR - Static variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
The character used to start a comment line in the scoring matrix file.
- commentChar() - Method in class net.maizegenetics.dna.snp.io.LineIndex
-
- commentChar(commentChar) - Method in class net.maizegenetics.dna.snp.io.LineIndexBuilder
-
- Companion - Static variable in class net.maizegenetics.analysis.ListPluginParameters
-
- compare(index1, index2) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- compare(index1, index2) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- compare(index1, index2) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Compares tags at given indices.
- compare(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
Compare two PE tags
- compare(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- compare(index1, index2) - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- compare(index1, index2) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- compare(sequence1, sequence2) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- compare(ef, of) - Static method in class net.maizegenetics.stats.statistics.ChiSquareTest
-
chi square test
- compare(o1, o2) - Method in class net.maizegenetics.util.StringNumberComparator
-
- compareAlignment(origFile, maskFile, impFile, noMask) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
-
Legacy approach for measuring accuracy, but need to maintain some tests.
- compareAlignment(impGT, keyGT, taxaPrefix) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
-
Calculates proportion imputed, homozygous proportion right, heterozygous proportion right
- CompareGenosBetweenHapMapFilesPlugin - Class in net.maizegenetics.analysis.gbs
-
- CompareGenosBetweenHapMapFilesPlugin() - Constructor for class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- CompareGenosBetweenHapMapFilesPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- CompareGenosBetweenHapMapFilesPlugin.SiteCompareType - Enum in net.maizegenetics.analysis.gbs
-
- compareHaplotypes(h0, h1, overlap, haplength) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- compareOriginalAgainstImputed(originalFile, imputedFile) - Static method in class net.maizegenetics.analysis.gbs.ProductionPipelineMain
-
Generates basic summary information about imputation such as change in sites or taxa count change in missing data change in heterozygosity how many sites changed their major allele
- compareSequence(queryLong, maxDivCheck) - Method in class net.maizegenetics.analysis.gbs.Barcode
-
Return the minimum sequence divergence between a query sequence and barcode with its overhang
- compareTags(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- compareTags(index1, t2) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- compareTags(t1, t2) - Static method in class net.maizegenetics.dna.tag.AbstractTags
-
- compareTo(arg0) - Method in class net.maizegenetics.analysis.clustering.Haplotype
-
- compareTo(cluster) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- compareTo(anotherBarcode) - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- compareTo(other) - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- compareTo(other) - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- compareTo(o) - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- compareTo(o) - Method in class net.maizegenetics.dna.map.Chromosome
-
Compares chromosomes numerically if both are numbers. Otherwise compares as strings.
- compareTo(o) - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- compareTo(o) - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- compareTo(o) - Method in class net.maizegenetics.dna.snp.io.ReadBedfile.BedFileRange
-
- compareTo(o) - Method in class net.maizegenetics.dna.tag.AbstractTag
-
- compareTo(otherLevel) - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- compareTo(c) - Method in class net.maizegenetics.taxa.Taxon
-
- compareTo(o) - Method in class net.maizegenetics.util.Tuple
-
Using this method (i.e. sorting Tuples) seems to imply both x and y are Comparable. If that's not the case, results are unpredictable.
- componentHidden(e) - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- componentMoved(e) - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- componentResized(e) - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- componentShown(e) - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- compose(input) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- compose(components) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- compositeAlignments() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- compositeAlignments() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- compositeAlignments() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns individual genotype tables within this genotype table.
- compositeAlignments() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- compositeAlignments() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- CompressedDoubleMatrix - Class in net.maizegenetics.analysis.association
-
- CompressedDoubleMatrix(kinship, theTree) - Constructor for class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- CompressedDoubleMatrix.kinshipMethod - Enum in net.maizegenetics.analysis.association
-
- compressedMatrix - Variable in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- CompressedMLMusingDoubleMatrix - Class in net.maizegenetics.analysis.association
-
- CompressedMLMusingDoubleMatrix(parentPlugin, dataset, kinshipMatrix, useCompression, useP3D, compression) - Constructor for class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- CompressedMLMusingDoubleMatrix(parentPlugin, dataset, kinshipMatrix, weights, useCompression, useP3D, compression) - Constructor for class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- compression - Variable in class net.maizegenetics.analysis.association.MLMPlugin
-
- compression - Variable in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- compressionType - Variable in class net.maizegenetics.analysis.association.MLMPlugin
-
- compressionType - Variable in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- computeAllDistances(tree, a, dist, idist, countEdges, epsilon) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
- computeBlockTable() - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes the block table. This method is a general specification of how the block table should be computed. It creates the block table according to the number of factors of each sequence. It then goes over each position of the block table, retrieves the corresponding factors from each sequence, and repasses the information to the subclasses that will do the actual computation of each block using the scoring scheme previously set.
- computeBoxCox(phenotypeValues, minimumValue, randomSeed, startLambda, endLambda, stepLambda) - Static method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformation
-
- computeColumnMaxima(matrix, col_maxima) - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
Computes the column maxima of a given matrix. It first sets up arrays of row and column indexes to simulate a copy of the matrix (where all operations will be performed). It then calls the recursive protected computeColumnMaxima method.
- computeColumnMaxima(col_maxima) - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
This method implements the SMAWK algorithm to compute the column maxima of a given matrix. It uses the arrays of row and column indexes to performs all operations on this 'fake' copy of the original matrix.
- computeDistance(tree, a, b) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
compute distance between two external nodes
- computeGenotypeR(site1, site2, a) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- computeHetBitDistances(theTBA, taxon1, taxon2) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute distance for a pair of taxa.
- computeHetBitDistances(theTBA, taxon1, taxon2, minSitesCompared) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute distance for a pair of taxa.
- computeHetBitDistances(theTBA, taxon1, taxon2, minSitesCompared, firstWord, lastWord, maskBadSet) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute distance for a pair of taxa. Optimized for calculations sites within a certain range of underlying word (64 sites chunks) in the TBit array
- computeHetBitDistances(iMj, iMn, jMj, jMn, minSitesCompared) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Calculation of distance using the bit vector of major and minor alleles.
- computeHetBitDistances(iMj, iMn, jMj, jMn, minSitesCompared, firstWord, lastWord) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Calculation of distance using the bit vector of major and minor alleles.
- computeHetBitDistancesThirdState(iMj, iMn, iMn2, jMj, jMn, jMn2, minSitesCompared) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Calculation of distance using the bit vector of the first three alleles.
- computeHetBitDistancesThirdState(iMj, iMn, iMn2, jMj, jMn, jMn2, minSitesCompared, firstWord, lastWord) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Calculation of distance using the bit vectors of the first three alleles.
- computeHetDistances(first, second, minSitesComp) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
- computeHetDistances(first, second, minSitesComp) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
-
- computeHetDistances(first, second, minSitesComp) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
-
- computeMatrix() - Method in class net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
-
Computes the dynamic programming matrix.
- computeMatrix() - Method in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
Computes the dynamic programming matrix.
- computeMatrix() - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Computes the dynamic programming matrix. If the scoring scheme is not compatible with the loaded sequences.
- computeOutputBorder(block, row, col, dim, lc, lr) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
-
Computes the output border of a block. This is performed in five steps: Retrieve the block's input border; Retrieve the block's complete DIST matrix; Create an interface to the
class OutMatrix matrix from the input border and DIST matrix; Use
class Smawk to compute all column maxima of the OUT matrix (SMAWK finds the index of the row that contains the maximum value of a column); Assemble the output border by extracting the maximum values of each column of the OUT matrix using the information obtained in the previous step.
- computeOutputBorder(block, row, col, dim, lc, lr) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Computes the output border of a block. This method works essentially in the same way as its global alignment counterpart: Retrieve the block's input border; Retrieve the block's complete DIST matrix; Create an interface to the
class OutMatrix matrix from the input border and DIST matrix; Use
class Smawk to compute all column maxima of the OUT matrix (SMAWK finds the index of the row that contains the maximum value of a column); Assemble the output border by extracting the maximum values of each column of the OUT matrix using the information obtained in the previous step. However, it also check if there is a better path starting inside the block (an S path) and oupdate the output border accordingly. It also checks if this block has any path of score higher than the maximum score found so far.
- computePairwiseAlignment() - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes the block table (the result depends on subclasses, see computeBlockTable for details) and requests subclasses to retrieve an optimal alignment between the loaded sequences. The actual product depends on the subclasses which can produce a global (see CrochemoreLandauZivUkelsonGlobalAlignment) or local alignment (see CrochemoreLandauZivUkelsonLocalAlignment).
- computePairwiseAlignment() - Method in class net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
-
Builds an optimal global alignment between the loaded sequences after computing the dynamic programming matrix. It calls the buildOptimalAlignment method after the computeMatrix method computes the dynamic programming matrix.
- computePairwiseAlignment() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Subclasses must implement this method to compute an alignment between the loaded sequences using the scoring scheme previously set. This methid is called by the getPairwiseAlignment method when needed.
- computePairwiseAlignment() - Method in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
Builds an optimal local alignment between the loaded sequences after computing the dynamic programming matrix. It calls the buildOptimalAlignment method after the computeMatrix method computes the dynamic programming matrix.
- computeRForAlleles(site1, site2, a) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- computeRForMissingness(site1, site2, a) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- computeScore() - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes the block table (the result depends on subclasses, see computeBlockTable for details) and requests subclasses to locate the score of the highest scoring alignment between the two sequences in the block table. The result depends on the subclasses, and either a global alignment (see CrochemoreLandauZivUkelsonGlobalAlignment) or local alignment score (see CrochemoreLandauZivUkelsonLocalAlignment) will be produced.
- computeScore() - Method in class net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
-
Computes the score of the best global alignment between the two sequences using the scoring scheme previously set. This method calculates the similarity value only (doesn't build the whole matrix so the alignment cannot be recovered, however it has the advantage of requiring O(n) space only).
- computeScore() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Subclasses must implement this method to compute the score of the alignment between the loaded sequences using the scoring scheme previously set. This methid is called by the getScore method when needed.
- computeScore() - Method in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
Computes the score of the best local alignment between the two sequences using the scoring scheme previously set. This method calculates the similarity value only (doesn't build the whole matrix so the alignment cannot be recovered, however it has the advantage of requiring O(n) space only).
- computeScore() - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Computes the score of the best local alignment between the two sequences using the scoring scheme previously set. This method calculates the similarity value only (doesn't build the whole matrix so the alignment cannot be recovered, however it has the advantage of requiring O(n) space only).
- computeZKZ(data, X, Z, kin, traitname) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
Computes ZKZ. If compression is specified then the compressed ZKZ is calculated along with compressed versions of Z and K.
- concatenate(dm, rows) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- concatenate(dm, rows) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- concatenate(dm, rows) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- concatenate(dm, rows) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- concatenate() - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- configFile() - Method in class net.maizegenetics.tassel.PreferencesDialog
-
Global configuration file
- configFile(value) - Method in class net.maizegenetics.tassel.PreferencesDialog
-
Set Config File. Global configuration file
- connConfigFile() - Method in class net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
-
DB connection config file
- connConfigFile(value) - Method in class net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
-
Set DB Config File. DB connection config file
- connConfigFile() - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
DB connection config file
- connConfigFile(value) - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
Set DB config file. DB connection config file
- connection(propertiesFile) - Static method in class net.maizegenetics.analysis.gobii.BMSConnection
-
- connection(host, user, password, dbName) - Static method in class net.maizegenetics.analysis.gobii.BMSConnection
-
- connection(propertiesFile) - Static method in class net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
-
Creates a Postgres database connection given a properties file
- connection(host, user, password, dbName) - Static method in class net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
-
Creates a Postgres database connection.
- connectToDatabaseOrDie(dbName, props) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- connectToDB(configFile) - Static method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
- connectToDB(configFile) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- cons(car, cdr) - Static method in class net.maizegenetics.util.db.Pair
-
- contains(o) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- contains(o) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- contains(hap) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- contains(s) - Method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
checks if the String is in the trie.
- contains(o) - Method in class net.maizegenetics.dna.snp.FilterList
-
- contains(sublevel) - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- contains(sublevel) - Method in interface net.maizegenetics.stats.linearmodels.Level
-
- contains(taxon) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- containsAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- containsAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- containsAll(c) - Method in class net.maizegenetics.dna.snp.FilterList
-
- containsClade(root, clade) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- containsKey(key) - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- containsNovelTaxa(root, taxa) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- containsSubtree(root, node) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- containsValue(value) - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- contig - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Contigs in Long array
- ContigencyTable - Class in net.maizegenetics.stats.statistics
-
Class for permuting contigency tables and determining the likelihood of the table. If determining of the probability of a 2x2 table use FisherExact as it is much faster.
- ContigencyTable(maxSize) - Constructor for class net.maizegenetics.stats.statistics.ContigencyTable
-
constructor for Contigency table
- contigFile() - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
Input file containing contigs in fasta format.
- contigFile(value) - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
Set Input Fasta Contig File. Input file containing contigs in fasta format.
- contigLength - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Length of contigs, 0 means contig doesn't exist
- contigLengthInLong - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Length of contigs in Long primitive data type, 0 means contig doesn't exist
- contigPETagCount() - Method in class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
Make contigs of PETagCounts from forward and backward tags
- ContigPETagCountPlugin - Class in net.maizegenetics.analysis.gbs
-
- ContigPETagCountPlugin() - Constructor for class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- ContigPETagCountPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- contigPETags() - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
Make contigs from forward and backward tags
- contribution1 - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- contribution2 - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- convergence - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- convert(input, outputClass) - Static method in class net.maizegenetics.plugindef.AbstractPlugin
-
- convert(instance, target) - Static method in class net.maizegenetics.util.db.TransformerService
-
- ConvertAlignmentCoordinatesPlugin - Class in net.maizegenetics.analysis.data
-
- ConvertAlignmentCoordinatesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
- convertDoubleArrayToFloat(doubleArray) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- convertFloatArrayToDouble(floatArray) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- convertGenotypesToParentCalls() - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- convertGenotypeStringToDiploidByteArray(diploidString) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Convert a genotype (diploid) string (e.g. ACGTA) to arrays of diploid bytes (e.g. {0,17,34,51,0})
- convertGenotypeTableSiteToVariantContext(genotypeTable, sites) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
Method to convert a list of positions into a single variantContext record If sites only has one element, it will just create genotypes for that position(Fixing indels with missing information) If sites has multiple consecutive elements, it is likely an indel This needs to walk through the sites and combine the alleles together ignoring - and + nucleotides
- convertGenotypeTableToVariantContextList(genotypeTable) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
Method to convert a genotype table to a List of VariantContexts This is done by walking through the genotypeTable's positions in order. To Handle indels, we need to process a set of positions at a time It will start with the first position and hold its index temporarily Combine consecutive indel positions into this index list. A consecutive position is one where the chromosomes match, and the current position is less than 1 physical position away from the previous We need to check less than one as an insertion has the same physical reference position If the consecutive position also contains an indel character "+" or "-" we need to add it to the block Otherwise(either non indel or non-consecutive) process the previous block and setup a new block with the current site
- convertGenotypeToDoubleProbability(genotype, sitesByTaxa) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- convertGenotypeToFloatProbability(genotype, sitesByTaxa) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- convertHaplotypeStringToAlleleByteArray(haploString) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Convert a haploid (allele) string (e.g. ACGTA) to arrays of allele bytes (e.g. {0,1,2,3,0})
- convertNames(tree, filename) - Static method in class net.maizegenetics.taxa.tree.NewickUtils
-
This converts tree node names based on the
conversion file specified.
- convertNegativeBranchLengthsToZeroLength(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
If the given node or the sub tree defined by that node have negative branch lengths, they'll have zeron branch lengths after a call to this function!
- convertNucleotideGenotypesToStringList(data) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Converts the byte representation of genotypes to string list of genotypes
- ConvertOldFastqToModernFormatPlugin - Class in net.maizegenetics.util
-
This plugin takes a single fastq or a directory of fastq files in the "old" format and converts them to the "modern" illumina format. The old format had multiple taxa combined in a single file, with barcodes attaached to each read sequence. The new fastQ format has the taxa (samples) each in individual files. THis method takes the old fastq and for each read block, subsets the sequence to start after the barcode (but including the initial cut site) and end after the ending cut site. The quality score is subsetted identically to the sequence so the 2 match. Files are written to a user defined directory.
- ConvertOldFastqToModernFormatPlugin() - Constructor for class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- ConvertOldFastqToModernFormatPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- convertParentCallsToNucleotides(popdata) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- convertTableReportToGuavaTable(tr) - Static method in class net.maizegenetics.util.TableReportUtils
-
- convertToHDF5(hdf5Outfile) - Method in class net.maizegenetics.dna.snp.io.BuilderFromVCF
-
Create a HDF5 version of file from the VCF file. This is useful in many cases where VCF files are too large to load fully into memory.
- convertToTBTByte() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- convertToTBTByte() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- ConvertTreeNamesPlugin - Class in net.maizegenetics.analysis.tree
-
- ConvertTreeNamesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- ConvertTreeNamesPlugin() - Constructor for class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- ConvertTreeNamesPluginKt - Class in net.maizegenetics.analysis.tree
-
- copy() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
This function returns a copy of the component Haplotypes not references to them.
- copy() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- copy() - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- copy() - Method in class net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
-
- copy() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- copy() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- copy() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- copy() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- copy() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- copyGenotypes(t4File, newT5File) - Static method in class net.maizegenetics.analysis.data.MigrateHDF5FromT4T5
-
- copyOrthogonalizedData() - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- copyTagMapRow(sourceTOPM, sourceRow, destRow, merge) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
This helps collapse identical reads from different regions of the genome together.
- copyUColumns() - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- CoreGenotypeTable - Class in net.maizegenetics.dna.snp
-
- CorePhenotype - Class in net.maizegenetics.phenotype
-
- CorePhenotype(attributes, types, name) - Constructor for class net.maizegenetics.phenotype.CorePhenotype
-
- correctSelfPhaseUsingCross(selfPhaseFilename, crossPhaseFilename, parent, chr, outfileName) - Method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- cosine(data1, data2) - Static method in class net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
-
Computes the cosine similarity of two vectors.
- cosineSimRank(data, row, col, k) - Static method in class net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
-
Rank all the rows according to their cosine similarity with the given row.
- COUNT - Static variable in enum net.maizegenetics.dna.WHICH_ALLELE
-
Count of the number of allele types
- countAllelesAtAllSites() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- countHeterozygousSites() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- countNotMissing() - Method in class net.maizegenetics.analysis.clustering.Haplotype
-
- countParameters(ps) - Static method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- countSortOrder(counts, descending) - Static method in class net.maizegenetics.analysis.imputation.RephaseParents
-
- countTags(keyFileS, enzyme, inputFileSWithBarcode, inputFileSWithoutBarcode, minCount, tagLengthInLong) - Method in class net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
-
Derives a PETagCount list for a pair of Fastq files.
- countTags(keyFileS, enzyme, fastqDirectory, outputDir, maxGoodReads, minCount) - Static method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
Derives a tagCount list for each fastq file in the fastqDirectory.
- countTags(myInput, myOutput, maxGoodReads, minCount, maxCount) - Static method in class net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
-
Derives a tagCount list for each fastq file in the fastqDirectory.
- countTags(keyFileS, enzyme, inputFileSWithBarcode, inputFileSWithoutBarcode, minCount, tagLengthInLong) - Method in class net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
-
Derives a PETagCount list for a pair of Qseq files.
- countTags(keyFileS, enzyme, qseqDirectory, outputDir, maxGoodReads, minCount) - Static method in class net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
-
Derives a tagCount list for each qseq file in the qseqDirectory.
- countTaxaSharedWith(hapCluster) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- countUnknownAndHeterozygotes(a) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
Sums the number of unknown and heterozgyous sites in a byte genotype
- covariance() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
If the box is checked, then the analysis will do an eigenvalue decomposition of the covariance matrix. If the box is unchecked, it will use a correlation matrix. Using the covariance matrix is recommended for genotypes while the correlation matrix is often used for phenotypes.
- covariance(value) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Set covariance (alternative = correlation). If the box is checked, then the analysis will do an eigenvalue decomposition of the covariance matrix. If the box is unchecked, it will use a correlation matrix. Using the covariance matrix is recommended for genotypes while the correlation matrix is often used for phenotypes.
- covariateAttributeList - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- covariateAttributeStream() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- covariateAttributeStream() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- covariateAttributeStream() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- CovariateModelEffect - Class in net.maizegenetics.stats.linearmodels
-
- CovariateModelEffect(covariate) - Constructor for class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- CovariateModelEffect(covariate, id) - Constructor for class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- CovariatePermutationTestSpliterator - Class in net.maizegenetics.analysis.modelfitter
-
A Spliterator that uses the covariate from an AdditiveSite to test it against a baseModel and a list of permuted data sets using a fixed effect linear model. This class is used as part of stepwise model fitting to process a list of AdditiveSites. The permutation test is used to determine the entry and exit limits to be used for model fitting.
- CovariatePermutationTestSpliterator(permutedData, siteList, baseModel) - Constructor for class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- create(maxTaxa, taxaWithTag) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Create a TaxaDistribution with only a single taxa with a tag. Very memory efficient, but needs conversion add an additional taxon with a tag
- create(maxTaxa) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Create an expandable TaxaDistribution with no initial values
- create(maxTaxa, taxaWithTags, depthOfTags) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Create an fixed TaxaDistribution with set values
- create(encodedTaxaDistribution) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Create an fixed TaxaDistribution with set values
- create(srcTaxaDist) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Copies a TaxaDistribution to an expandable TaxaDistribution. Can be used to convert a single TaxaDistribution to an expandable version
- create(maxTaxa, encodeTaxaDepths) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
Create expandable TaxaDistribution from encoded taxa distribution. The int[] encoding use first three bytes for taxa index, and last byte for depth as unsigned byte. Depths greater than 256 just increase.
- createAnnoHDF5WithHapMap(hapMapDir, outputFile, currChr) - Method in class net.maizegenetics.dna.pd.PDAnnotation
-
- createAnova() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Create pre- and post-scan anova reports.
- createAnova(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Create anova reports. Create pre- and post-scan anova reports.
- createAnovaReport - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createAnovaReport(createIt) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createBlock(factor1, factor2, row, col) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes a block of the block table, which corresponds to an alignment block between one factor of sequence 1 and one factor of sequence 2. See subclasses for actual implementation.
- createBlock(factor1, factor2, row, col) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
-
Creates and computes all information of an alignment block. Its main job is to compute the DIST column for the block. It then request the computeOutputBorder method to compute the block's output border.
- createBlock(factor1, factor2, row, col) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Creates and computes all information of an alignment block. This method works essentially in the same way as its global alignment counterpart. Its main job is to compute the DIST column for the block. It then request the computeOutputBorder method to compute the block's output border. It also computes all S, C and E-paths of this block. Finally, it checks if the C-path of this block is higher than the highest score found so far.
- createChart(dataset) - Method in class net.maizegenetics.analysis.chart.XYScatterAndLinePanel
-
- createChart(dataset) - Method in class net.maizegenetics.analysis.chart.XYScatterMultipleYPanel
-
- createEffects() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Create a report of marker effects based on the scan results.
- createEffects(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Create effects report. Create a report of marker effects based on the scan results.
- createEffectsPrescan() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Create a report of marker effects based on the results pre-scan.
- createEffectsPrescan(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Create prescan effects. Create a report of marker effects based on the results pre-scan.
- createFile(inTags, newHDF5file) - Static method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Initialize HDF5 TOPM from TagCounts file. The "MAXMAPPING"(set to 0), "TAGLENGTHINLONG", "tags" and "tagLength" are added.
- createFile(inTags, newHDF5file, maxMapping, maxVariants) - Static method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- createFirstColumnBlock(factor1, factor2, row) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes a block at the first column (column zero) of the block table, which corresponds to an alignment block between one factor of sequence 1 and an empty string. See subclasses for actual implementation.
- createFirstColumnBlock(factor1, factor2, row) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
-
Creates and computes all information of an alignment block of the first column of the block table. This is a special case of the createBlock method.
- createFirstColumnBlock(factor1, factor2, row) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Creates and computes all information of an alignment block of the first column of the block table. This is a special case of the createBlock method.
- createFirstRowBlock(factor1, factor2, col) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes a block at the first row (row zero) of the block table, which corresponds to an alignment block between one factor of sequence 2 and an empty string. See subclasses for actual implementation.
- createFirstRowBlock(factor1, factor2, col) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
-
Creates and computes all information of an alignment block of the first row of the block table. This is a special case of the createBlock method.
- createFirstRowBlock(factor1, factor2, col) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Creates and computes all information of an alignment block of the first column of the block table. This is a special case of the createBlock method.
- createFixedEffectsArray(factorList, covariateList, missing, numberOfObservations) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- createFixedEffectsArray(factorList, covariateList, missing) - Static method in class net.maizegenetics.stats.linearmodels.LinearModelUtils
-
- createFrom(values) - Method in interface net.maizegenetics.util.db.DBTuple
-
- createFrom(values) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- createHDF5GenotypeModule(h5w) - Static method in class net.maizegenetics.util.HDF5Utils
-
- createHDF5PositionModule(h5w) - Static method in class net.maizegenetics.util.HDF5Utils
-
- createHDF5TagModule(h5w, tagLengthInLong) - Static method in class net.maizegenetics.util.HDF5Utils
-
- createHDF5TaxaList(writer, exportList) - Static method in class net.maizegenetics.taxa.TaxaListBuilder
-
- createHDF5TaxaModule(h5w) - Static method in class net.maizegenetics.util.HDF5Utils
-
- CreateHybridGenotypesPlugin - Class in net.maizegenetics.analysis.data
-
- CreateHybridGenotypesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- createIdxValues(configFile, outputDir, datasetID, platformID, experimentID) - Static method in class net.maizegenetics.analysis.gobii.UpdateMarkerAndDNA_idxes
-
- createIndex() - Method in class net.maizegenetics.analysis.data.LIXPlugin
-
Create Index for given file.
- createIndex(value) - Method in class net.maizegenetics.analysis.data.LIXPlugin
-
Set Create Index. Create Index for given file.
- createMaskForAlignmentConflicts(unimpAlign, donorAlign, print) - Static method in class net.maizegenetics.analysis.imputation.FILLINDonorGenotypeUtils
-
Create mask for all sites where major & minor are swapped between GenotypeTables returns in this order [goodMask, swapMjMnMask, errorMask, invariantMask]
- createMergeOutfile(infiles, outfile) - Static method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
Determines the dimensions of the merged matrix, and creates a RandomAccessFile on disk large enough to hold the data.
- createMergeOutfile(infiles, outfile) - Static method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
Determines the dimensions of the merged matrix, and creates a RandomAccessFile on disk large enough to hold the data.
- createMouseInputListener() - Method in class net.maizegenetics.tassel.SeqViewerPanel.MyTableUI
-
- createNameGidMap(mappingFile, taxaField) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- createNode() - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
create a node
- createNode(id) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
create a node, with a specified identifier
- createNode(id, height) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
create a node, with a specified identifier
- createNode(node) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
constructor used to clone a node and all children
- createNode(children) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
- createNode(children, height) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
Create a node with the specified children, and the specified branch height
- createNodeBranchLength(branchLength, id) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
create a node, with a specified identifier
- createNodeBranchLength(branchLength, children) - Static method in class net.maizegenetics.taxa.tree.NodeFactory
-
Create a node with the specified children, and the specified branch length
- createNodeList() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
count and list external and internal nodes and compute heights of each node
- createNodeList() - Method in interface net.maizegenetics.taxa.tree.Tree
-
This method is called to ensure that the calls to other methods in this interface are valid.
- createOrderEnumerator(size) - Method in interface net.maizegenetics.stats.math.OrderEnumerator.OEFactory
-
For generating an ordering from 0..size-1. Enumerator doesn't have to actually produce
- createParametizedWrapper(parameters, lowerLimits, upperLimits, defaultValues) - Static method in class net.maizegenetics.taxa.tree.Parameterized.Utils
-
Create a wrapper around a set of double arrays to create a parameterized object (changes to parameterized object change given arrays)
- createParametizedWrapper(parameters, lowerLimits, upperLimits, defaultValues, parametersSE) - Static method in class net.maizegenetics.taxa.tree.Parameterized.Utils
-
Create a wrapper around a set of double arrays to create a parameterized object (changes to parameterized object change given arrays)
- createParentalByteGenos(genos, parentAGenos, parentBGenos, hets) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- createPermutedData() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- createPhenotypeFromRDataFrameElements(taxaArray, colNames, attributeType, dataVectors) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- createPhenotypeFromTransform(taxaListNames, variableNames, data, outputObjectName, types) - Static method in class net.maizegenetics.phenotype.PhenotypeUtils
-
- createPhenotypeObjectFromDB(phenos) - Static method in class net.maizegenetics.phenotype.PhenotypeUtils
-
- createPhenotypeObjectFromDB2(phenos) - Static method in class net.maizegenetics.phenotype.PhenotypeUtils
-
- createPositions(genotypes, translate) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- createPostgreSQLStatement(conn) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- createPostScanEffectsReport - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createPostScanEffectsReport(createIt) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createPreScanEffectsReport - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createPreScanEffectsReport(createIt) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createRandomDistribution(arraySize, proportionToFill, maxValue) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- createRefTagsFromBlast(chromStartEndFile, forwardP, reverseP, refTagPositionMap) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- createReportFromCurrentModel(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- createReportFromCurrentModelWithCI(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- createReportRowsFromCurrentModel(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- createReportRowsFromCurrentModelAfterScanCI(sflm) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- createResiduals() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Create a phenotype dataset of model residuals for each chromosome. For each chromosome, the residuals will be calculated from a model with all terms EXCEPT the markers on that chromosome.
- createResiduals(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Create residuals. Create a phenotype dataset of model residuals for each chromosome. For each chromosome, the residuals will be calculated from a model with all terms EXCEPT the markers on that chromosome.
- createResidualsByChr - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createResidualsByChr(createIt) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createResPhenotype(emma, taxa, traitName) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- createRootBlock(factor1, factor2) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Computes the root block of the block table. See subclasses for actual implementation.
- createRootBlock(factor1, factor2) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
-
Creates the root block. This is a special case of the createBlock method. No information is actually computed.
- createRootBlock(factor1, factor2) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Creates the root block. This is a special case of the createBlock method. No information is actually computed.
- createSmallCallTable(variants) - Static method in class net.maizegenetics.util.BuilderFromVCFUtil
-
- createStep() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Create a report of the which markers enter and leave the model as it is being fit.
- createStep(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Create step report. Create a report of the which markers enter and leave the model as it is being fit.
- createStepReport - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createStepReport(createIt) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- createSubPops(popdata, isNAM) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- createTaxa(genotypes, translate) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- createTaxaMap(conn, mappingFile) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- CreateTreePlugin - Class in net.maizegenetics.analysis.tree
-
- CreateTreePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Creates a new instance of CreateTreePlugin
- CreateTreePlugin.CLUSTERING_METHOD - Enum in net.maizegenetics.analysis.tree
-
- creatMergeTBTByTagCount(infileDirS, outfileS, tagCountFileS) - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- creatTagGeneticMappingInfoDatasets(startIndex, size) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Creat datasets in HDF5 holding genetic mapping information, which is used to test multiple alignment hypothesis
- creatTagGeneticMappingInfoGWDataset() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Creat dataset in HDF5 holding genome wide genetic mapping information, which is used to build training dataset to predict hypothesis genetic mapping
- creatTagMappingInfoDatasets(startIndex, size) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Creat datasets in HDF5 holding mapping information, which is used to annotate the TOPM with multiple alignment hypothesis
- criterionValue - Variable in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- criterionValue() - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- criterionValue(value) - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- criterionValue() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- criterionValue(value) - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- CrochemoreLandauZivUkelson - Class in net.maizegenetics.analysis.gbs.neobio
-
This abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
- CrochemoreLandauZivUkelsonGlobalAlignment - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
- CrochemoreLandauZivUkelsonLocalAlignment - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
- crossproduct() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- crossproduct(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- crossproduct() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- crossproduct(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- crossproduct() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- crossproduct(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- crossproduct() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- crossproduct(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- CrossProgenyEmissionMatrix - Class in net.maizegenetics.analysis.imputation
-
- CrossProgenyEmissionMatrix(hap, originalGenotypes, taxonIndex, siteIndices) - Constructor for class net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
-
- CrossProgenyEmissionMatrix(hapProbs, originalGenotypes, stateByObs, taxonIndex, siteIndices) - Constructor for class net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
-
- culledFiles(directoryFiles, keyFile) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Produces a list of fastq files that are represented by the plugin's keyfile
- currentBlockIndex - Variable in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- currentIndex - Variable in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- currentTraitName - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- currentTraitName - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- cutOrSnpPosition() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Cut Position
- cutOrSnpPosition(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Set cut position.
- data - Variable in class net.maizegenetics.analysis.gbs.neobio.Trie
-
This node's stored data.
- DATA_SOURCE - Static variable in class net.maizegenetics.util.db.LambdaTuplesContext
-
- DataAccessException - Exception in net.maizegenetics.util.db
-
General runtime Exception used to rethrow checked exceptions. It adds a bit of intelligence in that it adds an errorCode and state which it stored based on the wrapped exception (see SQL exception) User: julian3 Date: 2013/11/10 Time: 7:15 PM PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- DataAccessException() - Constructor for exception net.maizegenetics.util.db.DataAccessException
-
- DataAccessException(message) - Constructor for exception net.maizegenetics.util.db.DataAccessException
-
- DataAccessException(message, cause) - Constructor for exception net.maizegenetics.util.db.DataAccessException
-
- DataAccessException(cause) - Constructor for exception net.maizegenetics.util.db.DataAccessException
-
- DataAccessException(message, cause, enableSuppression, writableStackTrace) - Constructor for exception net.maizegenetics.util.db.DataAccessException
-
- dataAttributeList - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- dataAttributeStream() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- dataAttributeStream() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- dataAttributeStream() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- dataname - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- dataset() - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
Dataset Name
- dataset(value) - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
Set Dataset Name. Dataset Name
- DataSet - Class in net.maizegenetics.plugindef
-
This is a set of Datum.
- DataSet(list, creator) - Constructor for class net.maizegenetics.plugindef.DataSet
-
Creates a new instance of Datum
- DataSet(theDatum, creator) - Constructor for class net.maizegenetics.plugindef.DataSet
-
Convenience constructor for a single Datum
- DataSet(list, creator) - Constructor for class net.maizegenetics.plugindef.DataSet
-
Creates a new instance of Datum
- dataSetDescription() - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
(Optional) Short data set description to be added as an root level annotation under "dataSetDescription"
- dataSetDescription(value) - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
Set Data set description. (Optional) Short data set description to be added as an root level annotation under "/DataSetDescription"
- dataSetDescription() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
(Optional) Short data set description to be added as an root level annotation under "dataSetDescription"
- dataSetDescription(value) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Set Data set description. (Optional) Short data set description to be added as an root level annotation under "/DataSetDescription"
- dataSetDescription(dataSetDescription) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- dataSetName() - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
(Optional) Short data set name to be added as an root level annotation under "/DataSetName"
- dataSetName(value) - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
Set Data set name. (Optional) Short data set name to be added as an root level annotation under "dataSetName"
- dataSetName() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
(Optional) Short data set name to be added as an root level annotation under "/DataSetName"
- dataSetName(value) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Set Data set name. (Optional) Short data set name to be added as an root level annotation under "dataSetName"
- datasetName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Name of dataset for this data. Must match one the name of one of the administered datasets in the db.
- datasetName(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set Dataset Name. Name of dataset for this data. Must match one the name of one of the administered datasets in the db.
- datasetName() - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
Name of dataset whose marker and dnarun IDs are to be pulled
- datasetName(value) - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
Set dataset name. Name of dataset whose marker and dnarun IDs are to be pulled
- datasetName() - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
Name of dataset whose marker and dnarun IDs are to be pulled
- datasetName(value) - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
Set dataset name. Name of dataset whose marker and dnarun IDs are to be pulled
- dataSetName(dataSetName) - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- dataSetReturned(event) - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
- dataSetReturned(event) - Method in class net.maizegenetics.analysis.data.PassThroughPlugin
-
- dataSetReturned(event) - Method in class net.maizegenetics.pipeline.TasselPipeline
-
Returns Tassel data set after complete.
- dataSetReturned(event) - Method in class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- dataSetReturned(event) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
Returns data set after complete.
- dataSetReturned(event) - Method in class net.maizegenetics.plugindef.DefaultPluginListener
-
- dataSetReturned(event) - Method in interface net.maizegenetics.plugindef.PluginListener
-
Returns Tassel data set after complete.
- dataSetReturned(event) - Method in class net.maizegenetics.progress.PluginProgressUnit
-
- dataSetReturned(event) - Method in class net.maizegenetics.tassel.DataTreePanel
-
Returns Tassel data set after complete.
- DataTreePanel - Class in net.maizegenetics.tassel
-
- DataTreePanel(theQAF) - Constructor for class net.maizegenetics.tassel.DataTreePanel
-
- dataVector - Variable in class net.maizegenetics.plugindef.GenerateRCode.TableReportVectors
-
- Datum - Class in net.maizegenetics.plugindef
-
This wraps data elements used as input or output to Tassel modules.
- Datum(name, data, comment) - Constructor for class net.maizegenetics.plugindef.Datum
-
Creates a new instance of Datum
- datumList() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- datumList() - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- datumList() - Method in class net.maizegenetics.analysis.association.PhenotypeLM
-
- DAYS - Variable in interface net.maizegenetics.taxa.tree.Units
-
- dbConfigFile() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
DB connection config file
- dbConfigFile(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set dbConfigFile. DB connection config file
- dbConfigFile() - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
DB connection config file
- dbConfigFile(value) - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
Set dbConfigFile. DB connection config file
- dbConfigFile() - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
DB connection config file
- dbConfigFile(value) - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
Set dbConfigFile. DB connection config file
- dBFile() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Input database file with tags and taxa distribution
- dBFile(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Input DB. Input database file with tags and taxa distribution
- dBFile() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Name of output file (e.g. GBSv2.db)
- dBFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Set GBS DB File. Name of output file (e.g. GBSv2.db)
- dBName() - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
Database Name
- dBName(value) - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
Set Database Name. Database Name
- DBTuple - Interface in net.maizegenetics.util.db
-
A tuple is as defined in the relational model, where each element is defined by a name, and is ordered according to the order of elements in the resultant set User: julian3 Date: 2013/11/14 Time: 12:12 PM PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- dcoP - Variable in class net.maizegenetics.dna.map.TagMappingInfo
-
Double cross-over probability Round(Log2(P)), unknown Byte.MIN_VALUE
- dcoP - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Double cross-over probability Round(Log2(P)), unknown = Byte.MIN_VALUE
- deCode(evidenceByte) - Static method in enum net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
-
- decodeBySign(srcCompChunk) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- decodeBySign(source) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- decodeBySign(srcCompChunk) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- decodeBySign(source) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- decodeSnpName(name) - Static method in class net.maizegenetics.dna.snp.io.ReadNumericMarkerUtils
-
- DEFAULT - Static variable in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- DEFAULT_ATTRIBUTES_PATH - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- DEFAULT_CITATION - Static variable in class net.maizegenetics.plugindef.AbstractPlugin
-
- DEFAULT_LENGTH - Variable in interface net.maizegenetics.taxa.tree.BranchLimits
-
default branch length
- DEFAULT_MAX_NUMBER_ENTRIES - Static variable in class net.maizegenetics.util.ExceptionUtils
-
Default maximun number of entries.
- DEFAULT_NAME - Static variable in class net.maizegenetics.phenotype.TaxaAttribute
-
- DefaultDBTuple - Class in net.maizegenetics.util.db
-
Default implementation of a Tuple. It is a simple extension of an ArrayList and stored the values as an array User: julian3 Date: 2013/11/10 Time: 7:05 PM PROJECT: lambda_tuples DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- DefaultDBTuple(list) - Constructor for class net.maizegenetics.util.db.DefaultDBTuple
-
- DefaultDBTuple(values) - Constructor for class net.maizegenetics.util.db.DefaultDBTuple
-
- DefaultPluginListener - Class in net.maizegenetics.plugindef
-
- defaultValue() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- degree(n) - Method in class net.maizegenetics.util.DirectedGraph
-
- degree(n) - Method in interface net.maizegenetics.util.Graph
-
Gets the degree of a node
- degree(n) - Method in class net.maizegenetics.util.UndirectedGraph
-
- degreesOfFreedom() - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
-
- deleteByThreshold(threshold) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- deleteElements(name) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- deleteOddColumns() - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
This method simulates a deletion of odd rows by manipulating the col array of indexes. In fact, nothing is deleted, but the indexes are moved to the end of the array in a way that they can be easily restored by the restoreOddColumns method using a reverse approach.
- deleteOldData() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Delete exisiting Discovery data from DB
- deleteOldData(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Delete old data flag. True indicates we want the db tables cleared
- deleteOldData() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Delete exisiting DB
- deleteOldData(value) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Set Delete old data flag. True indicates we want the db tables cleared
- deleteOldData() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Delete exisiting Alignment data from DB
- deleteOldData(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Set Delete old data flag. True indicates we want the db tables cleared
- deleteOldData() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Delete exisiting SNP Quality data from DB
- deleteOldData(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Set Delete old data flag. True indicates we want the db tables cleared
- deleteOldData() - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
Delete existing SNP quality data from db tables
- deleteOldData(value) - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
Set Delete Old Data. Delete existing SNP quality data from db tables
- deleteRow(reduced_rows, k) - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
This method simulates a deletion of a row in the matrix during the reduce operation. It just moves the index to the end of the array in a way that it can be restored afterwards by the restoreRows method (nothing is actually deleted). Deleted indexes are kept in ascending order.
- deleteSelectedNodes() - Method in class net.maizegenetics.tassel.DataTreePanel
-
- deleteTaxon(taxonName) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- DELIMITER - Static variable in class net.maizegenetics.taxa.Taxon
-
- delta - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- dependentOnParameter(parameter) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- dependentOnParameter(parameter, value) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- dependentOnParameter(parameter, values) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- dependentOnParameter() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- dependentOnParameterValue() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- depth() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
Total depth
- depth() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- depth() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- depth() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns allele depth object (null if not present)
- DEPTH - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- depth() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- depth(taxon, site) - Method in class net.maizegenetics.dna.snp.score.AlleleDepth
-
Returns sum of all nucleotide depths at given taxon and site.
- depth() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- DEPTH_BYTE_MISSING - Static variable in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
- DEPTH_MISSING - Static variable in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
- depthByteToInt(depth) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
Converts byte depth to integer version. Positive depths value are exact, negative depths are log approximations
- depthByteToInt(depth) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
Converts byte arrays of depth to integer array version. Positive depths value are exact, negative depths are log approximations
- depthForAllele(taxon, site, allele) - Method in class net.maizegenetics.dna.snp.score.AlleleDepth
-
Same as value() but translates allele into scoreType
- depthForAlleles(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- depthForAlleles(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- depthForAlleles(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns depth count for each diploid allele at the given taxon and site.
- depthForAlleles(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- depthForAlleles(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- depthForSite(site) - Method in class net.maizegenetics.dna.snp.score.AlleleDepth
-
Returns sum of all nucleotide depths across all taxa at given site.
- depthForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.score.AlleleDepth
-
Returns sum of all nucleotide depths across all sites at given taxon.
- depthIntToByte(depth) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
Converts integer depth to byte version. Positive return values are exact, negative return values are log approximations
- depthIntToByte(depth) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
Converts integer array of depth to byte array version. Positive return values are exact, negative return values are log approximations
- depthIntToByte(depth) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthUtil
-
Converts a two dimensional integer array of depths to a 2D byte array version. Positive return values are exact, negative return values are log approximations
- depthMergeSelection() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Selection for How to Merge Depths
- depthMergeSelection(value) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Set Depth Merge Rule. Selection for How to Merge Depths
- depthOfGenotypesToMask() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Depth of genotypes to mask for accuracy calculation if depth information available
- depthOfGenotypesToMask(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Depth of genotypes to mask. Depth of genotypes to mask for accuracy calculation if depth information available
- depths() - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Distribution of taxa depths across all taxa. Taxa with zero depth are included in the array
- depthToOutput() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Output depth: write depths to the output hdf5 genotypes file
- depthToOutput(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
User sets true or false, indicating if they do or do not want depth information written to the HDF5 file.
- depthToOutput() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Output depth: write depths to the output hdf5 genotypes file
- depthToOutput(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
User sets true or false, indicating if they do or do not want depth information written to the HDF5 file.
- description(description) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- description() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- detailedSystemOutOnHaplotypes() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Details of taxa included in each haplotype to system out
- detailedSystemOutOnHaplotypes(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Detailed system out on haplotypes. Details of taxa included in each haplotype to system out
- determineKeyFormat(keyFile) - Static method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- determineQualityScoreBase(fastqFile) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Method for reading FastQ four line structure, and returning a string array with [sequence, qualityScore]
- df - Variable in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
-
- dfError - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- dfMarker - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- dfModel - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- dfsLabeledEdges(G, source) - Static method in class net.maizegenetics.util.GraphUtils
-
Produces edges in a depth-first search starting at source and labeled -1,0,1 for forward, reverse, and nontree (direction type). Based on http://www.ics.uci.edu/~eppstein/PADS/DFS.py by D. Eppstein, July, 2004
- dfsPostorderNodes(G, source) - Static method in class net.maizegenetics.util.GraphUtils
-
Produces nodes in a depth-first search post-ordering starting at source (i.e. listing node starting with the last node and headed toward source)
- dfsPreorderNodes(G, source) - Static method in class net.maizegenetics.util.GraphUtils
-
Produces nodes in a depth-first search pre-ordering starting at source (i.e. listing node starting with the source node)
- diagonal(diag) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- DIAGONAL_DIRECTION - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
A constant that indicates that the diagonal direction must be followed to reach the source of an optimal path in a block during the trace back procedure to retrieve a high scoring alignment.
- DialogUtils - Class in net.maizegenetics.gui
-
- diceWithMetaphone(s1, s2, ignoreCase, ignoreWhite, ignorePunc) - Static method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- DifferenceGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
-
- DifferenceGenotypeCallTable(base, hybrids, parents) - Constructor for class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- dim - Variable in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
The dimension of the OUT matrix.
- dimension - Variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Dimension of the (squared) matrix.
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- diploidAsString(site, value) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns String representation of diploid allele value at site.
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- diploidAsString(site, value) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns String representation of diploid allele value at site.
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- diploidAsString(site, value) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- DirectedGraph<T> - Class in net.maizegenetics.util
-
Class used to represent a directed graph The design is inspired by the Python networkx library (https://networkx.github.io/)
- DirectedGraph(nodes, adj, pred, wts) - Constructor for class net.maizegenetics.util.DirectedGraph
-
- direction - Variable in class net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
-
An array of directions that must be followed to reach the source of the highest scoring path for each entry in the output border.
- direction - Variable in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- direction() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- DirectoryCrawler - Class in net.maizegenetics.util
-
Directory crawler that matches REGEX or Glob patterns. Glob patterns are indicated by using the syntax:pattern approach that is used by PathMatcher. So to use glob "glob:*.{hmp,hmp.gz}"
- dirOfFiles() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
Directory contains files for sub-matrices. Can be text (.txt) containing chromosome / positions, Bed (.bed), or Position List (.json or .json.gz)
- dirOfFiles(value) - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
Set Dir Of Files. Directory contains files for sub-matrices. Can be text (.txt) containing chromosome / positions, Bed (.bed), or Position List (.json or .json.gz)
- discoverSNPsOnChromosome(targetChromo, locusLogDOS) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- DiscoverySNPCallerPlugin - Class in net.maizegenetics.analysis.gbs
-
This class aligns tags at the same physical location against one another, calls SNPs, and then outputs the SNPs to a HapMap file. It is multi-threaded, as there are substantial speed increases with it.
- DiscoverySNPCallerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- DiscoverySNPCallerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- DiscoverySNPCallerPluginV2 - Class in net.maizegenetics.analysis.gbs.v2
-
This class aligns tags at the same physical location against one another, calls SNPs, and then outputs the SNPs to a HapMap file. It is multi-threaded, as there are substantial speed increases with it.
- DiscoverySNPCallerPluginV2() - Constructor for class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- DiscoverySNPCallerPluginV2(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- DiscreteSitesFELM - Class in net.maizegenetics.analysis.association
-
- DiscreteSitesFELM(dataset, parentPlugin) - Constructor for class net.maizegenetics.analysis.association.DiscreteSitesFELM
-
- displayDecimal(out, number, width) - Method in class net.maizegenetics.util.FormattedOutput
-
print decimal number with a prespecified number of digits after the point
- displayInteger(out, num, maxNum) - Method in class net.maizegenetics.util.FormattedOutput
-
print integer, aligned to a reference number, (introducing space at the left side)
- displayIntegerWhite(out, maxNum) - Method in class net.maizegenetics.util.FormattedOutput
-
print whitespace of length of a string displaying a given integer
- displayLabel(out, label, width) - Method in class net.maizegenetics.util.FormattedOutput
-
print label with a prespecified length (label will be shortened or spaces will introduced, if necessary)
- displayNamPCsOnTASSELGUI(PCResults, chrVector, posVector, startPosVector, endPosVector, theGenotypesForCalculatingPCs) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- displayProjectedPCsOnTASSELGUI(ProjectedPCs, chrVector, posVector, startPosVector, endPosVector, theAlignmentForGenotype) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- dist - Variable in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
The DIST matrix of a block.
- dist(b1, b2, min) - Static method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Alternative to current IBS distance measure AA <> AA = 0 Aa <> Aa = 0 distance (normal IBS distance this is 0.5) AA <> aa = 1 distance
- dist(b1, b2, min) - Static method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Alternative to current IBS distance measure AA <> AA = 0 Aa <> Aa = 0 distance (normal IBS distance this is 0.5) AA <> aa = 1 distance
- dist(b1, b2, min) - Static method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
Alternative to current IBS distance measure AA <> AA = 0 Aa <> Aa = 0 distance (normal IBS distance this is 0.5) AA <> aa = 1 distance
- dist_column - Variable in class net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
-
The DIST column of this block.
- distance(data1, data2, isManhattan) - Static method in class net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
-
Compute Manhattan or Eulcidean distance between two vectors.
- distance2clusterIndex - Variable in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- distance_choice() - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- distance_choice(value) - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- distanceFrom(h0) - Method in class net.maizegenetics.analysis.clustering.Haplotype
-
Distance is defined as the sum of the distances between each pair of sites. If one or both of the sites are missing then the distance is zero. If the sites are equal the distance is zero. If both sites are homozygous but different, the distance is 2. If one site is heterozygous, the distance is 1.
- distanceMatrix() - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- DistanceMatrix - Class in net.maizegenetics.taxa.distance
-
Storage for pairwise distance matrices. Only stores half the matrix as it is symmetrical.
- DistanceMatrix(distance, taxa) - Constructor for class net.maizegenetics.taxa.distance.DistanceMatrix
-
Constructor taking distances array and taxa list. Use DistanceMatrixBuilder instead of this.
- DistanceMatrix(distances, taxa, annotations) - Constructor for class net.maizegenetics.taxa.distance.DistanceMatrix
-
Use DistanceMatrixBuilder instead of this.
- DistanceMatrix(dm) - Constructor for class net.maizegenetics.taxa.distance.DistanceMatrix
-
Constructor that clones a distance matrix.
- DistanceMatrix(dm, subset) - Constructor for class net.maizegenetics.taxa.distance.DistanceMatrix
-
Constructor that clones a distance matrix and for only the specified taxa.
- DistanceMatrixBuilder - Class in net.maizegenetics.taxa.distance
-
- DistanceMatrixPlugin - Class in net.maizegenetics.analysis.distance
-
- DistanceMatrixPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
- DistanceMatrixRangesPlugin - Class in net.maizegenetics.analysis.distance
-
- DistanceMatrixRangesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- DistanceMatrixUtils - Class in net.maizegenetics.taxa.distance
-
Utility functions for distance matrices
- DistanceMatrixWithCounts - Class in net.maizegenetics.taxa.distance
-
- divergence - Variable in class net.maizegenetics.dna.map.TagMappingInfo
-
Number of diverging bp (edit distance) from reference, unknown = Byte.MIN_VALUE
- divergence - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Number of diverging bp (edit distance) from reference, unknown = Byte.MIN_VALUE
- DiversityAnalyses - Class in net.maizegenetics.analysis.popgen
-
This method calculated estimates of nucleotide diversity (pi, theta, etc). In order to provide high performance, it establishes one nucleotide SitePattern, and then manipulates the weighting patterns for sliding windows and different types of sites. Total segregating sites needs to be adjusted for missing and gap data, as this will modify Theta and Tajima estimates
- DiversityAnalyses(aa, slidingWindow, start, end, window, step, thePolymorphismDistribution) - Constructor for class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
Constructor that uses a sliding window
- DiversityAnalyses(aa, slidingWindow, start, end, window, step) - Constructor for class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- divideChromosome(a, appoxSitesPerHaplotype, verboseOutput) - Static method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Divides a genome up into roughly equally sized blocks of sites
- divideChromosome(a, appoxSitesPerHaplotype) - Static method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- doesGenotypeDepthExist(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- doesGenotypeModuleExist(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- doesOverlapMatch(h0, h1, overlap, forward) - Static method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- doesTaxaModuleExist(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- doesTaxonHaveAllAnnotations(taxon, filters) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Tests whether a taxon has annotation values in the map
- doMerge(c0, c1, maxdiff) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
Tests whether two clusters are less than or equal to maxdiff distant. Uses clusterDistanceMaxPairDiff() to calculate distance.
- DominanceNormalizedIBSMatrix - Class in net.maizegenetics.analysis.distance
-
- DominanceRelationshipMatrix - Class in net.maizegenetics.analysis.distance
-
Compute Dominance Relationship Matrix for all pairs of taxa. Missing sites are ignored. http://www.genetics.org/content/198/4/1759.abstract
- donor1Taxon - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- donor2Taxon - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- donorDir() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Directory containing donor haplotype files from output of FILLINFindHaplotypesPlugin. All files with '.gc' in the filename will be read in, only those with matching sites are used
- donorDir(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Donor Dir. Directory containing donor haplotype files from output of FILLINFindHaplotypesPlugin. All files with '.gc' in the filename will be read in, only those with matching sites are used
- donorDir() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Directory containing donor haplotype files from output of the FILLINFindHaplotypesPlugin. All files with '.gc' in the filename will be read in, only those with matching sites are used
- donorDir(value) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Set Donor Dir. Directory containing donor haplotype files from output of the FILLINFindHaplotypesPlugin. All files with '.gc' in the filename will be read in, only those with matching sites are used
- DonorHaplotypes - Class in net.maizegenetics.dna.map
-
Defines the haplotypes and positions of a chromosomal segment
- DonorHaplotypes(chromosome, startPosition, endPosition, parent1index, parent2index) - Constructor for class net.maizegenetics.dna.map.DonorHaplotypes
-
- DonorHypoth - Class in net.maizegenetics.analysis.popgen
-
- DonorHypoth(targetTaxon, donor1Taxon, donor2Taxon, startBlock, focusBlock, endBlock, totalSites, mendelianErrors) - Constructor for class net.maizegenetics.analysis.popgen.DonorHypoth
-
- DonorHypoth(targetTaxon, donor1Taxon, donor2Taxon, startBlock, focusBlock, endBlock) - Constructor for class net.maizegenetics.analysis.popgen.DonorHypoth
-
- donorMapFile() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
tab-delimited File containing a TaxaColumn name to be used to map breakFile donors with a GID. This may be the same file that was used for adding germplasm and marker data.
- donorMapFile(value) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Set mappingFile. tab-delimited File containing a TaxaColumn name to be used to map breakFile donors with a GID. This may be the same file that was used for adding germplasm and marker data.
- dosage() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- dosage(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- dosage() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- dosage(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- dosage() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns dosage object (null if not present)
- dosage(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
- dosage() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- dosage(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- Dosage - Class in net.maizegenetics.dna.snp.score
-
- dosage() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- dosage(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- DosageBuilder - Class in net.maizegenetics.dna.snp.score
-
- doTagsByTaxaExist(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- doTagsExist(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- doTaxonCallsExist(reader, taxonName) - Static method in class net.maizegenetics.util.HDF5Utils
-
- doTaxonCallsExist(reader, taxon) - Static method in class net.maizegenetics.util.HDF5Utils
-
- DoubleFormat - Class in net.maizegenetics.util
-
- DoubleMatrix - Interface in net.maizegenetics.matrixalgebra.Matrix
-
- DoubleMatrixFactory - Class in net.maizegenetics.matrixalgebra.Matrix
-
- DoubleMatrixFactory(type) - Constructor for class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- DoubleMatrixFactory.FactoryType - Enum in net.maizegenetics.matrixalgebra.Matrix
-
- doubleValue(obs) - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- doubleValues() - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- dprime(value) - Method in class net.maizegenetics.analysis.popgen.LDResult.Builder
-
- dPrime() - Method in class net.maizegenetics.analysis.popgen.LDResult
-
- DPRIME - Static variable in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- duplicateHetsThreshold() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Threshold for defining heterozygous sites
- duplicateHetsThreshold(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Set HeterozygousThreshold. Threshold for defining heterozygous sites
- duplicateHetsThreshold() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Threshold for defining heterozygous sites
- duplicateHetsThreshold(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Set HeterozygousThreshold. Threshold for defining heterozygous sites
- DynamicBitStorage - Class in net.maizegenetics.dna.snp.bit
-
Provides rapid conversion routines and caching from byte encoding of nucleotides to bit encoding. Only two alleles are supported for each scope (e.g. Major and minor, or Reference and Alternate).
- DynamicBitStorage(genotype, allele, prefAllele) - Constructor for class net.maizegenetics.dna.snp.bit.DynamicBitStorage
-
- G - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- G_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- G_DIPLOID_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- gamma() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- gamma() - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- GammaDistribution - Class in net.maizegenetics.stats.statistics
-
gamma distribution. (Parameters: shape, scale; mean: scale*shape; variance: scale^2*shape)
- GammaFunction - Class in net.maizegenetics.stats.math
-
gamma function
- GAP_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- GAP_ALLELE_CHAR - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- GAP_ALLELE_STR - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- GAP_CHARACTER - Static variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Character that signals a gap in sequence.
- gap_cost - Variable in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
The cost of a gap (an insertion or deletion of a character).
- GAP_DIPLOID_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- gap_penalty() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
- gap_penalty(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Gap Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
- gap_penalty() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
- gap_penalty(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Gap Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
- gap_penalty() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
- gap_penalty(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Gap Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when when a gap is identified.
- GAP_TAG - Static variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Character that signals a gap in the score tag line of an alignment.
- gapAlignmentThreshold() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Maximum gap alignment allowed from the equation: IndelContrast / (IndelContrast/Non-IndelContrast) IC=Indel contrasts=Sum the number ACGT vs - NC=non-indel constrasts = Sum the number of ACGT vs ACGT ignore = - vs - Gapped Alignment ratio = IC/(IC+NC)
- gapAlignmentThreshold(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Maximum gap alignment allowed from the equation: IndelContrast / (IndelContrast/Non-IndelContrast) IC=Indel contrasts=Sum the number ACGT vs - NC=non-indel constrasts = Sum the number of ACGT vs ACGT ignore = - vs - Gapped Alignment ratio = IC/(IC+NC)
- gapped_seq1 - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
First gapped sequence.
- gapped_seq2 - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Second gapped sequence.
- gBSDBFile() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Name of output file (e.g. GBSv2.db)
- gBSDBFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Set GBS DB File. Name of output file (e.g. GBSv2.db)
- GBSEnzyme - Class in net.maizegenetics.analysis.gbs.v2
-
Determines which cut sites to look for, and sets them, based on the enzyme used to generate the GBS library. For two-enzyme GBS both enzymes MUST be specified and separated by a dash "-". e.g. PstI-MspI, SbfI-MspI The enzyme pair "PstI-EcoT22I" uses the Elshire common adapter while PstI-MspI, PstI-TaqI, and SbfI-MspI use a Y adapter (Poland et al. 2012)
- GBSEnzyme(enzyme) - Constructor for class net.maizegenetics.analysis.gbs.v2.GBSEnzyme
-
- GBSHDF5Constants - Class in net.maizegenetics.dna.tag
-
Path definitions for the HDF5 GBS file formats.
- GBSSeqToTagDBPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
Develops a discovery TBT file from a set of GBS sequence files. Keeps only good reads having a barcode and a cut site and no N's in the useful part of the sequence. Trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the common adapter. Originally the reference throughout was to "tag". This is being changed to "kmer" as the pipeline is a kmer alignment process.
- GBSSeqToTagDBPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- GBSSeqToTagDBPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- GBSUtils - Class in net.maizegenetics.analysis.gbs.v2
-
This class contains methods and constants used by various classes in the GBSv2 pipeline.
- gChr - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Genetic mapping chromosome of a tag, unknown = Integer.MIN_VALUE
- gChr - Variable in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
- GCTADistanceMatrix - Class in net.maizegenetics.analysis.distance
-
- genDeflation - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- genDeflation - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GeneralAnnotation - Interface in net.maizegenetics.util
-
Provide generalized annotations (descriptors).
- GeneralAnnotationStorage - Class in net.maizegenetics.util
-
- GeneralAnnotationStorage.Builder - Class in net.maizegenetics.util
-
- generalizedInverse() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- generalizedInverse() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- generalizedInverse() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- generalizedInverse() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- generalizedInverseWithRank(rank) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- generalizedInverseWithRank(rank) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- generalizedInverseWithRank(rank) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
inverts the matrix and returns the rank as the first element in rank[]. The original matrix is not modified.
- generalizedInverseWithRank(rank) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- GeneralPosition - Class in net.maizegenetics.dna.map
-
Provide information on a site and its annotations. This includes information on position, MAF, coverage. This class is immutable.
- GeneralPosition.Builder - Class in net.maizegenetics.dna.map
-
A builder for creating immutable CoreAnnotatedPosition instances. AnnotatedPositions are built off a base of a CorePosition, so build it first.
- generate(currentMatch) - Static method in class net.maizegenetics.plugindef.GeneratePluginCode
-
- generate(currentMatch, inputObject, outputObject) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- generateChromosomeResidualsFromCurrentModel() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- generateCombinedMatrix(aInverse, gStarInverse) - Static method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
Given the inverse of an A matrix (Pedigree Kinship matrix) and a G Matrix (Genetic Kinship Matrix) which contains mostly entries in the A Matrix creates a combined (H) matrix.
- generateKotlin(currentMatch) - Static method in class net.maizegenetics.plugindef.GeneratePluginCode
-
- generateMasterPositionList(alignments) - Static method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
Generate a list of unique positions given an array of alignments
- generateMasterTaxaList(alignments) - Static method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
Generate a list of unique taxa given an array of alignments
- GeneratePluginCode - Class in net.maizegenetics.plugindef
-
- GenerateRCode - Class in net.maizegenetics.plugindef
-
- GenerateRCode.PositionVectors - Class in net.maizegenetics.plugindef
-
- GenerateRCode.TableReportVectors - Class in net.maizegenetics.plugindef
-
- generateToolTip(dataset, series, item) - Method in class net.maizegenetics.analysis.chart.XYAndLineToolTipGenerator
-
- generateToolTip(dataset, series, item) - Method in class net.maizegenetics.analysis.chart.XYMultipleYToolTipGenerator
-
- GENERATIONS - Variable in interface net.maizegenetics.taxa.tree.Units
-
- GenericArrayPositions - Class in net.maizegenetics.analysis.avro
-
- GenericArrayPositions(positions) - Constructor for class net.maizegenetics.analysis.avro.GenericArrayPositions
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- GenericArrayTaxa - Class in net.maizegenetics.analysis.avro
-
- GenericArrayTaxa(taxa) - Constructor for class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- GenericMapAnnotations - Class in net.maizegenetics.analysis.avro
-
- GenericMapAnnotations(annotations) - Constructor for class net.maizegenetics.analysis.avro.GenericMapAnnotations
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- GenericRecordChromosome - Class in net.maizegenetics.analysis.avro
-
- GenericRecordGenotype - Class in net.maizegenetics.analysis.avro
-
- GenericRecordGenotype(genotypeSchema, genotype) - Constructor for class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- GenericRecordGenotypeTable - Class in net.maizegenetics.analysis.avro
-
- GenericRecordGenotypeTable(tasselSchema, table) - Constructor for class net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
-
- GenericRecordPosition - Class in net.maizegenetics.analysis.avro
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- GenericRecordPosition(position) - Constructor for class net.maizegenetics.analysis.avro.GenericRecordPosition
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- GenericRecordTaxon - Class in net.maizegenetics.analysis.avro
-
- GenericRecordTaxon(taxon) - Constructor for class net.maizegenetics.analysis.avro.GenericRecordTaxon
-
- GENETICMAMMPING - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- GENETICMAMMPINGGW - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- GENO_DESC - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
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- genoCounts() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genoCounts() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
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- genoCounts() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns counts of all diploid combinations from highest frequency to lowest for whole alignment. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Longs).
- genoCounts() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns counts of all diploid combinations from highest frequency to lowest for whole genotype table. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Longs).
- genoCounts() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genoCounts() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
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- GenomeAnnosDBQueryToPositionListPlugin - Class in net.maizegenetics.analysis.data
-
Reads a PostgreSQL query file and a genomeAnnosDB connection config file, checks that the query is a SELECT query for chr, position, etc.., executes the query, and turns the results into a PositionList with any result fields other that chr & position added as annotations.
- GenomeAnnosDBQueryToPositionListPlugin() - Constructor for class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
- GenomeAnnosDBQueryToPositionListPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
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- GenomeFeature - Class in net.maizegenetics.dna.map
-
Created by Jason Wallace on 7/2/14. This class stores a generic "feature" on a genome, such as a gene, transcript, exon, miRNA, etc. The intent is for this information to be read in from an external file (such as an Ensembl GFF/GTF file) and collated into a GenomeFeatureMap, but it could be used in other ways.
- GenomeFeatureBuilder - Class in net.maizegenetics.dna.map
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Created by jgw87 on 7/2/14. Builder class to create a GenomeFeature. All annoations are stored in a HashMap. Any annotation can be added through the addAnnotation() method, but the more common fields have their own convenience methods. Only the feature's own ID is required; all other annotations are optional
- GenomeFeatureBuilder() - Constructor for class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
Generic constructor which does nothing special
- GenomeFeatureBuilder(feature) - Constructor for class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
Constructor to build a new feature off of an existing one.
- GenomeFeatureMap - Class in net.maizegenetics.dna.map
-
Created by jgw87 on 7/2/14. A map to hold genome features for lookup by name and by location. The features themselves are hierarchical and so can be traced up and down the tree.
- GenomeFeatureMapBuilder - Class in net.maizegenetics.dna.map
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Created by jgw87 on 7/2/14. A Builder class to create a GenomeFeatureMap to identify genomic features. Can build piecemeal or read in from a file For now, not implementing functionality to make a new builder from an existing map.
- GenomeSequence - Interface in net.maizegenetics.dna.map
-
Defines the genome sequence of a chromosome
- genomeSequence(startSite, lastSite) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the partial genomic sequence from the specified start position to the specified end position. THe start/end positions are inclusive and the request is 0-based (though the alleles are stored in a 0-based byte array). Note the difference with chromosomes, which start with 1. Can only return 2.1 billion sites per call.
- genomeSequenceAsString(startSite, lastSite) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the partial genomic sequence from the specified start position to the specified end position. The start/end positions are inclusive and the request is 0-based (though the alleles are stored in a 0-based byte array). Note the difference with chromosomes, which start with 1. Can only return 2.1 billion sites per call.
- GenomeSequenceBuilder - Class in net.maizegenetics.dna.map
-
Builder for a chromosome genome sequence that hides the ReferenceGenomeSequence implementation. The sequence is read from a fasta file and stored in a byte array, 2 alleles packed per byte.
- genomeSize() - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the length of the entire genome
- genomeVersion() - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
Genome Version
- genomeVersion(value) - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
Set Genome Version. Genome Version
- genomeVersion() - Method in interface net.maizegenetics.dna.map.PositionList
-
Gets the Genome Assembly.
- genomeVersion(genomeVersion) - Method in class net.maizegenetics.dna.map.PositionListBuilder
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- genomeVersion() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genomeVersion() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genomeVersion() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Gets the Genome Assembly.
- genomeVersion() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genomeVersion() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- GENOMIC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
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- genomicSelection(phenotype, matrix, doCV, kFolds, nIter) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- GenomicSelectionPlugin - Class in net.maizegenetics.analysis.association
-
- GenomicSelectionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.association.GenomicSelectionPlugin
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- genosSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genosSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
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- genosSortedByFrequency(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return sorted list of diploid vales from highest frequency to lowest at given site in alignment. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Integers).
- genosSortedByFrequency(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return sorted list of diploid vales from highest frequency to lowest at given site in genotype table. Resulting double dimension array holds diploids (Strings) in result[0]. And the counts are in result[1] (Integers).
- genosSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genosSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
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- GenosToABHPlugin - Class in net.maizegenetics.analysis.data
-
Plugin to convert genotypes to parental comparisons and store them in an output file. The user can get outputs as A/H/B, 0/1/2, or 0/0.5/1 for a genotype matching parent A's genotype, heterozygous, or parent B's genotype respectively. If the genotype is neither A or B or a het combination of A/B (B/A) then it is coded as "NA".
- GenosToABHPlugin() - Constructor for class net.maizegenetics.analysis.data.GenosToABHPlugin
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- GenosToABHPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.GenosToABHPlugin
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- GenosToABHPlugin.OUTPUT_CHECK - Enum in net.maizegenetics.analysis.data
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- genotype(chrom, position) - Method in interface net.maizegenetics.dna.map.GenomeSequence
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Returns the allele value in a byte for the specified PHYSICAL position (1-based)
- genotype(chrom, positionObject) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the TASSEL encoding for the allele value in a byte for the specified PHYSICAL position
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotype(taxon, locus, physicalPosition) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
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- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotype(taxon, chromosome, physicalPosition) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- genotype(taxon, site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns diploid value (genotype) for a given taxon and site.
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- genotype(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns diploid value (genotype) for a given taxon and site.
- genotype(taxon, chromosome, physicalPosition) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns diploid values for given taxon, chromosome, and physical position. The chromosome and physical position should map to an unique site.
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotype(taxon, chromosome, physicalPosition) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotype(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotype(taxon, chromosome, physicalPosition) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotype(obs, site) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- genotype(theGenotype) - Method in class net.maizegenetics.phenotype.GenotypePhenotypeBuilder
-
- GENOTYPE_BLOCK_SIZE - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- GENOTYPE_BLOCK_SIZE - Static variable in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- GENOTYPE_TABLE_ANNOTATIONS - Static variable in interface net.maizegenetics.dna.snp.GenotypeTable
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- GenotypeAdditiveSite - Class in net.maizegenetics.analysis.modelfitter
-
GenotypeAdditiveSite is an AdditiveSite that takes a byte[] array of genotypes as input and converts them to a double[] array. It codes the homozygous major as 2, homozygous minor as 0 and het as 1. It then subtracts the mean value from all elements of the array and sets missing to zero (now the mean). For efficient storage, the values of 0,1,2,3 are stored in a byte array which indexes the double values.
- GenotypeAdditiveSite(site, chr, pos, id, selectionCriterion, genotype, majorAllele, majorAlleleFrequency) - Constructor for class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
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- genotypeAllSites(taxon) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAllSites(taxon) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAllSites(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns sequence of diploid allele values for all sites for given taxon. Each value in array is what would be returned by genotype().
- genotypeAllSites(taxon) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- genotypeAllSites(taxon) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns sequence of diploid allele values for all sites for given taxon. Each value in array is what would be returned by genotype().
- genotypeAllSites(taxon) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAllSites(taxon) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAllTaxa(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAllTaxa(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAllTaxa(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns sequence of diploid allele values for all taxa for given site. Each value in array is what would be returned by genotype().
- genotypeAllTaxa(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAllTaxa(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAllTaxa(site) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- genotypeArray(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeArray(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeArray(taxon, site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns diploid values for given taxon and site. Same values as genotype(), except two values are already separated into two bytes.
- genotypeArray(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
-
- genotypeArray(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns diploid values for given taxon and site. Same values as genotype(), except two values are already separated into two bytes.
- genotypeArray(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeArray(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAsString(chrom, position) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the haplotype allele value in a String for the specified physical position on the specified chromosome
- genotypeAsString(chrom, positionObject) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns the haplotype allele value in a String for the specified physical position on the specified chromosome
- genotypeAsString(chrom, startSite, endSite) - Method in interface net.maizegenetics.dna.map.GenomeSequence
-
Returns a string of haplotype allele values for the specified physical start and physical end positions on the specified chromosome.
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAsString(site, value) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAsString(site, value) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns string representation of diploid values returned by genotype() for given taxon and site. The default implementation separates The two allele values with a colon (:) delimiter. Nucleotide data will be represented by a single letter IUPAC code.
- genotypeAsString(site, value) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns String representation of allele value at site.
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- genotypeAsString(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns string representation of diploid values returned by genotype() for given taxon and site. The default implementation separates The two allele values with a colon (:) delimiter. Nucleotide data will be represented by a single letter IUPAC code.
- genotypeAsString(site, value) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns String representation of allele value at site.
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAsString(site, value) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAsString(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAsString(site, value) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAsStringArray(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAsStringArray(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAsStringArray(taxon, site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns string representation of diploid values returned by genotypeArray() for given taxon and site. Same two allele values as genotypeAsString(), except already separated into two Strings.
- genotypeAsStringArray(site, value) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Same as genotypeAsStringArray(taxon, site), except given value is converted for given site.
- genotypeAsStringArray(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns string representation of diploid values returned by genotypeArray() for given taxon and site. Same two allele values as genotypeAsString(), except already separated into two Strings.
- genotypeAsStringArray(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAsStringArray(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns string representation of diploid alleles for given taxon in specified range (end site excluded). Each value in string is what would be returned by genotypeAsString().
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns string representation of diploid alleles for given taxon in specified range (end site excluded). Each value in string is what would be returned by genotypeAsString().
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAsStringRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypeAsStringRow(taxon) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeAsStringRow(taxon) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeAsStringRow(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns string representation of diploid alleles for given taxon for all sites. Each value in string is what would be returned by genotypeAsString().
- genotypeAsStringRow(taxon) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns string representation of diploid alleles for given taxon for all sites. Each value in string is what would be returned by genotypeAsString().
- genotypeAsStringRow(taxon) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeAsStringRow(taxon) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- GenotypeCallTable - Interface in net.maizegenetics.dna.snp.genotypecall
-
Interface for genotype calls for a table of taxa and sites. GenotypeCallTable only contain information on the genotype calls - the call table does not have the TaxaList or PositionList. The calls are diploid genotype calls stored and retrieved as bytes. Conversions to string are also provided.
- GenotypeCallTableBuilder - Class in net.maizegenetics.dna.snp.genotypecall
-
Builder to construct a GenotypeCallTable. This builder is generally only used in complex situations, where the GenotypeTableBuilder does not suffice.
- genotypeComponent() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeComponent(value) - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeForAllSites(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Get all genotypes for given taxon.
- genotypeForAllSites(taxon) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- genotypeForAllTaxa(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Get all genotypes for given site.
- genotypeForAllTaxa(site) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- genotypeForAllTaxa(site) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- genotypeForAllTaxa(site) - Method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- genotypeForAllTaxa(site) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- genotypeForSiteRange(taxon, start, end) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Get all genotypes for given taxon from start site (inclusive) to end site (exclusive).
- genotypeIndices() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- genotypeMatrix() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeMatrix() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeMatrix() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns the immutable Genotype matrix. Taxa and Positions are not part of the matrix. This method is used for copying Genotype tables, when either the Taxa or Positions have changed.
- genotypeMatrix() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeMatrix() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- GenotypeMergeRule - Interface in net.maizegenetics.dna.snp.genotypecall
-
Defines the methods for merging the calls from two taxa. The merge rules need to be defined at the level of genotypic calls and for read depth. In general if depth is available, it will be used to merge.
- GenotypePhenotype - Class in net.maizegenetics.phenotype
-
This class holds phenotypes and genotypes for a set of Taxa.
- GenotypePhenotypeBuilder - Class in net.maizegenetics.phenotype
-
- genotypeRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- genotypeRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- genotypeRange(taxon, startSite, endSite) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns sequence of diploid allele values for given taxon in specified range (end site excluded). Each value in array is what would be returned by genotype().
- genotypeRange(taxon, startSite, endSite) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns sequence of diploid allele values for given taxon in specified range (end site excluded). Each value in array is what would be returned by genotype().
- genotypeRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- genotypeRange(taxon, startSite, endSite) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- genotypes() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- GENOTYPES - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- GENOTYPES_ALLELE_STATES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_ATTRIBUTES_PATH - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_LOCKED - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_MAX_NUM_ALLELES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_MODULE - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_NUM_TAXA - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_RETAIN_RARE_ALLELES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- GENOTYPES_SCORE_TYPE - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- genotypesToUnphasedSorted(genotypes) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- GenotypeSummaryPlugin - Class in net.maizegenetics.analysis.data
-
- GenotypeSummaryPlugin() - Constructor for class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- GenotypeSummaryPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- genotypeTable() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeTable(value) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeTable() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeTable(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeTable(genotypeTable) - Static method in class net.maizegenetics.analysis.avro.ImportAvro
-
- genotypeTable() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- genotypeTable(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
- GenotypeTable - Interface in net.maizegenetics.dna.snp
-
A representation of the SNP and indel variation for a set of taxa and genomic positions.
- genotypeTable() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- genotypeTable() - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- GenotypeTable.ALLELE_SORT_TYPE - Enum in net.maizegenetics.dna.snp
-
This defines the possible allele scope types.
- GenotypeTable.GENOTYPE_TABLE_COMPONENT - Enum in net.maizegenetics.dna.snp
-
Possible Components of a Genotype Table.
- GenotypeTableBuilder - Class in net.maizegenetics.dna.snp
-
Builder for GenotypeTables. New genotypeTables are built from a minimum of TaxaList, PositionList, and GenotypeCallTable. Depth and Scores are optional features of GenotypeTables.
- GenotypeTableMask - Interface in net.maizegenetics.gui
-
- GenotypeTableMask.MaskType - Enum in net.maizegenetics.gui
-
This defines the type of mask. reference - Mask created using taxon as reference. imputed - Mask created to identify imputed values. compared = Mask created to identify differences between two alignments.
- GenotypeTableMaskBoolean - Class in net.maizegenetics.gui
-
- GenotypeTableMaskBoolean(align, mask, name, type) - Constructor for class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- GenotypeTableMaskBoolean(align, mask, name, color, type) - Constructor for class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- GenotypeTableMaskGeneticDistance - Class in net.maizegenetics.gui
-
- GenotypeTableMaskReference - Class in net.maizegenetics.gui
-
- genotypeTableToDosageByteArray(genotype, useRef) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
This converts a genotype table to a double dimension dosage byte array.
- genotypeTableToPositionListOfArrays(positions) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- genotypeTableToPositionListOfArrays(genotype) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- genotypeTableToSampleNameArray(genotype) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
This converts the taxa of the specified genotype table to an array of taxa name strings.
- genotypeTableToSampleNameArray(taxa) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
This converts the taxa list to an array of taxa name strings.
- GenotypeTableUtils - Class in net.maizegenetics.dna.snp
-
Utility methods for comparing, sorting, and counting genotypes.
- GenotypeToAdditiveValuesPlugin - Class in net.maizegenetics.analysis.data
-
- GenotypeToAdditiveValuesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
-
- GenusKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for a genus of the taxon
- get(index) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- get(index) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- get(key) - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- get(key) - Method in class net.maizegenetics.analysis.avro.GenericRecordChromosome
-
- get(i) - Method in class net.maizegenetics.analysis.avro.GenericRecordChromosome
-
- get(key) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- get(i) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- get(key) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
-
- get(i) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
-
- get(key) - Method in class net.maizegenetics.analysis.avro.GenericRecordPosition
-
- get(i) - Method in class net.maizegenetics.analysis.avro.GenericRecordPosition
-
- get(key) - Method in class net.maizegenetics.analysis.avro.GenericRecordTaxon
-
- get(i) - Method in class net.maizegenetics.analysis.avro.GenericRecordTaxon
-
- get(index) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- get(taxon, site) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- get(index) - Method in class net.maizegenetics.dna.snp.FilterList
-
- get(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStatsFilterSite
-
- get(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStatsFilterTaxa
-
- get(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStatsSite
-
- get(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStatsTaxa
-
- get(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskedGenotypes
-
- get(taxon, site) - Method in interface net.maizegenetics.dna.snp.MaskMatrix
-
- get(taxon, site) - Method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- get(taxon, site) - Method in class net.maizegenetics.dna.snp.MaskSiteMatrix
-
- get(taxon, site) - Method in class net.maizegenetics.dna.snp.MaskTaxaMatrix
-
- get(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- get(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- get(row, col) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
The row and column coordinates are not checked to make sure they are in the matrix
- get(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- get(index) - Method in interface net.maizegenetics.util.BitSet
-
Returns true or false for the specified bit index.
- get(index) - Method in interface net.maizegenetics.util.BitSet
-
Returns true or false for the specified bit index
- get(index) - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- get(index) - Method in class net.maizegenetics.util.OpenBitSet
-
Returns true or false for the specified bit index.
- get(index) - Method in class net.maizegenetics.util.OpenBitSet
-
Returns true or false for the specified bit index
- get(row, column) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Gets value at given row and column.
- get(row, column) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- get(row, column) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- get(row, column) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- get(row, column) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- get(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- get(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getA() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getActualPostions() - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getActualSNPID() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getActualSNPID() - Method in interface net.maizegenetics.dna.map.Position
-
Returns SNP ID only if assigned. getSNPID() returns a default if not assigned.
- getAdjacentSiteIndexRange(siteIndex, siteNum) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getAdjusted(toAdjust, adjustmentFactor) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getAdjusted(toAdjust, adjustmentFactor) - Static method in class net.maizegenetics.stats.math.OrthogonalHints.Utils
-
- getAdjustedFactory(toAdjust, adjustmentFactor) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getAdjustmentMatrix() - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- getAlignerFromName(name) - Static method in enum net.maizegenetics.dna.map.TagMappingInfoV3.Aligner
-
- getAlignerFromValue(value) - Static method in enum net.maizegenetics.dna.map.TagMappingInfoV3.Aligner
-
- getAlignment() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Returns an annotated aligment if one was used for this LD this could be used to access information of locus position
- getAlignment() - Method in class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- getAlignment() - Method in interface net.maizegenetics.gui.GenotypeTableMask
-
- getAlignment() - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getAlignmentRetainRareAlleles() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getAllAllelesTaxaDistForSNP() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAllAllelesTaxaDistForSNP() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllAllelesTaxaDistForSNPEntries() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAllAllelesTaxaDistForSNPEntries() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllAnnotationEntries() - Method in interface net.maizegenetics.util.GeneralAnnotation
-
- getAllAnnotationEntries() - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getAllColumns(row) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Get all values for given row.
- getAllColumns(row) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- getAllColumns(row) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- getAllColumns(row) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- getAllColumns(row) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- getAllCountsForTagTissue(tag, tissue) - Method in interface net.maizegenetics.dna.tag.TagData
-
- getAllCountsForTagTissue(tag, tissue) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllCountsForTaxonTissue(taxon, tissue) - Method in interface net.maizegenetics.dna.tag.TagData
-
- getAllCountsForTaxonTissue(taxon, tissue) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllCountsForTissue(tissue) - Method in interface net.maizegenetics.dna.tag.TagData
-
- getAllCountsForTissue(tissue) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllele(alleleType) - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getAllele(alleleType) - Method in interface net.maizegenetics.dna.map.Position
-
Return the allele specified by alleleType, if unknown Alignment.Unknown is return
- getAlleleDepthsInTaxa() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getAlleleMap() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Provides an iterator that goes through all tags with non-empty alleleMaps.
- getAlleleMap() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAlleleMap() - Method in interface net.maizegenetics.dna.tag.TagData
-
Provides an iterator that goes through all tags with non-empty alleleMaps.
- getAlleleMap() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAlleleProbabilityInstance(numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- getAlleles(data, site) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- getAlleles(data, site) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- getAlleles(tag) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Provides all SNP allele calls associated with a given tag.
- getAlleles(tag) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAlleles(tag) - Method in interface net.maizegenetics.dna.tag.TagData
-
Provides all SNP allele calls associated with a given tag.
- getAlleles(tag) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllelesAtSite(site) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getAllelesSortedByFrequency(site) - Method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- getAllelesSortedByFrequency(data) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
This sorts alleles by frequency. Each cell in the given array contains a diploid value which is separated and counted individually. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploids are not supported.
- getAllelesSortedByFrequency(data, site) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
This sorts alleles in a given site by frequency. Each cell in the given array contains a diploid value which is separated and counted individually. Resulting double dimension array holds alleles (bytes) in result[0]. And the counts are in result[1]. Counts haploid values twice and diploid values once. Higher ploids are not supported.
- getAllelesSortedByFrequency(data, site) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- getAllelesSortedByFrequency(alignment, site) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- getAllelesTagTaxaDistForSNP(position) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution
- getAllelesTagTaxaDistForSNP(position) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAllelesTagTaxaDistForSNP(position) - Method in interface net.maizegenetics.dna.tag.TagData
-
For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution
- getAllelesTagTaxaDistForSNP(position) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAlleleStates(data, maxNumAlleles) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- getAllelesTaxaDistForSNP(position) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllNonRefTagAlignments(minscore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of all non-ref tags and their alignments This method calls getTagAlignmentsForTags(). All tag-tag alignments are return
- getAllNonRefTagAlignments(minscore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAllRefTagAlignments(minscore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of all alignments for reference tags This returns reftag to reftag alignments.
- getAllRefTagAlignments(minscore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAllRows(column) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Get all values for give column.
- getAllRows(column) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- getAllRows(column) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- getAllRows(column) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- getAllRows(column) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- getAllTagsTaxaMap() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Return all tag/taxadistribution stored in database. Returns a Hashmap of tag.taxadistributions
- getAllTagsTaxaMap() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getAllTagsTaxaMap() - Method in interface net.maizegenetics.dna.tag.TagData
-
Return all tag/taxadistribution stored in database. Returns a Hashmap of tag.taxadistributions
- getAllTagsTaxaMap() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllTaxa(group1, group2) - Static method in class net.maizegenetics.taxa.TaxaListUtils
-
Union joins the specified taxa.
- getAllTaxa(groups) - Static method in class net.maizegenetics.taxa.TaxaListUtils
-
- getAllTaxa(lists, sorted) - Static method in class net.maizegenetics.taxa.TaxaListUtils
-
Union joins the specified taxa.
- getAllTaxaNames(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getAllTissue() - Method in interface net.maizegenetics.dna.tag.TagData
-
Return the set of tissue
- getAllTissue() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getAllTraits() - Method in class net.maizegenetics.dna.pd.FolderParser
-
- getAlternateTagMappingInfo(index, mapIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getAlternating(primary, secondary) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getAlternatingFactory(primary, secondary) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getAltsForRef(ref) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- getAltsFromLine(mline, ref, isVCF, tabPos) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- getAncestor() - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
Returns this factor's ancestor factor.
- getAncestorSerialNumber() - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
This method is a shorthand to return the serial number of this factor's ancestor. Note that it does not check if this factor has an ancestor or not, therefore, if it is called on the root factor, a NullPointerException is raised.
- getAndClear(index) - Method in interface net.maizegenetics.util.BitSet
-
Clears a bit and returns the previous value. The index should be less than the BitSet size.
- getAndClear(index) - Method in class net.maizegenetics.util.OpenBitSet
-
- getAndClear(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getAndSet(index) - Method in interface net.maizegenetics.util.BitSet
-
Sets a bit and returns the previous value. The index should be less than the BitSet size.
- getAndSet(index) - Method in interface net.maizegenetics.util.BitSet
-
Sets a bit and returns the previous value. The index should be less than the BitSet size.
- getAndSet(index) - Method in class net.maizegenetics.util.OpenBitSet
-
Sets a bit and returns the previous value. The index should be less than the OpenBitSet size.
- getAndSet(index) - Method in class net.maizegenetics.util.OpenBitSet
-
Sets a bit and returns the previous value. The index should be less than the OpenBitSet size.
- getAndSet(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getAndSet(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getAnnotation() - Method in class net.maizegenetics.dna.map.Chromosome
-
- getAnnotation() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getAnnotation(key) - Method in class net.maizegenetics.dna.map.GenomeFeature
-
Get any annotation based on its key. If this feature lacks that annotation, it returns 'NA'
- getAnnotation() - Method in interface net.maizegenetics.dna.map.Position
-
- getAnnotation() - Method in class net.maizegenetics.taxa.Taxon
-
- getAnnotationAsMap() - Method in interface net.maizegenetics.util.GeneralAnnotation
-
- getAnnotationAsMap() - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getAnnotationKeys() - Method in interface net.maizegenetics.util.GeneralAnnotation
-
Returns all keys
- getAnnotationKeys() - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getAnnotationTypes() - Method in class net.maizegenetics.dna.pd.SiteAnnotation
-
Obtain complete listing of all annotations types available. Examples: Minor Allele Frequency
- getAnnotationValue(annotationType) - Method in class net.maizegenetics.dna.pd.SiteAnnotation
-
- getAnovaReport() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getAnovaReport() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- getAnovaReportWithCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getAnovaReportWithCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- getAttribute(name) - Method in interface net.maizegenetics.taxa.tree.AttributeNode
-
- getAttribute(name) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- getAttribute(node, name) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
- getAttribute(node, name) - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getAttributeNames() - Method in interface net.maizegenetics.taxa.tree.AttributeNode
-
- getAttributeNames() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- getAttributesStr(delimiter) - Method in class net.maizegenetics.dna.map.TagGWASMapInfo
-
- getAverageAnnotation(annoName) - Method in interface net.maizegenetics.util.GeneralAnnotation
-
Returns average annotation for a given annotation key
- getAverageAnnotation(annoName) - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getBackwardRead() - Method in class net.maizegenetics.dna.read.PERead
-
Return backward read
- getBarCodeCount() - Method in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
Returns the number of barcodes for the flowcell and lane
- getBarcodeString() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getBarLength() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getBarWithOverHangLength() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getBarWOverHang() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getBarWOverHangLong() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getBaseGenotypeTable() - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
Returns the high density base genotypeTable of the projection genotypeTable.
- getBaseline(c, width, height) - Method in class net.maizegenetics.gui.VerticalLabelUI
-
- getBaselineResizeBehavior(c) - Method in class net.maizegenetics.gui.VerticalLabelUI
-
- getBaseModel() - Method in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- getBasename(str) - Static method in class net.maizegenetics.util.Utils
-
Returns the base name of a string delimited with periods (i.e. Java Class).
- getBaseQuality(index, phredScale) - Method in class net.maizegenetics.dna.read.Read
-
Return quality value of base
- getBestMapIndex(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getBeta() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getBeta() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getBeta() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getBeta() - Method in class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
- getBiasAlternating(primary, secondary) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getBiasAlternatingFactory(primary, secondary) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getBins() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- getBit(index) - Method in interface net.maizegenetics.util.BitSet
-
Returns 1 if the bit is set, 0 if not. The index should be less than the BitSet size
- getBit(index) - Method in class net.maizegenetics.util.OpenBitSet
-
returns 1 if the bit is set, 0 if not. The index should be less than the OpenBitSet size
- getBit(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getBits() - Method in interface net.maizegenetics.util.BitSet
-
Expert: returns the long[] storing the bits
- getBits(startWord, endWord) - Method in interface net.maizegenetics.util.BitSet
-
Expert: returns the long[] storing the bits from start to end
- getBits(index) - Method in interface net.maizegenetics.util.BitSet
-
Expert: returns 64 bits at index.
- getBits() - Method in class net.maizegenetics.util.OpenBitSet
-
Expert: returns the long[] storing the bits
- getBits(index) - Method in class net.maizegenetics.util.OpenBitSet
-
- getBits(startWord, endWord) - Method in class net.maizegenetics.util.OpenBitSet
-
- getBits() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getBits(startWord, endWord) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getBits(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getBitSet() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
-
- getBlockChr() - Method in class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- getBlockChr(index) - Method in class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- getBlockIndex(tagIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Returns the block index based on the tag index in a full list
- getBlockNum() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Returns the number of block
- getBlockPos() - Method in class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- getBlockPos(index) - Method in class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- getBlockSize() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Returns the size of HDF5 block
- getBlockWithMinMinorCount(mjT, mnT, focusBlock, minMinorCnt, minMajorCnt) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
Given a start 64 site block, it expands to the left and right until it hits the minimum Minor Site count or MajorSiteCount in the target taxon
- getBlues(effect, restricted) - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getBlup() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getBlups() - Method in class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
- getBMSDB() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getBMSHost() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getBMSUser() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getBoolean(key) - Method in class net.maizegenetics.util.ArgsEngine
-
Gets the option.
- getBooleanPref(path, key, def) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getBottomPanel() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- getBottomPanel() - Method in class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- getBoxcoxAttributesStr(lamdas, delimiter) - Method in class net.maizegenetics.dna.map.TagGWASMapInfo
-
- getBranchLength() - Method in interface net.maizegenetics.taxa.tree.Node
-
Get the length of the branch attaching this node to its parent.
- getBranchLength() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Get the length of the branch attaching this node to its parent.
- getBranchLengthSE() - Method in interface net.maizegenetics.taxa.tree.Node
-
Get the length SE of the branch attaching this node to its parent.
- getBranchLengthSE() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Get the length SE of the branch attaching this node to its parent.
- getBufferedOutputStream(filename) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedReader(inSourceName) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedReader(inSourceName, bufSize) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedReader(file, bufSize) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedWriter(filename) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedWriter(filename, append) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedWriter(file) - Static method in class net.maizegenetics.util.Utils
-
- getBufferedWriter(file, append) - Static method in class net.maizegenetics.util.Utils
-
- getBuilder(tagSet) - Static method in class net.maizegenetics.analysis.rna.FindMatchByWordHash
-
- getBuilder(existingHDF5File) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Returns a builder to an existing, unfinished HDF5 genotypes file. Can be used if you want to add/modify annotations, etc, and/or call build() to finalize it
- getBuilder(hapmapFile) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromHapMap
-
- getBuilder(hapmapFile, listener) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromHapMap
-
- getBuilder(pedfile, mapfile, listener) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromPLINK
-
- getBuilder(infile) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCF
-
Create a builder for loading a VCF file into memory
- getBuilder(infile, listener) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCF
-
Create a builder for loading a VCF file into memory
- getBuilder() - Static method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.chart.QQDisplayPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.GetPositionListPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.GetTaxaListPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.HetsToUnknownPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.IdentityRecognitionPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.IndelsToUnknownPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.KmerCountingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.LIXPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MemoryUsagePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.PassThroughPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.SeparatePlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.SubtractGenotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.data.UnionAlignmentPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterDataSetPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.FastqToTBTPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.KmerToTBTPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.QseqToTBTPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.ListPluginParameters
-
- getButtonName() - Method in class net.maizegenetics.analysis.ListPlugins
-
- getButtonName() - Method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.analysis.tree.MergeTreesPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- getButtonName() - Method in class net.maizegenetics.analysis.workflow.WorkflowPlugin
-
- getButtonName() - Method in interface net.maizegenetics.plugindef.Plugin
-
Button name for this plugin to be used in buttons, etc.
- getButtonName() - Method in class net.maizegenetics.tassel.PreferencesDialog
-
- getButtonName() - Method in class net.maizegenetics.tassel.ShowParameterCachePlugin
-
- getButtonName() - Method in class net.maizegenetics.tassel.TasselLogging
-
- getButtonName() - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- getByteSeqFromLong(val) - Static method in class net.maizegenetics.dna.BaseEncoder
-
- getByteSeqFromLong(valA) - Static method in class net.maizegenetics.dna.BaseEncoder
-
- getCacheKey(taxon, site) - Static method in class net.maizegenetics.analysis.avro.AvroConstants
-
- getCacheKey(taxon, site) - Static method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- getCallAtVariableSiteForTag(site, tagIndex) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getCancelButton() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- getCar() - Method in class net.maizegenetics.util.db.Pair
-
- getCdr() - Method in class net.maizegenetics.util.db.Pair
-
- getCellRenderingType() - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getCensoredMajorityHaplotype(maxMinorFreq, maxMinorCount) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
This returns the majority haplotype for sites with either minor allele frequency below maxMinorFreq or minor allele count less than or equal to maxMinorCount. Missing is returned at sites not meeting the stated criteria.
- getChart() - Method in class net.maizegenetics.analysis.chart.BasicChartPanel
-
- getChartMode() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- getChecked(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getChecked(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- getChecked(row, col) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
The row and column coordinates are checked to make sure they fall in the matrix. If not an error is generated.
- getChecked(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- getChecksum(filename, protocol) - Static method in class net.maizegenetics.util.CheckSum
-
Allows user to specify the protocol, e.g. MD5, SHA-1, SHA-256
- getChecksumForString(str, protocol) - Static method in class net.maizegenetics.util.CheckSum
-
Allows user to specify the protocol, e.g. MD5, SHA-1, SHA-256
- getChild(n) - Method in interface net.maizegenetics.taxa.tree.Node
-
get child node
- getChild(n) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
get child node
- getChildCount() - Method in interface net.maizegenetics.taxa.tree.Node
-
Returns the number of children this node has.
- getChildCount() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Returns the number of children this node has.
- getChr(index) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getChr(tagIndex, mappingIndex) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return chromosome of a mapping
- getChrB(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getChrContig(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getChrF(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getChrIndex(chr) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getChromFromLine(mline, isVCF, tabPos) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- getChromosome(index) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getChromosome() - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- getChromosome() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getChromosome() - Method in interface net.maizegenetics.dna.map.Position
-
Return the locus (generally a chromosome) of a site
- getChromosome() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getChromosome(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns chromosome at give tag index.
- getChromosomeIndex(intChrName) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getChromosomeIndex(intChrName) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Finds the index in the myChromosomes[] (length = # of chromosomes) corresponding to the provided int version of the chromosome name
- getChromosomeNumber(siteIndex) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getChromosomeNumber() - Method in class net.maizegenetics.dna.map.Chromosome
-
Returns the integer value of the chromosome (if name is not a number then Integer.MAX_VALUE is returned)
- getChromosomes() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getChromosomes() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns an array whose values are the distinct chromosomes in this file, as stored in the chromosome[] array. The indices are arbitrary.
- getChromosomesFromCutPositions() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Return all chromosomes stored in database. Returns a list of distinct chromsome objects from the cutPosition table
- getChromosomesFromCutPositions() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getChromosomesFromCutPositions() - Method in interface net.maizegenetics.dna.tag.TagData
-
Return all chromosomes stored in database. Returns a list of distinct chromsome objects from the cutPosition table
- getChromosomesFromCutPositions() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getChroms() - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getChrPosMap() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- getChunkNum() - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
Return the total number of chunks
- getChunkNum(chunkSize) - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
Return the number of chunks at current chunkSize
- getChunkNum(tbtHDF5, chunkSize) - Static method in class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
Pre-calculate number of chunks when qsub genetic mapping
- getChunkNum(tbtHDF5, chunkSize) - Static method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
-
Pre-calculate number of chunks when qsub genetic mapping
- getChunkNum() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return the total number of chunks
- getChunkSize() - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
Return the chunk size (Number of tags in gt chunk)
- getChunkSize() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return the chunk size (Number of tags in a chunk)
- getCitation() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- getCitation() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- getCitation() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- getCitation() - Method in class net.maizegenetics.analysis.workflow.WorkflowPlugin
-
- getCitation() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getCitation() - Method in interface net.maizegenetics.plugindef.Plugin
-
Returns Citation for this plugin.
- getClade(i) - Method in class net.maizegenetics.taxa.tree.CladeSystem
-
get clade
- getClade(idGroup, internalNode, clade) - Static method in class net.maizegenetics.taxa.tree.CladeSystem
-
get clade for internal node
- getClade(root, clade) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- getCladeArray() - Method in class net.maizegenetics.taxa.tree.CladeSystem
-
get clade array
- getCladeCount() - Method in class net.maizegenetics.taxa.tree.CladeSystem
-
get number of clades
- getClades(idGroup, tree) - Static method in class net.maizegenetics.taxa.tree.CladeSystem
-
creates a clade system from a tree (using a pre-specified order of sequences)
- getClades(tree) - Static method in class net.maizegenetics.taxa.tree.CladeSystem
-
creates a clade system from a tree (using tree-induced order of sequences)
- getCladeSystems(trees) - Static method in class net.maizegenetics.taxa.tree.CladeSystem
-
- getClickedOK() - Method in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- getClonedDistances() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
Returns the distances as a 2-dimensional array of doubles. Matrix is cloned first so it can be altered freely.
- getClosedRangesAsPositions(bedfile) - Static method in class net.maizegenetics.dna.snp.io.ReadBedfile
-
Function that returns the 1-based closed Position ranges from a BED file as a RangeSet of Positions. NOTE: getRanges(bedFile) will be called which will shift the start in the BED file up by 1. Because of this the ranges returned will be 1-based Closed(Inclusive-Inclusive). This is NOT returning ranges in BED specification(0-based Inclusive-Exclusive).
- getClosestIndex(fromIndex, exclusion) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getClusterList() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- getClusterReport() - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- getClusters(rbt) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- getClusters(tbt) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- getClusterScores() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
After the initial cluster formation a Haplotype score equals the 1 / (number of clusters to which it belongs). Merging does not update the cluster score.
- getClusterSizes() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- getCmFromPosition(chromosome, position) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getCode() - Method in enum net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
-
- getCollapsedPETagCounts() - Method in class net.maizegenetics.dna.tag.PETagCounts
-
Collapse the PETagCounts and return a new collapsed PETagCounts object
- getColor() - Method in class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- getColor() - Method in interface net.maizegenetics.gui.GenotypeTableMask
-
- getColStart() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns the matrix column position where the paired alignment starts
- getColumnClass(columnIndex) - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- getColumnCount() - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- getColumnCount() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getColumnCount() - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getColumnCount() - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getColumnCount() - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getColumnCount() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getColumnCount() - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- getColumnCount() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getColumnCount() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getColumnCount() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getColumnCount() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getColumnCount() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getColumnCount() - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getColumnCount() - Method in class net.maizegenetics.util.HDF5TableReport
-
- getColumnCount() - Method in class net.maizegenetics.util.SimpleTableReport
-
- getColumnCount() - Method in interface net.maizegenetics.util.TableReport
-
Get the number of the columns
- getColumnName(col) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getColumnName(col) - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- getColumnName(col) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getColumnNameType() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getColumnObject(columnIndex) - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- getColumnRange(row, start, end) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Get values for given row from start column (inclusive) to end column (exclusive).
- getColumnRange(row, start, end) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- getColumnRange(row, start, end) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- getColumnRange(row, start, end) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- getColumnRange(row, start, end) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- getColumnWidth() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getCombined(first, numberOfFirstParameters, second, numberOfSecondParameters) - Static method in class net.maizegenetics.stats.math.OrthogonalHints.Utils
-
- getComment() - Method in class net.maizegenetics.plugindef.Datum
-
- getCommonAlleles() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getCommonTaxa(group1, group2) - Static method in class net.maizegenetics.taxa.TaxaListUtils
-
Intersect joins the specified taxa.
- getCommonTaxa(groups) - Static method in class net.maizegenetics.taxa.TaxaListUtils
-
Intersect joins the specified taxa.
- getCommonTaxa(groups, sorted) - Static method in class net.maizegenetics.taxa.TaxaListUtils
-
Intersect joins the specified taxa.
- getCompatibleTypes() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- getCompatibleTypes() - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- getCompatibleTypes() - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- getCompatibleTypes() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- getComplementBase(base) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns reverse complement for a sequence.
- getCompressedMatrix(km) - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- getCompressedZ(originalZ) - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- getCompressedZKZ(Z, km) - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- getConcatenatedName(theTDS) - Method in class net.maizegenetics.analysis.data.UnionAlignmentPlugin
-
- getConcatenatedTextAnnotations() - Method in interface net.maizegenetics.util.GeneralAnnotation
-
- getConcatenatedTextAnnotations() - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getConfigFile() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getConsecutiveRegions() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- getConstant(index) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getConstantFactory(index) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getContig(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getContig(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Return the contig of PE tag
- getContigCount() - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getContigCount() - Method in interface net.maizegenetics.dna.tag.PETags
-
Return total number of PE contigs
- getContigLength(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getContigLength(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Return the length of a contig
- getContigLengthInLong(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getContigLengthInLong(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Return the contig length in Long primitive data type
- getCopy() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getCopy() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getCopy() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getCopy() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getCopy() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getCopy() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
- getCopy() - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getCorrelationsForTags(tags) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Grab correlations for specified tags
- getCorrelationsForTags(tags) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getCount(x, y) - Method in class net.maizegenetics.taxa.distance.DistanceMatrixWithCounts
-
- getCountOfHaplotypesNotInThisCluster(cluster) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
Counts the number of Haplotypes in cluster that are not also in this cluster
- getCovariate() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- getCovariate(subset) - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- getCovariate() - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- getCovariate(subset) - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- getCovariate() - Method in class net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
-
- getCovariate(subset) - Method in class net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
-
- getCovariate() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getCovariateNoReindex() - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- getCovariateNoReindex(subset) - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- getCovariateWithReindex() - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- getCovariateWithReindex(subset) - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- getCreator() - Method in class net.maizegenetics.plugindef.DataSet
-
- getCumlativeP(a, b, c, d) - Method in class net.maizegenetics.stats.statistics.FisherExact
-
Calculates the one-tail P-value for the Fisher Exact test. Determines whether to calculate the right- or left- tail, thereby always returning the smallest p-value.
- getCurrentBlockIndex() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Returns current block index
- getCurrentIndex() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Returns current index
- getCurrentIndexWithinBlock() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Returns current index relative to current block
- getCurrentSize() - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- getCustomCompression() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- getCustomCompression() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getCutPosForStrandTagTaxaMap(chromosome, firstPosition, lastPosition, strand) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution Differs from getCutPositionTagTaxaMap() in that it now specifies on which strand the returned tags must appear.
- getCutPosForStrandTagTaxaMap(chromosome, firstPosition, lastPosition, direction) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getCutPosForStrandTagTaxaMap(chromosome, firstPosition, lastPosition, strand) - Method in interface net.maizegenetics.dna.tag.TagData
-
For a given snp position, Returns a Map of Allele with its associated Tag/TaxaDistribution Differs from getCutPositionTagTaxaMap() in that it now specifies on which strand the returned tags must appear.
- getCutPosForStrandTagTaxaMap(chromosome, firstPosition, lastPosition, direction) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getCutPositionTagTaxaMap(chromosome, firstPosition, lastPosition) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of positions and with associated map of Tags and their taxa distribution and their alignment direction. Warning: This can be a very large data structure for entire chromosomes. Only the best positions are returned.
- getCutPositionTagTaxaMap(chromosome, firstPosition, lastPosition) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getCutPositionTagTaxaMap(chromosome, firstPosition, lastPosition) - Method in interface net.maizegenetics.dna.tag.TagData
-
Map of positions and with associated map of Tags and their taxa distribution and their alignment direction. Warning: This can be a very large data structure for entire chromosomes. Only the best positions are returned.
- getCutPositionTagTaxaMap(chromosome, firstPosition, lastPosition) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getDARwinFilenames(base) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
Get DARwin file names.
- getData() - Method in class net.maizegenetics.analysis.gbs.neobio.Trie
-
Returns the data associated with this node.
- getData(i) - Method in class net.maizegenetics.plugindef.DataSet
-
- getData() - Method in class net.maizegenetics.plugindef.Datum
-
- getDataList() - Method in class net.maizegenetics.tassel.DataTreePanel
-
- getDataOfType(theClass) - Method in class net.maizegenetics.plugindef.DataSet
-
- getDataOfType(classes) - Method in class net.maizegenetics.plugindef.DataSet
-
- getDataOfTypeWithName(classes, names) - Method in class net.maizegenetics.plugindef.DataSet
-
- getDataOutputStream(filename, bufSize) - Static method in class net.maizegenetics.util.Utils
-
- getDataSet(list, creator) - Static method in class net.maizegenetics.plugindef.DataSet
-
Combines multiple data sets.
- getDataSet(data) - Static method in class net.maizegenetics.plugindef.DataSet
-
- getDataSet() - Method in class net.maizegenetics.plugindef.DataSet
-
- getDataSource() - Static method in class net.maizegenetics.util.db.LambdaTuplesContext
-
- getDataTreePanel() - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- getDataType() - Method in class net.maizegenetics.plugindef.Datum
-
- getDataWithName(name) - Method in class net.maizegenetics.plugindef.DataSet
-
- getDataWithName(names) - Method in class net.maizegenetics.plugindef.DataSet
-
- getDcoP(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getDcoP(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getDcoP(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getDcoP(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Round(Log2(P))
- getDecimalString(number, width) - Method in class net.maizegenetics.util.FormattedOutput
-
Returns a decimal string representation of a number with constrained width.
- getDefaultRendering(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getDefaultValue(n) - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- getDefaultValue(n) - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
get default value of parameter
- getDefaultValue(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- getDefaultValue(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- getDefaultValue(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- getDelimiter() - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
- getDelta() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getDepthMasksRendering(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getDepthMatrixForEncodedDepths(input) - Static method in class net.maizegenetics.dna.tag.TaxaDistBuilder
-
- getDescription() - Method in class net.maizegenetics.dna.read.Read
-
Return description of read
- getDescription() - Method in class net.maizegenetics.util.BasicFileFilter
-
- getDesiredIndices() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- getDfError() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getDfMarker() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getDfModel() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getDiagonalMatrix(diag) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getDiagonalPrefix(block) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
This method is a shorthand to retrieve the diagonal prefix of a block from the block table.
- getDimensionOfA() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getDiploidsSortedByFrequency(alignment, site) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
- getDiploidValue(a, b) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Combines two allele values into one diploid value. Assumed phased.
- getDiploidValuePhased(a, b) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Combines two allele values into one diploid value. Assumed phased.
- getDiploidValues(genotype) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Separates diploid allele value into it's two values.
- getDirectory(str) - Static method in class net.maizegenetics.util.Utils
-
Returns just the directory with the filename removed.
- getDistance(hap0, hap1) - Static method in class net.maizegenetics.analysis.clustering.Haplotype
-
- getDistance(hap0, hap1) - Static method in class net.maizegenetics.analysis.clustering.Haplotype
-
- getDistance(row, col) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getDistanceMatrix(alignment) - Static method in class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
- getDistanceMatrix(alignment, listener) - Static method in class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
- getDistances() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)
- getDistanceToRoot(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
determine distance to root
- getDivergence(tagIndex, mappingIndex) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return divergence of a mapping
- getDivergence(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getDivergence(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Blast doesn't have divergence, so it always return Byte.MIN_VALUE of Blast hits
- getDivergence(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getDivergence(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns Divergence
- getDivergenceOfTag(tagIndex) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getDnasampleName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
-
- getDomainBounds(includeInterval) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getDomainLowerBound(includeInterval) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getDomainUpperBound(includeInterval) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getDonorHaplotypes(taxon) - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- getDoublePref(path, key, def) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getDPrime(r, c) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Returns D' estimate for a given pair of numSites
- getEffectSize() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getEffectSize() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getEffectSize() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getEffectSize() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getEffectSize() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getEigenvalue(i) - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition
-
- getEigenvalue(i) - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- getEigenvalue(i) - Method in interface net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition
-
- getEigenvalue(i) - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLEigenvalueDecomposition
-
- getEigenvalue(i) - Method in class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- getEigenvalue(index) - Method in class net.maizegenetics.stats.PCA.ClassicMds
-
- getEigenvalueDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getEigenvalueDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- getEigenvalueDecomposition() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- getEigenvalueDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- getEigenvalueMatrix() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition
-
- getEigenvalueMatrix() - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- getEigenvalueMatrix() - Method in interface net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition
-
- getEigenvalueMatrix() - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLEigenvalueDecomposition
-
- getEigenvalueMatrix() - Method in class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- getEigenvalueMatrix() - Method in class net.maizegenetics.stats.PCA.PrinComp
-
- getEigenvalues() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition
-
- getEigenvalues() - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- getEigenvalues() - Method in interface net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition
-
- getEigenvalues() - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLEigenvalueDecomposition
-
- getEigenvalues() - Method in class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- getEigenValues() - Method in class net.maizegenetics.stats.PCA.PrinComp
-
- getEigenValuesAsColumnVector() - Method in class net.maizegenetics.stats.PCA.PrinComp
-
- getEigenvectors() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition
-
- getEigenvectors() - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition
-
- getEigenvectors() - Method in interface net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition
-
- getEigenvectors() - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLEigenvalueDecomposition
-
- getEigenvectors() - Method in class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- getEigenVectors() - Method in class net.maizegenetics.stats.PCA.PrinComp
-
- getEigenvectorsAs1dArray() - Method in class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- getElementAt(index) - Method in class net.maizegenetics.gui.AbstractAvailableListModel
-
- getElementAt(index) - Method in class net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
-
- getElementAt(index) - Method in class net.maizegenetics.gui.TableRowHeaderListModel
-
Returns the value at the specified index.
- getElementCount() - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- getElementCount() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getElementCount() - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getElementCount() - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getElementCount() - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getElementCount() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getElementCount() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getElementCount() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getElementCount() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getElementCount() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getElementCount() - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getElementCount() - Method in class net.maizegenetics.util.HDF5TableReport
-
- getElementCount() - Method in class net.maizegenetics.util.SimpleTableReport
-
- getElementCount() - Method in interface net.maizegenetics.util.TableReport
-
Get the total number of elements in the dataset. Elements = rowCount * columnCount;
- getEnd() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getEndPos() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getEndPosition() - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- getEndPosition(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getEndPosition(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
EndPosition of PEEnd1 is probably not the EndPosition of the tag
- getEndPosition(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getEndPosition(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns End Position of Tag
- getEnterLimit() - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- getErrorCode() - Method in exception net.maizegenetics.util.db.DataAccessException
-
- getErrordf() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getErrorRate() - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- getErrorSS() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getErrorSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
- getEvidence(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return the evidence
- getExceptionCauses(exception) - Static method in class net.maizegenetics.util.ExceptionUtils
-
This gets an exception's cause history. Only the message text is included (e.g. the exception's class names are not output).
- getExceptionCausesWithClassNames(exception) - Static method in class net.maizegenetics.util.ExceptionUtils
-
This gets an exception's cause history.
- getExistingHDF5Instance(reader) - Static method in class net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder
-
AlleleDepth is returned for an immutable HDF5 file
- getExitLimit() - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- getExportPluginExportDiploids() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getExportPluginIncludeTaxaAnnotations() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getExtension() - Method in class net.maizegenetics.util.BasicFileFilter
-
- getExternalNode(i) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Returns the ith external node.
- getExternalNode(i) - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getExternalNodeCount() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Returns the number of external nodes.
- getExternalNodeCount() - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getExternalNodes(root, store) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
Appends all external nodes from tree defined by root to Vector store
- getExternalNodes(root) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
Obtains all external nodes from tree defined by root and returns as an array
- getF() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getFactorModelEffect() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getFeatureFromId(id) - Method in class net.maizegenetics.dna.map.GenomeFeatureMap
-
- getFeatureIdFromGffAttributes(attributes) - Static method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
Parse a GFF attribute field to identify the name of the current GenomeFeature. Looks for 'ID=' and 'Name=' fields
- getFeaturesAtLocation(chrom, position) - Method in class net.maizegenetics.dna.map.GenomeFeatureMap
-
- getFeaturesAtLocation(chrom, position) - Method in class net.maizegenetics.dna.map.GenomeFeatureMap
-
Get a
HashSet of
class GenomeFeatures at a specified genome location Takes chromsome as a String for ones like "Pt", "scaffold487", etc.
- getFeaturesInRange(chrom, start, end) - Method in class net.maizegenetics.dna.map.GenomeFeatureMap
-
Get a
HashSet of
class GenomeFeatures at a specified genome location. Takes chromsome as a String for ones like "Pt", "scaffold487", etc.
- getFeaturesInRange(chrom, start, end) - Method in class net.maizegenetics.dna.map.GenomeFeatureMap
-
Get a
HashSet of
class GenomeFeatures at a specified genome location. Takes chromsome as a String for ones like "Pt", "scaffold487", etc.
- getFeaturesOfType(type) - Method in class net.maizegenetics.dna.map.GenomeFeatureMap
-
- getFile(chromosome, trait) - Method in class net.maizegenetics.dna.pd.FolderParser
-
- getFileChoice(data, datumArray) - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
- getFilename(str) - Static method in class net.maizegenetics.util.Utils
-
This returns the filename only. Preceding directories are removed and everything after last . is removed.
- getFilename(str, suffix) - Static method in class net.maizegenetics.util.Utils
-
This returns the filename only. Preceding directories are removed and suffix. If suffix not found, then everything after last . is removed.
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getFileReadyForClosing() - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
In implementations that use a RandomAccessFile for storage, this clears the RAM buffer of any remaining data, writes it to the file on disk, and closes the file.
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getFileReadyForClosing() - Method in class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- getFilterAlignPluginMaxFreq() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getFilterAlignPluginMinCount() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getFilterAlignPluginMinFreq() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getFilterBitSet() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- getFilteredInstance(genotype, translate) - Static method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- getFilteredInstance(alleleDepth, filter) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
- getFilteredInstance(base, translate) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
This creates a filtered AlleleDepth.
- getFilteredInstance(base, translate) - Static method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- getFilteredInstance(base, translate) - Static method in class net.maizegenetics.dna.snp.score.DosageBuilder
-
- getFilteredInstance(base, translate) - Static method in class net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
-
- getFilterTaxaPropsMaxHetFreq() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getFilterTaxaPropsMinHetFreq() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getFilterTaxaPropsMinNotMissingFreq() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getFirstCommonAncestor(nodes) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
For a set of nodes in the tree returns the common ancestor closest to all nodes (most recent common ancestor)
- getFirstCommonAncestor(nodeOne, nodeTwo) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
For two nodes in the tree returns the common ancestor closest to both nodes (most recent common ancestor)
- getFirstGeneticPosition(chromosome) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getFirstLowQualityPos(quality, minQual) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the position of the first low quality positions based on a quality fastq (?) string.
- getFirstLowQualityPos(quality, minQual, qualBase) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the position of the first low quality positions based on a quality fastq (?) string.
- getFlankingMarkerIndices(chromosome, geneticPosition) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getFloatStorageFeatures() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- getFocusEndSite() - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- getFocusStartSite() - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- getForwardRead() - Method in class net.maizegenetics.dna.read.PERead
-
Return forward read
- getFp() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getFpFromModelSS(modelss) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- getFullModelSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getFullyQualifiedClassNames(simpleName) - Static method in class net.maizegenetics.util.Utils
-
- getFullyQualifiedResourceNames(filename) - Static method in class net.maizegenetics.util.Utils
-
This returns a set of fully qualified resource names that match the specified filename.
- getGappedSequence1() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns the first gapped sequence.
- getGappedSequence2() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns the second gapped sequence.
- getGChr(index) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Return chromosome of genetic position
- getGEBVsAsDoubleMatrix() - Method in class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
- getGenericStorageFeatures() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- getGeneticDistanceMasksRendering(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getGeneticMappingInfo(tagIndex, geneticMapIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return tag genetic mapping information of a tag in one genetic map
- getGeneticMappingInfoGW(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getGeneticPos(markerIndex) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getGenotypeAfterUpdatingMissing() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
updates the genotype after missingObsForSite has changed
- getGenotypeAfterUpdatingMissing() - Method in class net.maizegenetics.analysis.association.AlleleProbabilityFELM
-
- getGenotypeAfterUpdatingMissing() - Method in class net.maizegenetics.analysis.association.DiscreteSitesFELM
-
- getGenotypeAfterUpdatingMissing() - Method in class net.maizegenetics.analysis.association.ReferenceProbabilityFELM
-
- getGenotypeAndUpdateMissing(missingObsBeforeSite) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- getGenotypeAndUpdateMissing(missingObsBeforeSite) - Method in class net.maizegenetics.analysis.association.AlleleProbabilityFELM
-
- getGenotypeAndUpdateMissing(missingObsBeforeSite) - Method in class net.maizegenetics.analysis.association.DiscreteSitesFELM
-
- getGenotypeAndUpdateMissing(missingObsBeforeSite) - Method in class net.maizegenetics.analysis.association.ReferenceProbabilityFELM
-
- getGenotypeCopyInstance(genotypeTable) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates a GenotypeTable with in-memory instance of GenotypeCallTable. Primarily needed for performance critical situations like imputation.
- getGenotypesCallsPath(taxon) - Static method in class net.maizegenetics.util.Tassel5HDF5Constants
-
- getGenotypesDepthPath(taxon) - Static method in class net.maizegenetics.util.Tassel5HDF5Constants
-
Deprecated.
- getGenotypesPedigreePath(taxon) - Static method in class net.maizegenetics.util.Tassel5HDF5Constants
-
- getGenotypesSiteScorePath(taxon, siteScoreType) - Static method in class net.maizegenetics.util.Tassel5HDF5Constants
-
- getGlobalMAF() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getGlobalMAF() - Method in interface net.maizegenetics.dna.map.Position
-
Return the minor allele frequency in a global scope
- getGlobalSiteCoverage() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getGlobalSiteCoverage() - Method in interface net.maizegenetics.dna.map.Position
-
Returns the proportion of genotypes scored at a given site
- getGOBIIDB() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getGOBIIUser() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getGPos(index) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Return site of genetic position
- getGRMFilenames(base) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
Get Genetic Relationship Matrix (grm) file names.
- getGroups(numberOfGroups) - Method in class net.maizegenetics.taxa.tree.TreeClusters
-
For a given number of groups this function returns the group membership for each taxon.
- getGroups(height) - Method in class net.maizegenetics.taxa.tree.TreeClusters
-
This function returns taxa group membership when the tree is cut at the designated height.
- getGVCFPositions() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- getGWASResult(trait) - Method in class net.maizegenetics.dna.pd.SiteAnnotation
-
Obtain GWAS result value for given trait
- getGWASTraits() - Method in class net.maizegenetics.dna.pd.SiteAnnotation
-
Obtain complete listing of all available traits for which GWAS traits may be available
- getHaplotype() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
The common haplotype of this cluster. The type is determined by the field ReturnHaplotype.
- getHaplotypeAsString() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
The common haplotype of this cluster. The type is determined by the field ReturnHaplotype.
- getHaplotypeList() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getHaplotypeNucleotide(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns the Nucleotide String for the given haploid allele value.
- getHDF5Alleles(reader, allele) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5AncestralAlleles(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5AncestralAlleles(reader, startSite, numSites) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5GenotypesCalls(reader, taxon) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5GenotypesDepth(reader, taxon) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5GenotypeSiteScores(reader, taxon, siteScoreType) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5GenotypeTaxaNumber(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5NucleotideInstance(writer, numSites) - Static method in class net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder
-
AlleleDepthBuilder is created and depths are stored in a HDF5 file. setDepth methods are used to set the depths. Finish the building with build()
- getHDF5PositionNumber(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5ReferenceAlleles(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5ReferenceAlleles(reader, startSite, numSites) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5TagCount(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5TagLengthInLong(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHDF5TaxaNumTaxa(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getHetTreatment() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getHomozygousInstance(genotype) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getHorizontalCenter() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getHorizontalPageSize() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getIBSDistance(iMajor, iMinor, jMajor, jMinor) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
Calculates the IBS distance between two taxa with bitsets for for major and minor allele
- getIBSDistance(iMajor, iMinor, jMajor, jMinor) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
- getIcon() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.chart.QQDisplayPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.GetPositionListPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.GetTaxaListPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.HetsToUnknownPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.IdentityRecognitionPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.IndelsToUnknownPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.KmerCountingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.LIXPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MemoryUsagePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.PassThroughPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.SeparatePlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.SubtractGenotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.data.UnionAlignmentPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterDataSetPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.FastqToTBTPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.KmerToTBTPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.QseqToTBTPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.ListPluginParameters
-
- getIcon() - Method in class net.maizegenetics.analysis.ListPlugins
-
- getIcon() - Method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.analysis.tree.MergeTreesPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- getIcon() - Method in class net.maizegenetics.analysis.workflow.WorkflowPlugin
-
- getIcon() - Method in interface net.maizegenetics.plugindef.Plugin
-
Icon for this plugin to be used in buttons, etc.
- getIcon() - Method in class net.maizegenetics.tassel.PreferencesDialog
-
- getIcon() - Method in class net.maizegenetics.tassel.ShowParameterCachePlugin
-
- getIcon() - Method in class net.maizegenetics.tassel.TasselLogging
-
- getIcon() - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- getID() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getID() - Method in class net.maizegenetics.dna.read.Read
-
Return ID of read
- getID() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getID() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getID() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getID() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getIdCorrelation(id) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- getIdentifier() - Method in interface net.maizegenetics.taxa.tree.Node
-
Returns the identifier for this node.
- getIdentifier() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Returns the identifier for this node.
- getIdentityMatrix(dim) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getIdGroup() - Method in class net.maizegenetics.taxa.tree.CladeSystem
-
get idGroup
- getIdGroup() - Method in class net.maizegenetics.taxa.tree.SplitSystem
-
get idGroup
- getIfHasEvidence(type, ifEvidence) - Method in enum net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
-
- getIfHasGeneticMapping() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return if the file has genetic mapping test result
- getIfHasGeneticMappingGW() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return if the file has genome wide genetic mapping annotation
- getIfHasMapping() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return if the file has alignment mapping annotation
- getIfPAV(index) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Return if this tag is PAV
- getImageHeight() - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getImageWidth() - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getIncludedSitesBasedOnFreqIgnoreMissing(aa, minimumProportion, maximumProportion, minimumCount) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
get sites to be included based on minimum frequency (the count of good bases, INCLUDING GAPS) and based on the proportion of good sites (INCLUDING GAPS) different from consensus
- getIncludedTraits() - Method in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- getIncrementalSSdf(effect) - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getIndex() - Method in enum net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
-
- getIndex() - Method in enum net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE
-
- getIndex() - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- getIndexOfTaxaName(taxon) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getIndexOfTaxaName(taxon) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getIndexOfTaxaName(taxon) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Get the index of a taxon based on its name
- getIndexOfTaxaName(taxon) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- getIndexOfTaxaName(taxon) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getIndicesOfSetBits() - Method in interface net.maizegenetics.util.BitSet
-
Return indices of set bits.
- getIndicesOfSetBits() - Method in class net.maizegenetics.util.OpenBitSet
-
- getIndicesOfSetBits() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getInput() - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- getInputs() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getInputStream(filename) - Static method in class net.maizegenetics.util.Utils
-
Gets input stream for given file.
- getInsertionPosition() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getInsertionPosition() - Method in interface net.maizegenetics.dna.map.Position
-
Return the insertion-position of a site. This will be zero for the main physical position and sequentially numbered (1, 2, 3,...) for any (if any) sites with the same
net.maizegenetics.dna.map.Position$getPosition(). This will mostly be used for insertions relative to the reference.
- getInstance(chromosome) - Static method in class net.maizegenetics.analysis.avro.GenericRecordChromosome
-
- getInstance(genotype) - Static method in class net.maizegenetics.analysis.distance.DominanceNormalizedIBSMatrix
-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375616/pdf/main.pdf p. 378
- getInstance(genotype, listener) - Static method in class net.maizegenetics.analysis.distance.DominanceNormalizedIBSMatrix
-
Same as other getInstance() but reports progress.
- getInstance(genotype) - Static method in class net.maizegenetics.analysis.distance.DominanceRelationshipMatrix
-
Compute Dominance Relationship Matrix for all pairs of taxa. Missing sites are ignored.
- getInstance(genotype, maxAlleles, variation, listener) - Static method in class net.maizegenetics.analysis.distance.DominanceRelationshipMatrix
-
Compute Dominance Relationship Matrix for all pairs of taxa. Missing sites are ignored.
- getInstance(genotype) - Static method in class net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
-
Compute Endelman Kinship Matrix. Maximum alleles per site to evaluate defaults to 2.
- getInstance(genotype, maxAlleles) - Static method in class net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
-
Compute Endelman Kinship Matrix
- getInstance(genotype, listener) - Static method in class net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
-
Compute Endelman Kinship Matrix. Maximum alleles per site to evaluate defaults to 2.
- getInstance(genotype, maxAlleles, listener) - Static method in class net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
-
Compute Endelman Kinship Matrix
- getInstance(genotype) - Static method in class net.maizegenetics.analysis.distance.GCTADistanceMatrix
-
Compute Normalized_IBS (GCTA) kinship for all pairs of taxa. Missing sites are ignored. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/pdf/main.pdf Equation-3
- getInstance(genotype, listener) - Static method in class net.maizegenetics.analysis.distance.GCTADistanceMatrix
-
Same as other getInstance() but reports progress.
- getInstance(theAlignment) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute observed distances for all taxa. Missing sites are ignored.
- getInstance(theAlignment, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute observed distances for all taxa. Missing sites are ignored.
- getInstance(theAlignment, minSiteComp, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute observed distances for all taxa. Missing sites are ignored.
- getInstance(theAlignment, minSiteComp, trueIBS, listener, useThirdState) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix
-
Compute observed distances for all taxa. Missing sites are ignored.
- getInstance(genotype) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
-
- getInstance(genotype, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
-
- getInstance(genotype, minSiteComp, trueIBS, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
-
- getInstance(genotype) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
-
- getInstance(genotype, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
-
- getInstance(genotype, minSiteComp, trueIBS, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
-
- getInstance(genotype, taxonIndex) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrixOneByAll
-
- getInstance(genotype, taxonIndex, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrixOneByAll
-
- getInstance(genotype, taxonIndex, minSiteComp, listener) - Static method in class net.maizegenetics.analysis.distance.IBSDistanceMatrixOneByAll
-
- getInstance(hdf5Filename) - Static method in class net.maizegenetics.dna.map.PositionListBuilder
-
Creates a new position list based on an existing HDF5 file.
- getInstance(reader) - Static method in class net.maizegenetics.dna.map.PositionListBuilder
-
Creates a new builder based on an existing HDF5 file reader.
- getInstance(numSites) - Static method in class net.maizegenetics.dna.map.PositionListBuilder
-
Generates a generic position list when no position information known
- getInstance(positions) - Static method in class net.maizegenetics.dna.map.PositionListBuilder
-
Creates in memory of PositionList from the an array of positions.
- getInstance(numTaxa, numSites, siteScoreType, taxaList) - Static method in class net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
-
- getInstance(writer, numSites, siteScoreType, taxaList) - Static method in class net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
-
- getInstance(reader, siteScoreType) - Static method in class net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
-
- getInstance(genoTables) - Static method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
This factory method combines given genoTables. If only one genotypeTable, then it is returned unchanged. Otherwise, this requires that each genotypeTable has the same Taxa in the same order.
- getInstance(genoTables, isUnion) - Static method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
This factory method combines given genoTables. If only one genotypeTable, then it is returned unchanged. If isUnion equals true, a union join of the Identifiers will be used to construct the combination. Any genotypeTable not containing one of the Identifiers will return unknown value for those locations. If isUnion equals false, a intersect join of the Identifiers will be used.
- getInstance(base, annoName, symbol, threshold, mode) - Static method in class net.maizegenetics.dna.snp.FilterAndMaskGVCFGenomeSequence
-
- getInstance(base, taxa, positions, translate) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(genotypes, positions, redirectSites) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
For use when converting between coordinate systems.
- getInstance(a, subTaxaList) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
This returns GenotypeTable with only specified subTaxaList. Defaults to retain unknown taxa.
- getInstance(genotype, subTaxaList, retainUnknownTaxa) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
This returns FilterGenotypeTable with only specified subTaxaList. If retainUnknownTaxa is true then Alignment will return unknown values for missing taxa.
- getInstance(genotypes, subSites) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(genotypes, subSites, includeSites) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(a, siteNamesToKeep) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(a, siteNamesToKeep) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(a, subPositionList) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(a, chromosome, startPhysicalPos, endPhysicalPos) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(a, chromosome, startPhysicalPos, endPhysicalPos) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(a, chromosome) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(genotypes, startSite, endSite) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
Factory method that returns genotypes FilterGenotypeTable viewing sites between start site (inclusive) and end site (inclusive).
- getInstance(a, startSite, endSite, includeSites) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstance(genotypeCallTables) - Static method in class net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
-
- getInstance(numTaxa, numSites) - Static method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
Get Genotype Builder given number of taxa and sites. Performance optimized for site loop inside taxon loop. Default is unphased and NucleotideAlignmentConstants.NUCLEOTIDE_ALLELES encoding.
- getInstance(numTaxa, numSites, phased, record) - Static method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- getInstance(numTaxa, numSites, phased, filename) - Static method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- getInstance(numTaxa, numSites, phased, isOneLetter, index, filename) - Static method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- getInstance(genotypeCallTables, taxonMap, positionMap) - Static method in class net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
-
- getInstance(alleleCounts, stats, numIndices, index) - Static method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- getInstance(orig, newIndex) - Static method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- getInstance(original, newGenotypes) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstance(genotype, positionList, taxaList, alleleDepth, alleleProbability, referenceProbability, dosage, annotations) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Standard approach for creating a new Alignment
- getInstance(genotype, positionList, taxaList, alleleDepth) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstance(genotype, positionList, taxaList) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstance(genotype, positionList, taxaList, hdf5File) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates a new HDF5 file alignment based on existing Genotype, PositionList, and TaxaList.
- getInstance(a, hdf5File) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates a new HDF5 file alignment based on an existing alignment.
- getInstance(hdf5File) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstance(base, mask) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstance(paFile, baseHighDensityAlignmentFile) - Static method in class net.maizegenetics.dna.snp.io.ProjectionGenotypeIO
-
Returns a genotypeTable based on a projection genotype file and high density genotype table
- getInstance(paFile, baseHighDensityAlignment) - Static method in class net.maizegenetics.dna.snp.io.ProjectionGenotypeIO
-
Returns a genotypeTable based on a projection genotype file and high density genotype table
- getInstance(numTaxa, numSites, isSiteOptimized) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstance(orig) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstance(genotype, predicate) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstance(genotype, predicate) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstance(genoTables, taxaMergeRule, positionMergeRule) - Static method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- getInstance(baseAlignment, allBreakPoints) - Static method in class net.maizegenetics.dna.snp.ProjectionBuilder
-
- getInstance(writer, numSites) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
AlleleDepthBuilder is created and depths are stored in a HDF5 file. setDepth methods are used to set the depths. Finish the building with build()
- getInstance(numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
This returns an AlleleDepthBuilder where depths are stored in memory.
- getInstance(reader) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
This creates an AlleleDepth instance from an existing HDF5 file.
- getInstance(writer, numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- getInstance(reader) - Static method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- getInstance(writer, numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.DosageBuilder
-
- getInstance(numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.DosageBuilder
-
- getInstance(reader) - Static method in class net.maizegenetics.dna.snp.score.DosageBuilder
-
- getInstance(writer, numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
-
- getInstance(numTaxa, numSites, taxaList) - Static method in class net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
-
- getInstance(reader) - Static method in class net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
-
- getInstance(translateTaxa, translateSite) - Static method in class net.maizegenetics.dna.snp.TranslateBuilder
-
- getInstance(base, translate) - Static method in class net.maizegenetics.dna.snp.TranslateBuilder
-
- getInstance(numBaseIndices) - Static method in class net.maizegenetics.dna.snp.TranslateIndexBuilder
-
- getInstance(base) - Static method in class net.maizegenetics.dna.snp.TranslateIndexBuilder
-
- getInstance(numBaseIndices, base) - Static method in class net.maizegenetics.dna.snp.TranslateIndexBuilder
-
- getInstance(parentFrame) - Static method in class net.maizegenetics.gui.PrintHeapAction
-
- getInstance() - Static method in class net.maizegenetics.gui.VerticalLabelUI
-
- getInstance(nrows, ncols, values, columnMajor) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getInstance(nrows, ncols, dblValue) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getInstance() - Static method in class net.maizegenetics.plugindef.DefaultPluginListener
-
- getInstance() - Static method in class net.maizegenetics.progress.ProgressPanel
-
- getInstance(cme, me) - Static method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getInstance(covariate, me) - Static method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getInstance(size) - Static method in class net.maizegenetics.stats.statistics.FisherExact
-
Static method to get instance
- getInstance(alignment, masks, dataTreePanel) - Static method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getInstance(topm, dataTreePanel) - Static method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getInstance(alignment, dataTreePanel) - Static method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getInstance(theTableSource) - Static method in class net.maizegenetics.tassel.TableReportPanel
-
- getInstance(filter) - Static method in class net.maizegenetics.tassel.TableReportPanel
-
- getInstance(topm) - Static method in class net.maizegenetics.tassel.TableReportPanel
-
- getInstance(taxaList) - Static method in class net.maizegenetics.tassel.TableReportPanel
-
- getInstance(positionList) - Static method in class net.maizegenetics.tassel.TableReportPanel
-
- getInstance(parentFrame) - Static method in class net.maizegenetics.tassel.TasselLogging
-
- getInstance(taxa) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- getInstance(numTaxa) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- getInstance(numTaxa) - Static method in class net.maizegenetics.taxa.TaxaListBuilder
-
- getInstance() - Static method in class net.maizegenetics.util.FormattedInput
-
create new instance of this object (note that there is no public constructor because this class is a singleton!)
- getInstance() - Static method in class net.maizegenetics.util.FormattedOutput
-
create instance of this class (note that there is no public constructor as this class is a singleton)
- getInstance(numRows, numColumns) - Static method in class net.maizegenetics.util.SuperByteMatrixBuilder
-
This returns a SuperByteMatrix designed for better performance when column iteration loop inside row iteration loop.
- getInstance(tableName, columnNames) - Static method in class net.maizegenetics.util.TableReportBuilder
-
- getInstance(tableName, numColumns) - Static method in class net.maizegenetics.util.TableReportBuilder
-
- getInstance(tableName, columnNames, filename) - Static method in class net.maizegenetics.util.TableReportBuilder
-
- getInstance(bitSet) - Static method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getInstanceCompareAlignments(align1, align2, name, type) - Static method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getInstanceCompareReference(align) - Static method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getInstanceCompareReference(align, id) - Static method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getInstanceCompareReference(align, index) - Static method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getInstanceCompareReference(align, id) - Static method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getInstanceCompareReference(align, ref, name) - Static method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getInstanceCompareReference(align, id, distances) - Static method in class net.maizegenetics.gui.GenotypeTableMaskGeneticDistance
-
- getInstanceCompareReference(align, id, distances) - Static method in class net.maizegenetics.gui.GenotypeTableMaskGeneticDistance
-
- getInstanceCompareReference(align, index, distances) - Static method in class net.maizegenetics.gui.GenotypeTableMaskGeneticDistance
-
- getInstanceCompareReference(align) - Static method in class net.maizegenetics.gui.GenotypeTableMaskReference
-
- getInstanceCompareReference(align, id) - Static method in class net.maizegenetics.gui.GenotypeTableMaskReference
-
- getInstanceCompareReference(align, id) - Static method in class net.maizegenetics.gui.GenotypeTableMaskReference
-
- getInstanceCompareReference(align, index) - Static method in class net.maizegenetics.gui.GenotypeTableMaskReference
-
- getInstanceCopy(genotype) - Static method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- getInstanceCopy(matrix) - Static method in class net.maizegenetics.util.SuperByteMatrixBuilder
-
- getInstanceFromModel(baseModel, dataList) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- getInstanceFromVectors(basisVectors, dataList) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- getInstanceMaskIndels(genotype) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstanceOnlyMajorMinor(genotype) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- getInstanceRemoveHeterozygous(genotype) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstanceRemoveHomozygous(genotype) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstanceRemoveIDs(a, subTaxaList) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
Removes specified IDs.
- getInstanceRemoveIndels(genotype) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstanceRemoveMinorSNPs(genotype) - Static method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- getInstanceRemoveSiteNames(a, siteNamesToRemove) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstanceRemoveSiteNames(a, siteNamesToRemove) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstances(parentFrame) - Static method in class net.maizegenetics.analysis.workflow.WorkflowPlugin
-
- getInstanceSingleValue(numRows, numColumns, value) - Static method in class net.maizegenetics.util.SuperByteMatrixBuilder
-
- getInstanceSortTaxaAlphabetically(genotypes) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstanceTaxaOrderedByGeneticDistance(genotypes, taxon) - Static method in class net.maizegenetics.dna.snp.FilterGenotypeTable
-
- getInstanceTranspose(numTaxa, numSites) - Static method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
Get Genotype Builder given number of taxa and sites. Performance optimized for taxon loop inside site loop. Default is unphased and NucleotideAlignmentConstants.NUCLEOTIDE_ALLELES encoding.
- getInstanceTranspose(numRows, numColumns) - Static method in class net.maizegenetics.util.SuperByteMatrixBuilder
-
This returns a SuperByteMatrix designed for better performance when row iteration loop inside column iteration loop.
- getInstanceTranspose(matrix) - Static method in class net.maizegenetics.util.SuperByteMatrixBuilder
-
This returns a SuperByteMatrix that performs better in the reverse row / column iteration nesting than the given matrix.
- getIntegerLevels(originalLevels) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getIntegerLevels(originalLevels, ids) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getIntegerLevels(genotypes, ids) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getIntegerLevels(originalLevels, ids) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getIntegerLevels(originalLevels) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getIntegerLevels(originalLevels) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getIntegerLevelsSortedByGenotype(originalLevels, ids) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getInternalNode(i) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Returns the ith internal node.
- getInternalNode(i) - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getInternalNodeCount(root) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
- getInternalNodeCount() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Returns the number of internal nodes.
- getInternalNodeCount() - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getInternalNodes(root, store) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
Appends all internal nodes from tree defined by root to Vector store
- getInternalNodes(root, includeRoot) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
Obtains all internal nodes from tree defined by root and returns as an array
- getInternalParameterBoundaries(parameter, storage) - Method in interface net.maizegenetics.stats.math.OrthogonalHints
-
A boundary is a value of a parameter for which values lower than the boundary and values higher than the boundary are better treated as two separate functions (IE, they are only piecewise connected), and minimisation should be performed over both ranges individually (and then the true minimum taken as the minimuma of the ranges)
- getInternalParameterBoundaries(base, parameter) - Static method in class net.maizegenetics.stats.math.OrthogonalHints.Utils
-
- getInterval(chromosome, position) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getIntFromLong(val) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Split a 2-bit encoded long into 2 integers.
- getIntFromSeq(seq) - Static method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryUtils
-
- getIntFromSeq(seq) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns an int for a sequence in a String NOTE: this version leaves the padding at the FRONT of the sequence. This is to facilitate SPARK machine-learning IT is preferable to have a smaller int when creating the sequence. Padding at the end gives a larger value. Currently this is only used for monetdb encoding. The ints can be converted back to sequence by the existing getSequenceFromInt() method. User needs to know where padding was added to correctly analyze the sequence.
- getIntPref(path, key, def) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getIntStorageFeatures() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- getInverse(exclude) - Method in class net.maizegenetics.stats.linearmodels.SymmetricMatrixInverterDM
-
Calculates a new inverse when rows/columns of the original matrix have been removed. Each element of exclude corresponds to a row/column of the matrix. If exclude is true, then that row/column in removed.
- getInverse(exclude, size) - Method in class net.maizegenetics.stats.linearmodels.SymmetricMatrixInverterDM
-
Calculates a new inverse when rows/columns of the original matrix have been removed. Each element of exclude corresponds to a row/column of the matrix. If exclude is true, then that row/column in removed.
- getInverseOfXtX() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getInverseOfXtX() - Method in class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
- getInvH() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getIsAccumulateResults() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getItemCount(parm1) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getItemCount(parm1) - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getItemCount(parm1) - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getIterator() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getIUPACAllele(allele) - Static method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- getJavaPackages() - Static method in class net.maizegenetics.util.Utils
-
- getKey(taxon, site) - Static method in class net.maizegenetics.analysis.avro.AvroConstants
-
- getKey(taxon, site) - Static method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- getKnownVariants() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getKnownVariants() - Method in interface net.maizegenetics.dna.map.Position
-
Returns the nature of the polymorphism {"ACTAT","-"} or {"A","C","G"} or {"100","103","106"}
- getLabel(id, defaultLabel) - Method in class net.maizegenetics.taxa.tree.LabelMapping
-
- getLabelCount() - Method in class net.maizegenetics.taxa.tree.CladeSystem
-
get number of labels
- getLabelCount() - Method in class net.maizegenetics.taxa.tree.SplitSystem
-
get number of labels
- getLabelIdentifier(id) - Method in class net.maizegenetics.taxa.tree.LabelMapping
-
- getLabelInstance(label) - Static method in class net.maizegenetics.plugindef.PluginParameter
-
- getLaneAnnotatedTaxaList(keyPath, fastQpath) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Returns an annotated taxaList based on a Keyfile for GBS
- getLaneAnnotatedTaxaList(keyPath, fastQpath, useNew) - Static method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- getLastGeneticPosition(chromosome) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getLDForSitePair(rMj, rMn, cMj, cMn, minMinorCnt, minCnt, minR2, myFisherExact, site1Index, site2Index) - Static method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Method for estimating LD between a pair of bit sets. Since there can be tremendous missing data, minimum minor and minimum site counts ensure that meaningful results are estimated. Site indices are merely there for annotating the LDResult.
- getLDType() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getLeafCount(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
Return the number of terminal leaves below this node or 1 if this is a terminal leaf.
- getLeafIdGroup(tree) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
get list of the identifiers of the external nodes
- getLeftPrefix(block) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
This method is a shorthand to retrieve the left prefix of a block from the block table.
- getLeftTailedP(a, b, c, d) - Method in class net.maizegenetics.stats.statistics.FisherExact
-
Calculates the left-tail P-value for the Fisher Exact test.
- getLength() - Method in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
- getLength() - Method in class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
Return the length of the genomic sequence
- getLength() - Method in class net.maizegenetics.dna.map.Chromosome
-
- getLengthB() - Method in class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Return length of backward sequence
- getLengthF() - Method in class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Return length of forward sequence
- getLevelCounts() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getLevelCounts() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getLevelCounts() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getLevelCounts() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getLevelCounts() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getLevels() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getLibraryID() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
-
- getLinearModel() - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- getLinearModel() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getLinkageDiseqDisplayPlugin(type) - Method in class net.maizegenetics.pipeline.TasselPipeline
-
- getListCellRendererComponent(list, value, index, isSelected, cellHasFocus) - Method in class net.maizegenetics.gui.RowHeaderRenderer
-
- getListeners() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getListOfTaxa(filename) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- getLnLikelihood() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getLnProbObsGivenState(state, obs) - Method in class net.maizegenetics.analysis.imputation.EmissionProbability
-
- getLnProbObsGivenState(state, obs, node) - Method in class net.maizegenetics.analysis.imputation.EmissionProbability
-
- getLnTransitionProbability(state1, state2) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- getLocale() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getLoci() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getLoci() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns Loci created from getChromosomes().
- getLocus() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- getLocus() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getLocus(tagIndex) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getLocus(tagIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Get Chromosome representing chromosome for given tag.
- getLocusReport(minTaxaWithLocus, varSiteKept) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getLocusStr() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getLogDebug() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getLogs() - Method in class net.maizegenetics.util.ChangeLog
-
- getLogSendToConsole() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getLogXDim() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getLogYDim() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getLongArrayFromSeq(seq) - Static method in class net.maizegenetics.dna.BaseEncoder
-
- getLongArrayFromSeq(seq, paddedLength) - Static method in class net.maizegenetics.dna.BaseEncoder
-
- getLongArrayFromSeq(seq) - Static method in class net.maizegenetics.dna.tag.AbstractTag
-
- getLongFromSeq(seq) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns a long for a sequence in a String
- getLongSeqFromByteArray(b) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the 2-bit encoded long represented by 32 bytes representing
class NucleotideAlignmentConstants representation. It is padded by As if shorter than 32 bytes, -1 returned if longer than 32. The byte array values must be 0-3. If the array contains a value outside that range returns -1.
- getLookupTable() - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getLowerCorner() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- getLowerLimit(n) - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- getLowerLimit(n) - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
get lower parameter limit
- getLowerLimit(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- getLowerLimit(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- getLowerLimit(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.BarChartPanel
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.BasicChartPanel
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.HistogramPanel
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.PieChartPanel
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.XYScatterAndLinePanel
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.XYScatterMultipleYPanel
-
- getMainComponent() - Method in class net.maizegenetics.analysis.chart.XYScatterPanel
-
- getMajorAlleleFromSnpset(snpset, alpha) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- getMajorAlleleFromSnpset(snpset) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- getMajorityHaplotype() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
The majority haplotype of this cluster where each site is assigned value of the major allele within the cluster.
- getManhattanDistance(loc, t, nsnps) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- getMapOfTaxonByAnnotation(taxaList, annotation) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Create a Multimap of all the taxa associated with a particular annotation value.
- getMapP(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getMapP(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getMapP(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getMapP(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
- getMappingIndicesOfAligner(alignerName) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return the map indices of an aligner
- getMappingInfo(tagIndex, mapIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return tag mapping information of a tag in one map
- getMappingInfoChunk(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return mapping information of a while chunk, avoid issues while multi threads are trying to get TMI info, specifically for hypothesis genetic mapping
- getMappingNum(index) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return the number of mapping (multiple alignments)
- getMappingNum() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return number of mapping result
- getMapSize() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
-
Returns map size
- getMarginalSSdf(effect) - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getMarker(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getMarkerEffectReport() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getMarkerEffectReport() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- getMarkerEffectReportWithCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getMarkerEffectReportWithCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- getMarkerFp() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getMarkerName(marker) - Static method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getMarkerNameFromLine(mline, isVCF, tabPos, mapsetname) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- getMarkerNumber(marker) - Static method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getMarkerPosition(marker) - Static method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getMarkers() - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getMarkerSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
- getMask(taxon, site) - Method in interface net.maizegenetics.gui.GenotypeTableMask
-
- getMask(taxon, site) - Method in class net.maizegenetics.gui.GenotypeTableMaskBoolean
-
- getMask(taxon, site) - Method in class net.maizegenetics.gui.GenotypeTableMaskGeneticDistance
-
- getMask(taxon, site) - Method in class net.maizegenetics.gui.GenotypeTableMaskReference
-
- getMaskBitSet() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- getMaskInstance(base, mask) - Static method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
- getMaskInstance(base, mask) - Static method in class net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
-
- getMaskInstance(base, mask) - Static method in class net.maizegenetics.dna.snp.score.DosageBuilder
-
- getMaskInstance(base, mask) - Static method in class net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
-
- getMaskType() - Method in class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- getMaskType() - Method in interface net.maizegenetics.gui.GenotypeTableMask
-
- getMatrix() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getMatrixCopy() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getMaxFreq() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getMaxHeapSizeMB() - Static method in class net.maizegenetics.util.Utils
-
Returns max heap size in MB.
- getMaximumDistance(hap) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getMaximumPathLengthLengthToLeaf(root) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
- getMaximumSize(c) - Method in class net.maizegenetics.gui.VerticalLabelUI
-
- getMaxNodeDepth(root) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
- getMaxNumVariants() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getMaxNumVariants() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getMaxNumVariants() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns maximum number of variants stored per tag.
- getMaxp() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- getMaxp() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getMaxP() - Method in class net.maizegenetics.gui.ReportDestinationDialog
-
- getMaxStartPosition() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getMaxTagLength() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getMaxThreads() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getMD5Checksum(filename) - Static method in class net.maizegenetics.util.CheckSum
-
- getMeanCladeHeight(clade, trees) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- getMeanLocation(loc, size, t, add, nsnps) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- getMeanLocation(locs) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- getMeanSubtreeHeight(subtree, trees) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- getMedianQuality(phredScale) - Method in class net.maizegenetics.dna.read.Read
-
Return median quality of read
- getMemoryUse() - Static method in class net.maizegenetics.util.Sizeof
-
- getMenu() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
Returns menu that can be added to main menu bar.
- getMenu() - Method in interface net.maizegenetics.plugindef.Plugin
-
Returns menu that can be added to main menu bar.
- getMergedClusters(candidateClusters, maxdiff) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
Merges clusters whose maximum pairwise difference is less than maxdiff. Clusters are tested sequentially. That is, if two clusters are merged, they become the new head cluster against which remaining clusters are tested for merging.
- getMergedInstance(dh1, dh2) - Static method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- getMergedPETagCounts(another, ifCollapsed) - Method in class net.maizegenetics.dna.tag.PETagCounts
-
Merge two PETagCounts objects
- getMetaData() - Method in class net.maizegenetics.plugindef.PluginEvent
-
- getMGID() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
-
- getMinCount() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getMinFreq() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getMinimumPathLengthLengthToLeaf(root) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
- getMinimumSize(c) - Method in class net.maizegenetics.gui.VerticalLabelUI
-
- getMinStartPosition() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getMinTagLength() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getMismatchInLong(longSeq1, longSeq2) - Method in class net.maizegenetics.analysis.gbs.PolymorphismFinder
-
- getMismatchInLong(longSeq1, longSeq2) - Method in class net.maizegenetics.analysis.gbs.UTagPairFinder
-
- getModelcfmSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getModelcfmSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
- getModeldf() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getModelEffects() - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- getModelSS() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getMostProbableIntegerStateSequence() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
-
- getMostProbableStateSequence() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithm
-
- getMostProbableStateSequence() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
-
- getMrkBlups() - Method in class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
- getMrkEstsAsDoubleMatrix() - Method in class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
- getMultiMaps(index) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getMultiMaps(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getMultiMaps(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getMultiMaps(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
- getName() - Method in class net.maizegenetics.dna.map.Chromosome
-
- getName() - Method in enum net.maizegenetics.dna.map.TagMappingInfoV3.Aligner
-
- getName() - Method in class net.maizegenetics.plugindef.Datum
-
- getName() - Method in class net.maizegenetics.taxa.Taxon
-
- getNameList(pedigree) - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- getNamSubPopulation(taxonname) - Static method in class net.maizegenetics.analysis.imputation.SubpopulationFinder
-
- getNamSubPopulation(taxon) - Static method in class net.maizegenetics.analysis.imputation.SubpopulationFinder
-
- getNewChar() - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
Returns this factor's new character.
- getNext() - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
Returns this factor's next factor.
- getNext() - Method in class net.maizegenetics.dna.tag.FastqReader
-
Returns single entry in fastq file consisting of 4 Strings.
- getNext() - Method in interface net.maizegenetics.stats.math.OrderEnumerator
-
The next value in the enumeration
- getNextBoolean() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextByte() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextBytes(bs) - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextChar() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextColor() - Static method in class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- getNextDouble() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextFloat() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextInt() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextLong() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNextShort() - Static method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Access a default instance of this class, access is synchronized
- getNodeByName(tree, name) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
- getNodeByName(root, name) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
- getNodeHeight() - Method in interface net.maizegenetics.taxa.tree.Node
-
Get the height of this node relative to the most recent node.
- getNodeHeight() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Get the height of this node relative to the most recent node.
- getNonMissingBytes(allData, missing) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- getNonMissingDoubles(allData, missing) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- getNonMissingDoubles(allData, missing) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- getNonMissingElements(array, missing) - Static method in class net.maizegenetics.stats.linearmodels.LinearModelUtils
-
- getNonMissingElements(array, missing) - Static method in class net.maizegenetics.stats.linearmodels.LinearModelUtils
-
- getNonMissingValues(allData, missing) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- getNonMissingValues(allData, missing) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- getNucleotideAlleleByte(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns haploid byte value for given nucleotide value. Only right-most four bits used.
- getNucleotideAlleleByte(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns haploid byte value for given nucleotide value. Only right-most four bits used.
- getNucleotideAlleleValue(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns char allele for allele byte encoding. THis is called from junit tests in ReferenceGenomeSequenceTest.java
- getNucleotideComplement(nucleotide) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns the Nucleotide Complement of given byte encoded nucleotide. A returns T. T returns A. C returns G. G returns C. Otherwise given nucleotide is returned.
- getNucleotideDiploidByte(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns diploid byte value for given nucleotide value. First four bits contain first allele value. And second four bits contain second allele value.
- getNucleotideDiploidByte(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns diploid byte value for given nucleotide value. First four bits contain first allele value. And second four bits contain second allele value.
- getNucleotideDiploidComplement(diploidAllele) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns the Nucleotide Complement of the given diploid byte encoded alleles.
- getNucleotideDiploidIUPACComplement(diploidAllele) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns the Nucleotide Complement of the given diploid IUPAC encoded alleles.
- getNucleotideIUPAC(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns the IUPAC String for the given diploid allele value.
- getNucleotideIUPACChar(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns the IUPAC char for the given diploid allele value.
- getNucleotideRendering(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getNull() - Static method in class net.maizegenetics.stats.math.OrthogonalHints.Utils
-
- getNullTag() - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- getNullTag() - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getNullTag() - Method in interface net.maizegenetics.dna.tag.Tags
-
Returns a polyA string of length 32*getTagSizeInLong()
- getNum() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
-
- getNumAccumulateIntervals() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getNumber() - Method in interface net.maizegenetics.taxa.tree.Node
-
return the index of this node
- getNumber() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- getNumberLines(filename) - Static method in class net.maizegenetics.util.Utils
-
Return number of lines in given file.
- getNumberLinesNotHashOrBlank(filename) - Static method in class net.maizegenetics.util.Utils
-
Return number of lines in given file that doesn't begin with Hash (#) and isn't blank.
- getNumberOfChunks() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getNumberOfClusters() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- getNumberOfGroups() - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- getNumberOfLevels() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getNumberOfLevels() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getNumberOfLevels() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getNumberOfLevels() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getNumberOfLevels() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getNumberOfSites() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getNumberOfStates() - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- getNumberOfSublevels() - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- getNumberOfSublevels() - Method in interface net.maizegenetics.stats.linearmodels.Level
-
- getNumberOfTagsPerChunk() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getNumberOfTaxaWithTag(readIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getNumberOfTaxaWithTag(readIndex) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Get the number of taxa with a given tag It is count of the taxa with readCount>0
- getNumberTaxaCovered() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getNumColumns() - Method in class net.maizegenetics.util.ColumnMatrix
-
- getNumColumns() - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Return number of columns.
- getNumColumns() - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- getNumColumns() - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- getNumColumns() - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- getNumColumns() - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- getNumericCodingForAdditiveModel(marker, allele) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getNumericCodingForAdditiveModel(marker, allele) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getNumOfAlign(tagIndex, mapIndex) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Return number of alignment in an aligner
- getNumOfAlignAll(tagIndex) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Return number of alignment hypotheses across all aligners, excluding PEEnd1 and PEEnd2
- getNumOfRank0(tagIndex, mapIndex) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Return the number of Rank0 in an aligner
- getNumParameters() - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- getNumParameters() - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
get number of parameters
- getNumParameters() - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- getNumParameters() - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- getNumParameters() - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- getNumRows() - Method in class net.maizegenetics.util.ColumnMatrix
-
- getNumRows() - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Return number of rows.
- getNumRows() - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- getNumRows() - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- getNumRows() - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- getNumRows() - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- getNumWords() - Method in interface net.maizegenetics.util.BitSet
-
Expert: gets the number of longs in the array that are in use
- getNumWords() - Method in class net.maizegenetics.util.OpenBitSet
-
Expert: gets the number of longs in the array that are in use
- getNumWords() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- getOkButton() - Method in class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- getOpenDir(parent) - Static method in class net.maizegenetics.gui.FileBrowserUtils
-
- getOpenDir() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getOpenFile(parent) - Static method in class net.maizegenetics.gui.FileBrowserUtils
-
- getOpenFiles() - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- getOrdered(size) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getOrderedFactory() - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getOrthogonalizedData() - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- getOutformat() - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getOutput() - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- getOutputFileName() - Method in class net.maizegenetics.gui.ReportDestinationDialog
-
- getOutputName() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- getOutputName() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getOverlapIdentity() - Method in class net.maizegenetics.dna.read.PERead
-
Return identity of overlap of PE
- getOverlapLength() - Method in class net.maizegenetics.dna.read.PERead
-
Return length of overlap of PE
- getp() - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- getP(a, b, c, d) - Method in class net.maizegenetics.stats.statistics.FisherExact
-
calculates the P-value for this specific state
- getPackagesFromClassPath(classpath) - Static method in class net.maizegenetics.util.Utils
-
- getPairIndex(index) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return the index of the tag which is the other end of PE
- getPairwiseAlignment() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Return the last pairwise alignment computed (if any) or request subclasses to compute one and return the result by calling the computePairwiseAlignment method. The sequences must already be loaded and a scoring scheme must already be set.
- getPanel() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
GUI Panel for this plugin.
- getPanel() - Method in class net.maizegenetics.plugindef.AbstractPluginAction
-
GUI Panel for associated plugin.
- getPanel() - Method in interface net.maizegenetics.plugindef.Plugin
-
GUI Panel for this plugin.
- getPanel() - Method in interface net.maizegenetics.plugindef.PluginAction
-
GUI Panel for associated plugin.
- getParameter(key) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getParameter(key) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getParameter(key) - Method in interface net.maizegenetics.plugindef.Plugin
-
Returns parameter value for given parameter key.
- getParameter(key) - Method in interface net.maizegenetics.plugindef.Plugin
-
Returns parameter value for given parameter key.
- getParameter(n) - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- getParameter(n) - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
get model parameter
- getParameter(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- getParameter(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- getParameter(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- getParameterFields() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getParameters(source) - Static method in class net.maizegenetics.taxa.tree.Parameterized.Utils
-
- getParametersSE() - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- getParent() - Method in interface net.maizegenetics.taxa.tree.Node
-
Returns the parent node of this node.
- getParent() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Returns the parent node of this node.
- getParent1index() - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- getParent2index() - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- getParentalGenotype(genos, parentIndices, site) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- getParentFrame() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
Parent Frame for this plugin. Can be null.
- getParentFrame() - Method in interface net.maizegenetics.plugindef.Plugin
-
Parent Frame for this plugin. Can be null.
- getParentFromGffAttributes(attributes) - Static method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
Parse a GFF attribute field to identify the parent of the current GenomeFeature. Tricky b/c of the different ways it can be represented. There's a hierarchy of accepted answers, with 'parent_id', 'Parent=', 'transcript_id', and 'gene_id' taken in that order. If nothing is found, returns an empty string ("")
- getParentHaplotypes(previousParents, candidates, overlap, forward) - Static method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- getParentHaplotypesV1(previousParents, candidates, overlap, forward) - Static method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- getPathLengthInfo(root) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
Calculates max/min lengths of paths from root to leaf, taking into account branch lengths
- getPBest(tagIndex) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Return the most significant p-value across all hypotheses
- getPContig() - Method in class net.maizegenetics.dna.read.PERead
-
Return Pcontig read Return null when there is no Pcontig
- getPERead(index) - Method in class net.maizegenetics.dna.read.PEFastqChunk
-
Return PE read
- getPEReadNum() - Method in class net.maizegenetics.dna.read.PEFastqChunk
-
Return number of PE read
- getPermutationReport() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getPermutationReport() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- getPermutedData() - Method in class net.maizegenetics.stats.linearmodels.WithinPopulationPermuter
-
- getPersistPreferences() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getPev() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getPhaseForSite(site) - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- getPhenotypeFromB4RMergeDuplicates(dbURL, db, userName, password, studyName, taxaName, variableName) - Static method in class net.maizegenetics.analysis.b4r.B4RPhenotypeUtils
-
- GetPhenotypeFromB4RPlugin - Class in net.maizegenetics.analysis.b4r
-
- GetPhenotypeFromB4RPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
- getPhenotypeFromB4RWithDuplicates(dbURL, db, userName, password, studyName, taxaName, variableName) - Static method in class net.maizegenetics.analysis.b4r.B4RPhenotypeUtils
-
- getPhenotypeFromB4RWithRepNumber(dbURL, db, userName, password, studyName, taxaName, variableName, repNumber) - Static method in class net.maizegenetics.analysis.b4r.B4RPhenotypeUtils
-
- getPhredScale() - Method in class net.maizegenetics.dna.read.FastqChunk
-
Return phred score scale of the fastq, 33 or 64
- getPhredScale() - Method in class net.maizegenetics.dna.read.PEFastqChunk
-
Return phred score scale of the fastq, 33 or 64
- getPhysicalMapPositions() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Get all of the physical map positions associated with the ref tags.
- getPhysicalMapPositions(chromosome, firstPosition, lastPosition) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Get the unique list of positions for ref tags for a specific chromosome within a range.
- getPhysicalMapPositions() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getPhysicalMapPositions(chromosome, firstPosition, lastPosition) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getPhysicalPositions() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- getPhysPos(markerIndex) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getPlateName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
-
- getPLINKAlleleByte(value) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromPLINK
-
Returns haploid byte value for given PLINK value. Only right-most four bits used.
- getPlugin() - Method in class net.maizegenetics.plugindef.AbstractPluginAction
-
Return associated plugin.
- getPlugin() - Method in interface net.maizegenetics.plugindef.PluginAction
-
Return associated plugin.
- getPluginInstance(className, frame) - Static method in interface net.maizegenetics.plugindef.Plugin
-
- getPluginInstance(className, frame, isInteractive) - Static method in interface net.maizegenetics.plugindef.Plugin
-
Gets instance of Plugin
- getPluginListener() - Method in class net.maizegenetics.plugindef.ThreadedPluginListener
-
- getPosEndB(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getPosEndContig(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getPosEndF(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getPosFromLine(mline, isVCF, tabPos) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- getPosition(siteIndex) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getPosition() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getPosition() - Method in interface net.maizegenetics.dna.map.Position
-
Return the physical position of a site
- getPositionArray(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getPositionArray(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getPositionArray(index) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getPositionArray(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns chromosome, strand, and start position for given tag.
- getPositionFromCm(chromosome, cM) - Method in class net.maizegenetics.analysis.imputation.AGPMap
-
- getPositionList() - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getPositionList(bedfile) - Static method in class net.maizegenetics.dna.snp.io.ReadBedfile
-
Gets position list from specified bed file.
- GetPositionListPlugin - Class in net.maizegenetics.analysis.data
-
- GetPositionListPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.GetPositionListPlugin
-
- getPositions() - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getPositionsOfVariableSites() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getPossibleCharts() - Static method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- getPossibleGraphicOutFormats() - Static method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getPosStartB(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getPosStartContig(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getPosStartF(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getPred() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getPredictedValues() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getPrediction(index) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Return prediction value from model
- getPref(path, key, def) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getPreferredSize(c) - Method in class net.maizegenetics.gui.VerticalLabelUI
-
- getPreviousRegionStats() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- getPrincipalComponents() - Method in class net.maizegenetics.stats.PCA.PrinComp
-
calculated as data * eigenvectors
- getPrincipalCoordinate(index) - Method in class net.maizegenetics.stats.PCA.ClassicMds
-
- getProbObsGivenState(state, obs) - Method in class net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
-
- getProbObsGivenState(state, obs, site) - Method in class net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
-
- getProbObsGivenState(state, obs) - Method in class net.maizegenetics.analysis.imputation.EmissionProbability
-
- getProbObsGivenState(state, obs, node) - Method in class net.maizegenetics.analysis.imputation.EmissionProbability
-
- getProgressPanel() - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- getProtocolChecksum(filename, protocol) - Static method in class net.maizegenetics.util.CheckSum
-
Allows user to specify the protocol, e.g. MD5, SHA-1, SHA-256
- getPVal(r, c) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Returns P-value estimate for a given pair of numSites. If there were only 2 alleles at each locus, then the Fisher Exact P-value (one-tail) is returned. If more states then the permuted Monte Carlo test is used.
- getQRDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getQRDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- getQRDecomposition() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- getQRDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- getQual() - Method in class net.maizegenetics.dna.read.Read
-
Return quality string
- getQual(startIndex, endIndex) - Method in class net.maizegenetics.dna.read.Read
-
Return quality string from startIndex to endIndex
- getQuantAnnotation(annoName) - Method in interface net.maizegenetics.util.GeneralAnnotation
-
Returns all annotation value for a given annotation key
- getQuantAnnotation(annoName) - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getRandom() - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- getRandomNode(tree) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
Returns a uniformly distributed random node from the tree, including both internal and external nodes.
- getRandomParameterValue(parameter) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- getRangeBounds() - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getRanges(bedFile) - Static method in class net.maizegenetics.dna.snp.io.ReadBedfile
-
Function to parse the bedFile and create a List of BedFileRanges. The positions stored in BedFileRange are 1-based inclusive exclusive. This is done by adding 1 to both the start and end position from the BED file.
- getRangesAsPositionMap(bedfile) - Static method in class net.maizegenetics.dna.snp.io.ReadBedfile
-
Function that returns the 1-based Position ranges from a BED file as a RangeMap of Positions to the annotated name of the region. NOTE: getRanges(bedFile) will be called which will shift the start and end positions in the BED file up by 1. Because of this the ranges returned will be 1-based Closed-Open(Inclusive-Exclusive). This is NOT returning ranges in BED specification(0-based Inclusive-Exclusive).
- getRangesAsPositions(bedfile) - Static method in class net.maizegenetics.dna.snp.io.ReadBedfile
-
Function that returns the 1-based Position ranges from a BED file as a RangeSet of Positions. NOTE: getRanges(bedFile) will be called which will shift the start and end positions in the BED file up by 1. Because of this the ranges returned will be 1-based Closed-Open(Inclusive-Exclusive). This is NOT returning ranges in BED specification(0-based Inclusive-Exclusive).
- getRank() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- getRank() - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- getRank() - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition
-
- getRank() - Method in interface net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
-
- getRead() - Method in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
- getRead() - Method in class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
- getRead(index) - Method in class net.maizegenetics.dna.read.FastqChunk
-
Return Fastq read
- getRead(index) - Method in interface net.maizegenetics.dna.tag.Reads
-
Get the compressed read sequence in a long array for a given index
- getRead(i) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getReadB() - Method in class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Return backward sequence in Long array
- getReadCount(tagIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getReadCount(index) - Method in class net.maizegenetics.dna.tag.PETagCounts
-
Return read count of a PE tag
- getReadCount(index) - Method in interface net.maizegenetics.dna.tag.Reads
-
Gets the count of a particular read. If index does not exist it return -1
- getReadCount(index) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getReadCount(index) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getReadCountDistributionForTaxon(taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Returns the read count for a specified tag and taxon
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getReadCountForTagTaxon(tagIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- getReadCountForTaxa(readIndex, taxaIndex) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getReadCountsForTaxa(readIndex) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getReadF() - Method in class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Return forward sequence in Long array
- getReadIndex(read) - Method in interface net.maizegenetics.dna.tag.Reads
-
Gets the first index of a read (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.
- getReadIndex(read) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
Gets the first index of a read (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.
- getReadIndexForPositionIndex(posIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- getReadIndexForPositionIndex(posIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getReadIndexForPositionIndex(posIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getReadIndexForPositionIndex(posIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Consider removing this. -Terry
- getReadIndexSet(read) - Method in interface net.maizegenetics.dna.tag.Reads
-
Gets the set indices of matching reads (the only one if a unique list). If the read is not found then it returns a null array indicating its insertion point.
- getReadIndexSet(read) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getReadLength() - Method in class net.maizegenetics.dna.read.Read
-
Return read length
- getReadNum() - Method in class net.maizegenetics.dna.read.FastqChunk
-
Return number of Fastq read
- getReadTotal() - Method in interface net.maizegenetics.dna.tag.Reads
-
This is the number of different reads in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct reads if readUnique is true
- getReadTotal() - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getRealColumnCount() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getRealColumnIndex(col) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getRealEigenvalues() - Method in class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- getRealElementAt(index) - Method in class net.maizegenetics.gui.AbstractAvailableListModel
-
- getRealElementAt(index) - Method in class net.maizegenetics.gui.SiteNamesAvailableListModel
-
- getRealElementAt(index) - Method in class net.maizegenetics.gui.TaxaAvailableListModel
-
- getRealNames() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getRealSize() - Method in class net.maizegenetics.gui.AbstractAvailableListModel
-
- getRefAlignmentsForRefTags(refTags, minscore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of all alignments for specified ref tags having minimum specified score. minscore = 0 means get all tags. This returns refTag to refTag alignments from the reftag_reftag_Alignments table. It does not include refTag to non-refTag alignments.
- getRefAlignmentsForRefTags(refTags, minscore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getRefAlignmentsForTags(tags, minscore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of all reftag alignments for specified non-ref tags. All tags on the list must be non-ref tags as the tagID is pulled from the tagTagIDMap.
- getRefAlignmentsForTags(tags, minscore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getRefChromPosList(chrom) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- getReferenceMasksRendering(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getReferenceProbabilityRendering(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getRefGeno(site) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getRefTags() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Set of all reference tags
- getRefTags() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getRemoveButton() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- getRenderingType() - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getRenderingTypes() - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getRenderingTypes() - Method in class net.maizegenetics.gui.TOPMGenotypeTableCellRenderer
-
- getRes() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getResidualPhenotypesByChromosome() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getResiduals() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getResidualSS() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getResidualSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- getRestricted() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getRestricted(toRestrict, minimum, range) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getRestrictedFactory(toRestrict, minimum, range) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getReverseComplement(seq, len) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the reverse complement of a sequence already encoded in a 2-bit long.
- getReverseComplement(seq) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the reverse complement of a sequence already encoded in a 2-bit long. The entire long (32-bp) is reverse complemented.
- getReverseComplement(seq) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the reverse complement of a arrays of sequences already encoded in a 2-bit long.
- getReverseComplement(seq) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns a string based reverse complement. Get around issues with the poly-A tailing in the 2-bit encoding approach.
- getReverseComplementarySeq() - Method in class net.maizegenetics.dna.read.Read
-
Return reverse complementary sequence
- getReverseComplementarySeq(startIndex, endIndex) - Method in class net.maizegenetics.dna.read.Read
-
Return reverse complementary sequence
- getReverseQual() - Method in class net.maizegenetics.dna.read.Read
-
Return reverse quality string
- getRightTailedP(a, b, c, d) - Method in class net.maizegenetics.stats.statistics.FisherExact
-
Calculates the right-tail P-value for the Fisher Exact test.
- getRightTailedPQuick(a, b, c, d, maxP) - Method in class net.maizegenetics.stats.statistics.FisherExact
-
Calculates the right-tail P-value for the Fisher Exact test.
- getRobinsonFouldsDistance(t1, t2) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees
- getRobinsonFouldsDistance(s1, t2) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees
- getRobinsonFouldsRescaledDistance(t1, t2) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
- getRobinsonFouldsRescaledDistance(s1, t2) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
computes Robinson-Foulds (1981) distance between two trees rescaled to a number between 0 and 1
- getRoot() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Returns the root node of this tree.
- getRoot() - Method in interface net.maizegenetics.taxa.tree.Tree
-
- getRootFactor() - Method in class net.maizegenetics.analysis.gbs.neobio.FactorSequence
-
Returns the root factor, the one that starts the list of factors.
- getRow(row) - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
Returns specified row.
- getRow(row) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getRow(row) - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getRow(row) - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getRow(row) - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getRow(row) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getRow(row) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getRow(row) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getRow(rowLong) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
Returns specified row.
- getRow(rowLong) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
Returns specified row.
- getRow(row) - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getRow(row) - Method in class net.maizegenetics.util.HDF5TableReport
-
- getRow(row) - Method in class net.maizegenetics.util.SimpleTableReport
-
Returns specified row.
- getRow(row) - Method in interface net.maizegenetics.util.TableReport
-
Returns specified row.
- getRowCount() - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- getRowCount() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getRowCount() - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getRowCount() - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getRowCount() - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getRowCount() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getRowCount() - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- getRowCount() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getRowCount() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getRowCount() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getRowCount() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getRowCount() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getRowCount() - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getRowCount() - Method in class net.maizegenetics.util.HDF5TableReport
-
- getRowCount() - Method in class net.maizegenetics.util.SimpleTableReport
-
- getRowCount() - Method in interface net.maizegenetics.util.TableReport
-
Get the number of rows
- getRowHeaders() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getRowStart() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns the matrix row position where the paried alignement starts
- getRSqr(r, c) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Returns r^2 estimate for a given pair of numSites
- getS() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- getS() - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- getS() - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition
-
- getS() - Method in interface net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
-
for the decomposition of A, A = USV'
- getSampleSize(r, c) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Get number of gametes included in LD calculations (after missing data was excluded)
- getSaveDir(parent) - Static method in class net.maizegenetics.gui.FileBrowserUtils
-
- getSaveDir() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getSaveFile() - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getSaveFile(parent) - Static method in class net.maizegenetics.gui.FileBrowserUtils
-
- getSaveFileByChooser(fileExtensions) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getSaveFileByChooser(fileExtensions, parent) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- getSaveFiles() - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericRecordChromosome
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericRecordPosition
-
- getSchema() - Method in class net.maizegenetics.analysis.avro.GenericRecordTaxon
-
- getScore() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getScore() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns the score for this alignment.
- getScore() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Returns the score of the last alignment computed (if any) or request subclasses to compute one and return the result by calling the computeScore method. The sequences must already be loaded and a scoring scheme must already be set.
- getScore(tagIndex, mappingIndex) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return score of a mapping
- getScore(i, j) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- getScore(s1, s2, ignoreCase, ignoreWhite, ignorePunc, technique) - Static method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getScore(s1, s2, ignoreCase, ignoreWhite, ignorePunc, technique, delimiter) - Static method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getScoreTagLine() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns the score tag line.
- getSelectedButton() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- getSelectedButton() - Method in class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- getSelectedTasselDataSet() - Method in class net.maizegenetics.tassel.DataTreePanel
-
- getSelection(rows, columns) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getSelection(rows, columns) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- getSelection(rows, columns) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Creates a new matrix consisting or the rows and columns of this matrix in the order specified. If rows or columns is null then all rows or columns, respectively, will be included
- getSelection(rows, columns) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- getSelectionFromDoubleArray(original, nrows, ncols, rows, columns) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getSeq() - Method in class net.maizegenetics.dna.read.Read
-
Return read
- getSeq(startIndex, endIndex) - Method in class net.maizegenetics.dna.read.Read
-
Return read from startIndex to endIndex
- getSequence() - Method in interface net.maizegenetics.taxa.tree.Node
-
Returns the sequence at this node, in the form an array of bytes.
- getSequence() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Returns the sequence at this node, in the form of an array of bytes.
- getSequenceFromInt(val) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Return a string representation of the 2-bit encoded Integer (16bp).
- getSequenceFromLong(val, len) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Return a string representation of the 2-bit encoded long.
- getSequenceFromLong(val) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Return a string representation of an array of 2-bit encoded longs.
- getSequenceFromLong(val) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Return a string representation of the 2-bit encoded long.
- getSequenceFromLong(val, length) - Static method in class net.maizegenetics.dna.tag.AbstractTag
-
Return a string representation of an array of 2-bit encoded longs.
- getSequenceString() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Returns the sequence at this node, in the form of a String.
- getSerialNumber() - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
Returns this factor's serial number.
- getSeries1() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- getSeries2() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- getSeries3() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- getSeriesCount() - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getSeriesCount() - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getSeriesCount() - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getSeriesKey(series) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getSeriesKey(series) - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getSeriesKey(series) - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getSeriesName(series) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getSeriesName(series) - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getSeriesName(series) - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getSFString(numbers, sf, delimiter) - Method in class net.maizegenetics.util.FormattedOutput
-
- getSFString(number, sf) - Method in class net.maizegenetics.util.FormattedOutput
-
- getShuffled(size) - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getShuffledFactory() - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getSignificance(deltaL, df) - Static method in class net.maizegenetics.stats.statistics.LikelihoodRatioTest
-
compute significance level for the differences in log-likelihood (based on chi-square distribution)
- getSingularValueDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getSingularValueDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- getSingularValueDecomposition() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- getSingularValueDecomposition() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- getSingularValues() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- getSingularValues() - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- getSingularValues() - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition
-
- getSingularValues() - Method in interface net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
-
for the decomposition of A, A = USV'
- getSiteCompareType(alleles1, alleles2) - Static method in class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- getSiteCount() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Returns the counts of the numSites in the alignment
- getSiteCount() - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- getSiteIncremental(taxaList) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Build an alignment site by site in memory
- getSiteIncremental(taxaList, numberOfPositions, newHDF5File) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Build an GenotypeTable by site block (1<<16 sites). Number of positions (sites) must be known from the beginning. Positions and genotypes must be added by block
- getSiteIndex(chr, pos) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
Return index of nearest site of given position
- getSiteInstance(genotype) - Static method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- getSiteNamesToCovariates() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSiteNamesToFactors() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSiteNamesToKeep() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSiteNamesToRemove() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSiteNum() - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getSitesToCovariateButton() - Method in class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- getSitesToCovariatesIndex() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSitesToFactorsButton() - Method in class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- getSitesToFactorsIndex() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSitesToKeep() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- getSize() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- getSize() - Static method in enum net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
-
- getSize() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getSize() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getSize() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getSize() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns number of tags.
- getSize() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getSize() - Method in class net.maizegenetics.gui.AbstractAvailableListModel
-
- getSize() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
-
- getSize() - Method in class net.maizegenetics.gui.TableRowHeaderListModel
-
Returns the length of the list.
- getSize() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getSize() - Method in class net.maizegenetics.plugindef.DataSet
-
- getSize() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getSize() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getSize() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getSize() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getSize() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
Returns the number of taxa which is also the number of rows and columns that the distance matrix has.
- getSliderPosition() - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getSliderPositionAsSite() - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- getSNPCallsQuant(callBiallelicSNPsWithGap, includeReferenceTag) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getSNPCallsQuant(refSeq, callBiallelicSNPsWithGap) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getSNPCallsVCF(callBiallelicSNPsWithGap, includeReferenceTag) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getSnpCount() - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- getSNPID() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getSNPID() - Method in interface net.maizegenetics.dna.map.Position
-
Return the ID (name) for a site
- getSNPPositionQS(myMap) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
For a given map of chromosome/posiiton, Returns a map of chromsome (string) and Tuple (position,qualityScore)
- getSNPPositionQS(myMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getSNPPositionQS(myMap) - Method in interface net.maizegenetics.dna.tag.TagData
-
For a given map of chromosome/posiiton, Returns a map of chromsome (string) and Tuple (position,qualityScore)
- getSNPPositionQS(myMap) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getSNPPositions() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Create the unique list of SNPs (variants) based on all alleles.
- getSNPPositions(minSupportValue) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Create the unique list of SNPs (variants) based on all alleles. Only alleles with support values greater than the minSupportValue are considered.
- getSNPPositions(minQualityScore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Create the unique list of SNPs (variants) based on all alleles. Only positions with minimum quality score equal to or greater than the u are considered.
- getSNPPositions() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getSNPPositions(minSupportValue) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getSNPPositions(minQualityScore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getSNPPositions() - Method in interface net.maizegenetics.dna.tag.TagData
-
Create the unique list of SNPs (variants) based on all alleles.
- getSNPPositions(minSupportValue) - Method in interface net.maizegenetics.dna.tag.TagData
-
Create the unique list of SNPs (variants) based on all alleles. Only alleles with support values greater than the minSupportValue are considered.
- getSNPPositions(minQualityScore) - Method in interface net.maizegenetics.dna.tag.TagData
-
Create the unique list of SNPs (variants) based on all alleles. Only positions with minimum quality score equal to or greater than the u are considered.
- getSNPPositions() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getSNPPositions(minSupportValue) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getSNPPositions(minQualityScore) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getSNPPositionsForChromosomes(startChr, endChr) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Get SNPs for specified chromosomes
- getSNPPositionsForChromosomes(startChr, endChr) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getSNPPositionsForChromosomes(startChr, endChr) - Method in interface net.maizegenetics.dna.tag.TagData
-
Get SNPs for specified chromosomes
- getSNPPositionsForChromosomes(startChr, endChr) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getSplit(i) - Method in class net.maizegenetics.taxa.tree.SplitSystem
-
get split
- getSplit(idGroup, internalNode, split) - Static method in class net.maizegenetics.taxa.tree.SplitUtils
-
get split for branch associated with internal node
- getSplitCount() - Method in class net.maizegenetics.taxa.tree.SplitSystem
-
get number of splits
- getSplits(idGroup, tree) - Static method in class net.maizegenetics.taxa.tree.SplitUtils
-
creates a split system from a tree (using a pre-specified order of sequences)
- getSplits(tree) - Static method in class net.maizegenetics.taxa.tree.SplitUtils
-
creates a split system from a tree (using tree-induced order of sequences)
- getSplitVector() - Method in class net.maizegenetics.taxa.tree.SplitSystem
-
get split vector
- getStackTrace(exception, max) - Static method in class net.maizegenetics.util.ExceptionUtils
-
This sends an exception's stack trace to the specified logger. The max parameter defines the maximun number of entries to send to the logger. Setting max to a negative number sends all the entries in the stack track to the logger.
- getStart() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getStartPos() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getStartPos(tagIndex, mappingIndex) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return start position of a mapping
- getStartPosition(index) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getStartPosition() - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- getStartPosition(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getStartPosition(index) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns start position of given tag.
- getState() - Method in exception net.maizegenetics.util.db.DataAccessException
-
- getSteps() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- getStepSize() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getStrand(tagIndex) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getStrand() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getStrand(tagIndex, mappingIndex) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return strand of a mapping
- getStrand(value) - Static method in interface net.maizegenetics.dna.map.Position
-
- getStrand(value) - Static method in interface net.maizegenetics.dna.map.Position
-
- getStrand() - Method in interface net.maizegenetics.dna.map.Position
-
Return the strand for a site definition
- getStrand() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getStrand(tagIndex) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getStrand(tagIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns Strand for given tag.
- getStrandB(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getStrandContig(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getStrandF(index) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- getStrandFromLine(mline, isVCF, tabPos) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
- getStrandStr() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- getStrandStr() - Method in interface net.maizegenetics.dna.map.Position
-
- getString(key) - Method in class net.maizegenetics.util.ArgsEngine
-
Gets the value for a valued option.
- getStringGenotype(site) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getSublevel(sublevel) - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- getSublevel(sublevel) - Method in interface net.maizegenetics.stats.linearmodels.Level
-
- getSublevels() - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- getSublevels() - Method in interface net.maizegenetics.stats.linearmodels.Level
-
- getSubSample(sample) - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getSubSample(sample) - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getSubSample(sample) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getSubSample(sample) - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getSubSample(sample) - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getSubsetOfA(exclude) - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getSubtree(root, node) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- getSuggestedOrdering(defaultOrdering) - Method in interface net.maizegenetics.stats.math.OrthogonalHints
-
If there is a "best" ordering to use it can be specified here, if not should return null
- getSum() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getSumSquares() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getTableCellRendererComponent(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- getTableCellRendererComponent(table, value, isSelected, hasFocus, row, col) - Method in class net.maizegenetics.gui.TOPMGenotypeTableCellRenderer
-
- getTableColumnNames() - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- getTableColumnNames() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getTableColumnNames() - Method in class net.maizegenetics.analysis.popgen.PolymorphismDistribution
-
- getTableColumnNames() - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getTableColumnNames() - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getTableColumnNames() - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getTableColumnNames() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getTableColumnNames() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getTableColumnNames() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getTableColumnNames() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getTableColumnNames() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getTableColumnNames() - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getTableColumnNames() - Method in class net.maizegenetics.util.HDF5TableReport
-
- getTableColumnNames() - Method in class net.maizegenetics.util.SimpleTableReport
-
Return column names for the table
- getTableColumnNames() - Method in interface net.maizegenetics.util.TableReport
-
Get the names of the columns
- getTableData() - Method in class net.maizegenetics.analysis.popgen.PolymorphismDistribution
-
- getTableDisplayPlugin(filename, flag) - Method in class net.maizegenetics.pipeline.TasselPipeline
-
- getTableTitle() - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- getTableTitle() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getTableTitle() - Method in class net.maizegenetics.analysis.popgen.PolymorphismDistribution
-
- getTableTitle() - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getTableTitle() - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getTableTitle() - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getTableTitle() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getTableTitle() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getTableTitle() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getTableTitle() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getTableTitle() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getTableTitle() - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getTableTitle() - Method in class net.maizegenetics.util.HDF5TableReport
-
- getTableTitle() - Method in class net.maizegenetics.util.SimpleTableReport
-
Return the name for the title of the ANOVA
- getTableTitle() - Method in interface net.maizegenetics.util.TableReport
-
Get the title of the table
- getTag(index) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- getTag(index) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTag(index) - Method in interface net.maizegenetics.dna.tag.Tags
-
Get the compressed read sequence in a long array for a given index
- getTag(index) - Method in class net.maizegenetics.dna.tag.UTagPairs
-
- getTagAlignmentApproaches() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
- getTagAlignmentApproaches() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagAlignmentApproaches() - Method in interface net.maizegenetics.dna.tag.TagData
-
- getTagAlignmentApproaches() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagAlignmentsForRefTag(refTag, minscore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of all non-reftag alignments for specified ref tag.
- getTagAlignmentsForRefTag(refTag, minscore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagAlignmentsForTags(tags, minscore) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Method returns a map of all tag (non-ref) alignments for specified non-ref tags. All tags on the list must be non-ref tags as the tagID is pulled from the tagTagIDMap.
- getTagAlignmentsForTags(tags, minscore) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagB(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagB(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Get the compressed backward tag sequence in a long array for a given index
- getTagBLength(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagBLength(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Returns the length in bp of a backward tag
- getTagCount() - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- getTagCount() - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagCount() - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagCount() - Method in interface net.maizegenetics.dna.tag.PETags
-
This is the number of different PE tags in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct tags if readUnique is true
- getTagCount() - Method in class net.maizegenetics.dna.tag.TagCounts
-
I don't know why we have 4 or 5 methods with different names that do exactly the same thing. I'm just putting this here because it's defined in the abstract class and its absence is causing problems.
- getTagCount() - Method in interface net.maizegenetics.dna.tag.Tags
-
This is the number of different tags in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct tags if readUnique is true
- getTagCutPosition(tag) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Get the cut position associated with a list of tags. Return a map of Tag/CutPosition The Position object is returned to facilitate grabbing both physical position and strand information.
- getTagCutPosition(tagSet) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
Get the cut position associated with each tag in a set. Return a map of Tag/Position from which the cut position/strand will be pulled. This is used in debugging with the SNPCutPosTagVerificationPlugin
- getTagCutPosition(tag) - Method in interface net.maizegenetics.dna.tag.TagData
-
Get the cut position associated with a list of tags. Return a map of Tag/CutPosition The Position object is returned to facilitate grabbing both physical position and strand information.
- getTagCutPosition(tagSet) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
Get the cut position associated with each tag in a set. Return a map of Tag/Position from which the cut position/strand will be pulled. This is used in debugging with the SNPCutPosTagVerificationPlugin
- getTagCutPositions(onlyBest) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Get all of the genomic cut positions associated with all tags. Positions in the position list are annotated with cigarAlignment, isBest, alignmentApproach, and supportValue.
- getTagCutPositions(chromosome, firstPosition, lastPosition, onlyBest) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Get the unique list of position that tags to for a specific chromosome within a range.
- getTagCutPositions(chromosome, firstPosition, lastPosition, onlyBest) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagCutPositions(onlyBest) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagCutPositions(onlyBest) - Method in interface net.maizegenetics.dna.tag.TagData
-
Get all of the genomic cut positions associated with all tags. Positions in the position list are annotated with cigarAlignment, isBest, alignmentApproach, and supportValue.
- getTagCutPositions(chromosome, firstPosition, lastPosition, onlyBest) - Method in interface net.maizegenetics.dna.tag.TagData
-
Get the unique list of position that tags to for a specific chromosome within a range.
- getTagCutPositions(onlyBest) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagCutPositions(chromosome, firstPosition, lastPosition, onlyBest) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagDepth(taxon, position) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
- getTagDepth(taxon, position) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagDepth(taxon, position) - Method in interface net.maizegenetics.dna.tag.TagData
-
- getTagDepth(taxon, position) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagF(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagF(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Get the compressed forward tag sequence in a long array for a given index
- getTagFLength(index) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagFLength(index) - Method in interface net.maizegenetics.dna.tag.PETags
-
Returns the length in bp of a forward tag
- getTagGWASMapInfo(tagIndex) - Method in class net.maizegenetics.dna.map.TagGWASMap
-
- getTagIndex(read) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
This may return one of multiple identical 64 bp tags, which are essentially differnt in full-length PE tags
- getTagIndex(tagF, tagB) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagIndex(read) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagIndex(tagF, tagB) - Method in interface net.maizegenetics.dna.tag.PETags
-
Gets the index of a PE tag (including forward and backward) (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.
- getTagIndex(read) - Method in interface net.maizegenetics.dna.tag.Tags
-
Gets the first index of a read (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.
- getTagIndexFirst(readFirst) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagIndexSet(read) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return the range of identical 64 bp tags, [0,3] means {0,1,2} are identical. When the read doesn't exist, return null
- getTagIndexSet(read) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagIndexSet(read) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getTagIndexSet(read) - Method in interface net.maizegenetics.dna.tag.Tags
-
Gets the set indices of matching reads (the only one if a unique list). If the read is not found then it returns a null array indicating its insertion point.
- getTagIndexWithLongestSeq(read) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Return the index of 64 bp tag with alignment of longest PE tag, when there are multiple identical 64 bp tags. When the tag is not found, return -1
- getTagLength(index) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- getTagLength(index) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagLength() - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagLength(index) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getTagLength(index) - Method in interface net.maizegenetics.dna.tag.Tags
-
Returns the length in bp of a particular tag
- getTagLength(index) - Method in class net.maizegenetics.dna.tag.UTagPairs
-
- getTagLengthArray() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getTagLengthInLong() - Method in class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Return tag length in Long primitive data type
- getTagLookTable() - Method in class net.maizegenetics.analysis.gbs.TagMatchFinder
-
- getTagNum() - Method in class net.maizegenetics.dna.tag.UTagPairs
-
- getTagPair(tc, etr) - Method in class net.maizegenetics.analysis.gbs.UNetworkFilter
-
- getTagPath(tag) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getTags() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash
-
Returns a unmodifiable list of the tags (reference sequences)
- getTags() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Set of all tags
- getTags() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTags() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getTags() - Method in interface net.maizegenetics.dna.tag.TagData
-
Set of all tags
- getTags() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTags(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getTagsArray() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- GetTagSequenceFromDBPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
This plugin queries a GBSv2 sql database for existing tags. If the user specifies a tag, and the tag is found, a tab-delimited file is written containing that tag sequence. If the tag is NOT found, a tab-delimited file is written that shows the tag and "not found". If no tag sequence is specified, the method will print out all tag sequences stored in the specified db. If input db not found, plugin throws an exception. If output directory doesn't exist, plugin throws an exception
- GetTagSequenceFromDBPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- GetTagSequenceFromDBPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- GetTagSequenceFromDBPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- getTagsForAllele(position, allele) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Return all tags that call a particular SNP position allele. Empty list is returned if there are no tags.
- getTagsForAllele(allele) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Return all tags that call a particular SNP position allele. Empty list is returned if there are no tags.
- getTagsForAllele(position, allele) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagsForAllele(allele) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagsForAllele(position, allele) - Method in interface net.maizegenetics.dna.tag.TagData
-
Return all tags that call a particular SNP position allele. Empty list is returned if there are no tags.
- getTagsForAllele(allele) - Method in interface net.maizegenetics.dna.tag.TagData
-
Return all tags that call a particular SNP position allele. Empty list is returned if there are no tags.
- getTagsForAllele(position, allele) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagsForAllele(allele) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagsForSNPPosition(position) - Method in interface net.maizegenetics.dna.tag.TagData
-
Return all tags that cover a particular SNP position. Empty list is returned if there are no tags.
- getTagsForSNPPosition(position) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagsForTaxon(taxon) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Returns the list of tags present of a taxon. Note this could be a very compute intensive request.
- getTagsForTaxon(taxon) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagsForTaxon(taxon) - Method in interface net.maizegenetics.dna.tag.TagData
-
Returns the list of tags present of a taxon. Note this could be a very compute intensive request.
- getTagsForTaxon(taxon) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagSizeInLong() - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- getTagSizeInLong() - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
- getTagSizeInLong() - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- getTagSizeInLong() - Method in interface net.maizegenetics.dna.tag.PETags
-
Returns the number of long use to represent the sequence
- getTagSizeInLong() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getTagSizeInLong() - Method in interface net.maizegenetics.dna.tag.Tags
-
Returns the number of longs use to represent the sequence
- getTagsNameMap() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Map of all tags with associated names
- getTagsNameMap() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagsNameMap() - Method in interface net.maizegenetics.dna.tag.TagData
-
Map of all tags with associated names
- getTagsNameMap() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagsTaxaMap(cutPosition) - Method in interface net.maizegenetics.dna.tag.TagData
-
For a given genomic position returns of the map tags and their distribution.
- getTagsTaxaMap(cutPosition) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTagsWithDepth(minimumDepth) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
- getTagsWithDepth(minimumDepth) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTagsWithDepth(minimumDepth) - Method in interface net.maizegenetics.dna.tag.TagData
-
- getTagsWithDepth(minimumDepth) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- GetTagTaxaDistFromDBPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
This plugin takes a GBSv2 database as input, queries for the tags and their taxa distribution, and creates a tab-delimited file of tag and taxa-distribution. IT can be used for verifying data in the db. The user may supply a file with tab-delimited columns specifying on which tags to present data. The input "tag" file must have at least 1 column named "TAGS" (any case - Tags/TAGS/tags). Other data in the file will be ignored. Output: A tab-delimited file where the first column is the tag, and subsequent columns indicate taxa found in the db. The values in the "taxa" columns are the number of occurranes of that tag for that taxa.
- GetTagTaxaDistFromDBPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- GetTagTaxaDistFromDBPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- GetTagTaxaDistFromDBPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- getTasselClasses() - Static method in class net.maizegenetics.util.Utils
-
- getTaxaCount() - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- getTaxaCount() - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getTaxaCount() - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getTaxaCount() - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Returns the number of taxa (samples)
- getTaxaCount() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getTaxaCountForRead(readIndex) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getTaxaDistribution(tag) - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Returns the TaxaDistribution for a given taxa. If distribution data is not available, null is returned.
- getTaxaDistribution(tag) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTaxaDistribution(tag) - Method in interface net.maizegenetics.dna.tag.TagData
-
Returns the TaxaDistribution for a given taxa. If distribution data is not available, null is returned.
- getTaxaDistribution(tag) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTaxaGroupAlignments(a, parentIndex, snpIndices) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- getTaxaIncremental(positionList) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates an in memory builder for addition by taxon. Each taxon can only be added once, i.e. merging is not possible
- getTaxaIncremental(positionList, mergeRule) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates an in memory builder for addition by taxon, which permits the merging of taxa.
- getTaxaIncremental(genotypeTable, mergeRule) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates a builder initialized with the Genotypes in a existing GenotypeTable. The position list and initial taxa list is derived from the positions, taxa, and genotypes already in the GenotypeTable. The initial GenotypeTable is not changed as it is immutable.
- getTaxaIncremental(positionList, newHDF5File) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Create a new taxa incremental HDF5 GenotypeTableBuilder
- getTaxaIncrementalWithMerging(newHDF5File, positionList, mergeRule) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Creates a new taxa incremental HDF5 GenotypeTableBuilder to which replicate taxa can be added
- getTaxaIndex() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getTaxaInMarkerSSdf() - Method in class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
- getTaxaInstance(genotype) - Static method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- getTaxaList() - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getTaxaList() - Method in interface net.maizegenetics.dna.tag.RepGenData
-
Returns the taxa list associated with taxa distribution
- getTaxaList() - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- getTaxaList() - Method in interface net.maizegenetics.dna.tag.TagData
-
Returns the taxa list associated with taxa distribution
- getTaxaList() - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- getTaxaList() - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Return taxa list of this alignment.
- getTaxaList() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
Return TaxaList of this alignment.
- getTaxaList() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getTaxaList() - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- GetTaxaListPlugin - Class in net.maizegenetics.analysis.data
-
- GetTaxaListPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.GetTaxaListPlugin
-
- getTaxaName() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getTaxaName(taxaIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getTaxaName(taxaIndex) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getTaxaName(taxaIndex) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Returns the name of a taxon
- getTaxaName(taxaIndex) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getTaxaNames() - Method in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
Returns the taxaNames for the flowcell and lane
- getTaxaNames() - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getTaxaNames() - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- getTaxaNames() - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Returns an array of taxa names
- getTaxaNames() - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- getTaxaNum() - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getTaxaReadBitsForTag(tagIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getTaxaReadBitsForTag(tagIndex) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
The presence/absence of the taxa in a bitSet format (1=present, 0=absent)
- getTaxaReadCountsForTag(tagIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- getTaxaReadCountsForTag(tagIndex) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Returns all read counts for a specified tag index.
- getTaxon() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- getTaxon() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getTaxon(i) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getTaxon(reader, taxonName) - Static method in class net.maizegenetics.util.HDF5Utils
-
- getTaxonIndex() - Method in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
- getTaxonIndex(taxonName) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- getTaxonName() - Method in class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Return taxon name of the sequence
- getTaxonName() - Method in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
Return taxon name implied by the barcode sequence
- getTaxonName() - Method in class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
- getTaxonPath(taxon) - Static method in class net.maizegenetics.util.Tassel5HDF5Constants
-
- getTaxonSiteFromKey(keyStr) - Static method in class net.maizegenetics.analysis.avro.AvroConstants
-
- getTBTIndexOfTag(tagIndex) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getTechnique() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- getTestSite() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getTestSiteName() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getTextAnnotation(annoName) - Method in interface net.maizegenetics.util.GeneralAnnotation
-
Returns all annotation value for a given annotation key
- getTextAnnotation(annoName) - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- getTheBarcodes(index) - Method in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
- getTheFileType() - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- getThis() - Method in class net.maizegenetics.tassel.DataTreePanel
-
- getTissueDepths(tissueNum, taxaNum) - Method in class net.maizegenetics.taxa.TaxaTissueDist
-
- getTissueIndex() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- getTolerance() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.chart.QQDisplayPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.GetPositionListPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.GetTaxaListPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.HetsToUnknownPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.IdentityRecognitionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.IndelsToUnknownPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.KmerCountingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.LIXPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MemoryUsagePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.PassThroughPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SeparatePlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SubtractGenotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.data.UnionAlignmentPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterDataSetPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.FastqToTBTPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.KmerToTBTPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.QseqToTBTPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.ListPluginParameters
-
- getToolTipText() - Method in class net.maizegenetics.analysis.ListPlugins
-
- getToolTipText() - Method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
Tool Tip Text for this plugin
- getToolTipText(e) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- getToolTipText() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.analysis.tree.MergeTreesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- getToolTipText() - Method in class net.maizegenetics.analysis.workflow.WorkflowPlugin
-
- getToolTipText() - Method in interface net.maizegenetics.plugindef.Plugin
-
Tool Tip Text for this plugin
- getToolTipText() - Method in class net.maizegenetics.tassel.PreferencesDialog
-
- getToolTipText() - Method in class net.maizegenetics.tassel.ShowParameterCachePlugin
-
- getToolTipText() - Method in class net.maizegenetics.tassel.TasselLogging
-
- getToolTipText() - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- getTOPMIndexOfTag(tagIndex) - Method in class net.maizegenetics.dna.map.TagLocus
-
- getTopPrefix(block) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
This method is a shorthand to retrieve the top prefix of a block from the block table.
- getTotalCount() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- getTotalNReads() - Method in class net.maizegenetics.dna.map.TagLocus
-
- getTotalReadCount() - Method in class net.maizegenetics.dna.tag.PETagCounts
-
Return total read count of PE tags
- getTrait() - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getTransitionProbability(state1, state2) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- getTranslations() - Method in class net.maizegenetics.dna.snp.TranslateIndex
-
Returns all the translated indices.
- getTree() - Method in class net.maizegenetics.tassel.DataTreePanel
-
- getTwoClusters(gt, parentIndex) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- getTwoClusters(inputAlignment, minGametesPerTaxon) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- getTwoTailedP(a, b, c, d) - Method in class net.maizegenetics.stats.statistics.FisherExact
-
Calculates the two-tailed P-value for the Fisher Exact test. In order for a table under consideration to have its p-value included in the final result, it must have a p-value less than the original table's P-value, i.e. Fisher's exact test computes the probability, given the observed marginal frequencies, of obtaining exactly the frequencies observed and any configuration more extreme. By "more extreme," we mean any configuration (given observed marginals) with a smaller probability of occurrence in the same direction (one-tailed) or in both directions (two-tailed).
- getType() - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- getType() - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- getTypeChangeMap() - Method in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- getU(transpose) - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- getU(transpose) - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- getU(transpose) - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition
-
- getU(transpose) - Method in interface net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
-
for the decomposition of A, A = USV'
- getUColumns() - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- getUnanimousHaplotype() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
The unanimous haplotype of this cluster. Only monomorphic sites are reported. Others will be unknown.
- getUniqueMapOfTaxonByAnnotation(taxaList, annotation) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Create a Map of all the taxa associated with a particular annotation value. If there would be a duplicate mapping, then an Optional.empty() is returned.
- getUniqueMappingOfAligner(tagIndex, alignerName) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Return unique mapping (chr and startPosition) from an aligner, return null if it has multiple equally good position or doesn't align. This is used to block positions for genetic mapping
- getUniquePositions(chromosome) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getUniquePositions(chromosome) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- getUniquePositions(chromosome) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- getUniquePositions(chromosome) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns the set of unique positions for the given chromosome
- getUnits() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Return the units that this tree is expressed in.
- getUnits() - Method in interface net.maizegenetics.taxa.tree.Tree
-
Gets the units that this tree's branch lengths and node heights are expressed in.
- getUnits() - Method in interface net.maizegenetics.taxa.tree.UnitsProvider
-
- getUnknownInstance(genotype) - Static method in class net.maizegenetics.dna.snp.bit.DynamicBitStorage
-
- getUnphasedDiploidValue(a, b) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Combines two allele values into one diploid value. In alphabetical order
- getUnphasedDiploidValueNoHets(g1, g2) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Combines two genotype values into one diploid value. Returns unknown if either parent is heterozygous or unknown, or alleles are swapped.
- getUnphasedNucleotideGenotypeBuilder(numTaxa, numSites) - Static method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
Get Genotype Builder given number of taxa and sites. Performance optimized for site loop inside taxon loop. Default is unphased and NucleotideAlignmentConstants.NUCLEOTIDE_ALLELES encoding.
- getUnphasedSortedDiploidValue(genotype) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Ensures diploid value in alphabetical order
- getUnrootedBranchCount(center) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
returns number of branches centered around an internal node in an unrooted tree
- getUnselectedButton() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- getUnselectedButton() - Method in class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- getUpperCorner() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- getUpperLimit(n) - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- getUpperLimit(n) - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
get upper parameter limit
- getUpperLimit(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- getUpperLimit(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- getUpperLimit(n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- getUsage() - Method in class net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
-
- getUsage() - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- getUsage() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- getUsage() - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- getUsage() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- getUsage() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getUsage() - Method in interface net.maizegenetics.plugindef.Plugin
-
Gets the Usage Statement for this Plugin.
- getUsageHTML() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- getUTA() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getV(transpose) - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- getV(transpose) - Method in class net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition
-
- getV(transpose) - Method in class net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition
-
- getV(transpose) - Method in interface net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
-
for the decomposition of A, A = USV'
- getValue() - Method in enum net.maizegenetics.dna.map.TagMappingInfoV3.Aligner
-
- getValueAt(row, col) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getValueAt(rowLong, col) - Method in class net.maizegenetics.dna.map.PositionListTableReport
-
- getValueAt(rowLong, col) - Method in class net.maizegenetics.dna.map.TOPMTableReport
-
- getValueAt(row, col) - Method in class net.maizegenetics.dna.snp.FilterTableReport
-
- getValueAt(row, col) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- getValueAt(row, col) - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- getValueAt(row, col) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- getValueAt(row, col) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- getValueAt(row, col) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- getValueAt(rowIndex, columnIndex) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
- getValueAt(row, col) - Method in class net.maizegenetics.taxa.TaxaListTableReport
-
- getValueAt(row, col) - Method in class net.maizegenetics.util.AbstractTableReport
-
- getValueAt(row, col) - Method in class net.maizegenetics.util.HDF5TableReport
-
- getValueAt(row, col) - Method in class net.maizegenetics.util.SimpleTableReport
-
- getValueAt(row, col) - Method in interface net.maizegenetics.util.TableReport
-
Returns value at given row and column.
- getValueFromName(name) - Static method in enum net.maizegenetics.dna.map.TagMappingInfoV3.Aligner
-
- getVariableTagSizeInLong(index) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- getVariantDef() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getVariantDef(tagIndex, variantIndex) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getVariantDef(tagIndex, variantIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns variant definition at given tag and variant index.
- getVariantDef() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns variant definitions for all tags. First index of result is tag and second is variant.
- getVariantDefArray(tagIndex) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
Returns an array containing all variant definitions for the tag at the supplied index.
- getVariantDefArray(tagIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns an array containing all variant definitions for given tag.
- getVariantDefByReference() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
Provides the reference
- getVariantOff() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getVariantOff() - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns variant position offsets for all tags. First index of result is tag and second is variant.
- getVariantOffByReference() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getVariantPosOff(tagIndex, variantIndex) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- getVariantPosOff(tagIndex, variantIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns variant position offset from start position at given tag and variant index.
- getVariantPosOffArray(tagIndex) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
Returns an array containing all variant position offsets for the tag at the supplied index.
- getVariantPosOffArray(tagIndex) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Returns an array containing all variant position offsets for given tag.
- getVariants(inputLine) - Static method in class net.maizegenetics.dna.tag.SAMUtils
-
Parses an input line from a SAM file to determine all variants.
- getVarRan() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getVarRes() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- getWindows(ispoly, windowSize) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- getWinSize() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- getWinSize() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- getWords(prefix) - Method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
get the words in the trie with the given prefix
- getX(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getX(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getX(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getX() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getX(row) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getX() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getX() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getX() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getX() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getX() - Method in class net.maizegenetics.util.Tuple
-
- getXDim() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getXName() - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getXName() - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getXName() - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getXtX() - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getXtX() - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getXtX() - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getXtX() - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getXtX() - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getXtX2(cme) - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getXtX2(fme) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getXtX2(ncme) - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getXtXGM() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- getXtXGM() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- getXtXGM() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- getXtXGM() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- getXTXpart() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- getXty(y) - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getXty(y) - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getXty(y) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getXty(y) - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getXtY(X, Y) - Static method in class net.maizegenetics.stats.linearmodels.ModelEffectUtils
-
- getXty(y) - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getY(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- getY(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- getY(series, item) - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- getY(row) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
- getY() - Method in class net.maizegenetics.util.Tuple
-
- getYDim() - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- getyhat(beta) - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- getyhat() - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- getyhat(beta) - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getyhat(beta) - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getyhat(beta) - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- getZero() - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- getZeroFactory() - Static method in class net.maizegenetics.stats.math.OrderEnumerator.Utils
-
- gMatrix() - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
Kinship Matrix
- gMatrix(value) - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
Set Kinship Matrix. Kinship Matrix
- GOBII_DB - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- GOBII_DB_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- GOBII_IFLUtils - Class in net.maizegenetics.analysis.gobii
-
This class contains utility methods for pulling values out of hmp or vcf files needed when creating the intermediate files for loading into GOBII postgres and monetdb instances
- GOBII_TOP - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- GOBII_USER - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- GOBII_USER_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- GOBIIAvroGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
-
- GOBIIDbUtils - Class in net.maizegenetics.analysis.gobii
-
These methods were largely borrowed from Jeff's privatemaizegenetics GenomeAnnosDB.java, then modified as needed for GOBII postgres access. Currently, this file is ONLY connecting to postgres, not monetd. if plugins are created that need to connect to monetdb, a new connectToDB() method for monetdb must be created, or the existing one will need to be changed to indicate the database type for connection. For connecting to a monetdb instance, see example in privatemaizegenetics.lynn.MonetdbFileProcessing.MonetDBQtoPosList.connectToDBOrDie
- GOBIIGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
-
- GOBIIPlugin - Class in net.maizegenetics.analysis.gobii
-
- GOBIIPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- GOBIIPostgresConnection - Class in net.maizegenetics.analysis.gobii
-
- gPos - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Genetic mapping position of a tag, unknown = Integer.MIN_VALUE
- gPos - Variable in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
- Graph<T> - Interface in net.maizegenetics.util
-
Created by Eli Rodgers-Melnick on 7/2/2014 This interface is implemented by graphs, both directed and undirected. The design is inspired by the Python networkx library (https://networkx.github.io/)
- Graph.GraphType - Enum in net.maizegenetics.util
-
- GraphBuilder<T> - Class in net.maizegenetics.util
-
Builder for graphs, directed and undirected
- GraphBuilder(type) - Constructor for class net.maizegenetics.util.GraphBuilder
-
Generic constructor
- GraphUtils<T> - Class in net.maizegenetics.util
-
Functions used for Graph traversal and analysis
- groupMembers - Variable in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- guiName(guiName) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- guiName() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- GVCFGenomeSequence - Interface in net.maizegenetics.dna.map
-
Created by zrm22 on 3/27/17. Interface is used to store GenomeSequences defined by a GATK generated GVCF file
- GVCFGenomeSequenceBuilder - Class in net.maizegenetics.dna.map
-
Created by zrm22 on 3/27/17.
- GVCFLine(lineNum, line) - Constructor for class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- GWAS - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- GWAS_IFLPlugin - Class in net.maizegenetics.analysis.gobii
-
The tables populated from this plugin are described in TAS-1162 The plugin takes files of gwas data and adds them to the gwas_data in a GOBII instance. It is assume the gwas_method and gwas_experiment tables associated with this data have already been populated. These are all proprietary tables currently only in use by Buckler Lab. TO speed up procesing, the experimentId and methodIds are hard-coded in the juint that calls this plugin. Those tables are generally small, and if you have to go to it to get the name, you might as well just input the ID anda save GOBII IFL processing time. The values stored in the "values" column will be stored as "real" in the gwas_data table This is because there is 1 "value" field, which holds values for all data, of any type. The method table will provide specifics on how to interpret each statistic. In addition to the .gz files of gwas data, a mapping file of phenotype names to IDs is created - data pulled from b4R table.
- GWAS_IFLPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- GWAS_IFLPlugin() - Constructor for class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- GWASMappingPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- gwasPValue - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
P-value of genetic mapping of a tag
- IBS_DISTANCE_MATRIX_AVE_TOTAL_SITES - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- IBS_DISTANCE_MATRIX_NUM_ALLELES - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- IBS_DISTANCE_MATRIX_TRUE_IBS - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- IBS_DISTANCE_MATRIX_TYPE - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- IBSDistanceMatrix - Class in net.maizegenetics.analysis.distance
-
This class calculates an identity by state matrix. It is scaled so only non-missing comparison are used. It conducts bit level calculations of IBS for genotypes. Only the two most common alleles are used in the distance calculations.
- IBSDistanceMatrix2Alleles - Class in net.maizegenetics.analysis.distance
-
- IBSDistanceMatrix3Alleles - Class in net.maizegenetics.analysis.distance
-
- IBSDistanceMatrixOneByAll - Class in net.maizegenetics.analysis.distance
-
- IBSERROR_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- IBSERRORRATE_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- IBSMAJORCORR_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- IBSMINORCORR_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- IBSMINORERRORRATE_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- id() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- id(id) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- IdentifierSynonymizer - Class in net.maizegenetics.taxa
-
User: Ed Date: Mar 30, 2005 Time: 1:39:47 PM
- IdentifierSynonymizer(preferredTaxa, alternateTaxaSets) - Constructor for class net.maizegenetics.taxa.IdentifierSynonymizer
-
- IdentifierSynonymizer(preferredTaxa, alternateTaxaSets, technique) - Constructor for class net.maizegenetics.taxa.IdentifierSynonymizer
-
- IdentifierSynonymizer(preferredTaxa, alternateTaxaSets, technique, delimiter) - Constructor for class net.maizegenetics.taxa.IdentifierSynonymizer
-
- IdentifierSynonymizer(preferredTaxa, alternateTaxa) - Constructor for class net.maizegenetics.taxa.IdentifierSynonymizer
-
- identifySitesOfFlankingMarkers(site, chrVector, posVector, theGenotypesForCalculatingPCs, pg, chr) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- identity(n) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- IdentityRecognitionPlugin - Class in net.maizegenetics.analysis.data
-
- IdentityRecognitionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.IdentityRecognitionPlugin
-
- ifMap - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
If the tag is mapped by aligner
- ifPAV - Variable in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
- ifRef - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
If the tag is reference tag
- ifUnique - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
If the tag is unique to one position in genome
- ignoreDepth() - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
If genotypic depth information is present in the input file, ignore it (i.e., do not write depth information to the output files). Default: keep depth.
- ignoreDepth(value) - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
Set Ignore Depth. If genotypic depth information is present in the input file, ignore it (i.e., do not write depth information to the output files). Default: keep depth.
- importAnnotatedTaxaList(filename) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
- ImportAvro - Class in net.maizegenetics.analysis.avro
-
- importJSONToFilter(filename) - Static method in class net.maizegenetics.dna.snp.io.FilterJSONUtils
-
- importPositionListFromJSON(filename) - Static method in class net.maizegenetics.dna.snp.io.JSONUtils
-
- importTaxaListFromJSON(filename) - Static method in class net.maizegenetics.dna.snp.io.JSONUtils
-
Imports taxa list from JSON file.
- ImportUtils - Class in net.maizegenetics.dna.snp
-
Methods for importing GenotypeTables from various file formats.
- improveImputedProgenyStates() - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- ImputationAccuracyPlugin - Class in net.maizegenetics.analysis.imputation
-
This evaluates the accuracy of an imputed genotype. First input genotype should be the original. Second should be the masked genotype. Third should be the imputed genotype.
- ImputationAccuracyPlugin() - Constructor for class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- ImputationAccuracyPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- ImputationByMean - Class in net.maizegenetics.analysis.numericaltransform
-
Imputation of the missing data by mean of the respective column.
- ImputationPlugin - Class in net.maizegenetics.analysis.numericaltransform
-
- ImputationPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
Creates a new instance of the ImputationPlugin
- ImputationUtils - Class in net.maizegenetics.analysis.imputation
-
- impute(data) - Static method in class net.maizegenetics.analysis.numericaltransform.ImputationByMean
-
Impute the missing values.
- impute(data, k, isManhattan, isCosine) - Static method in class net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
-
Impute all the missing values.
- IMPUTE_DOM - Static variable in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- imputeAll() - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- imputeAllHetCalls() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Write all imputed heterozygous calls as such, even if the original file has a homozygous call. (Not recommended for inbred lines.)
- imputeAllHetCalls(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Impute all het calls. Write all imputed heterozygous calls as such, even if the original file has a homozygous call. (Not recommended for inbred lines.)
- imputeCrossFromParents(progeny, hap0, hap1) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- imputeCrossFromParentsUsingProbabilities(progeny, hapProb0, hapProb1, probObsGivenState) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- ImputeCrossProgeny - Class in net.maizegenetics.analysis.imputation
-
- imputed - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- imputedDominance() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Should the plugin impute a value for dominance if data is missing. If false, the dominance score in the design matrix will be 0 for missing genotypes.
- imputedDominance(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Impute Dominance Score. Should the plugin impute a value for dominance if data is missing. If false, the dominance score in the design matrix will be 0 for missing genotypes.
- imputedFile() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
The output file containing the imputed progeny genotypes in hapmap format.
- imputedFile(value) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
Set Imputed Genotypes Output File. The output file containing the imputed progeny genotypes in hapmap format.
- imputedHDF5GenotypeFile() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Target, unfinished HDF5 (*.h5) file containing imputed genotypes to be updated
- imputedHDF5GenotypeFile(value) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Set Imputed HDF5 Genotype File. Target, unfinished HDF5 (*.h5) file containing imputed genotypes to be updated
- imputeDonorFile() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Impute the donor file itself
- imputeDonorFile(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Impute donor file. Impute the donor file itself
- imputeLinkageMarkers(interval, hapmapFormat, origsnpFile, snpfilePattern, outfilePattern) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- imputeLinkageMarkersAcrossFamilies(interval, hapmapFormat, excludeTaxa) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- imputeLinkageMarkersFrom1106(interval) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- ImputeProgenyStatesPlugin - Class in net.maizegenetics.analysis.imputation
-
- ImputeProgenyStatesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
- imputeUsingViterbiFiveState(a, probHeterozygous, familyName) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- imputeUsingViterbiFiveState(a, probHeterozygous, familyName, useVariableRecombitionRates) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- inbredCoef - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- inbreedF(val) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Set inbreeding coefficient (default=Float.NaN)
- InbreedFKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for inbreeding coefficient of the taxon
- includeBranchLengths() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Whether to include branch lengths for Newick formatted files.
- includeBranchLengths(value) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Set Include Branch Lengths. Whether to include branch lengths for Newick formatted files.
- includeGaps() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Include sites where major or minor allele is a GAP
- includeGaps(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Include Gaps. Include sites where major or minor allele is a GAP
- includeGaps() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Include sites where major or minor allele is a GAP
- includeGaps(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Include Gaps. Include sites where major or minor allele is a GAP
- includeParents(include) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- includeRareAlleles() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Include the rare alleles at site (3 or 4th states)
- includeRareAlleles(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Include Rare Alleles. Include the rare alleles at site (3 or 4th states)
- includeSites() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Include Sites
- includeSites(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Include Sites.
- includeSites() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- includeTaxa() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Include Taxa
- includeTaxa(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Set Include Taxa.
- includeTaxa() - Method in class net.maizegenetics.dna.snp.FilterTaxa
-
- includeTaxaAnnotations() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Whether to include taxa annotations if format supports taxa annotations.
- includeTaxaAnnotations(value) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Set Include Taxa Annotations. Whether to include taxa annotations if format supports taxa annotations.
- IncompatibleScoringSchemeException - Exception in net.maizegenetics.analysis.gbs.neobio
-
Signals that an scoring scheme is not compatible with the sequences being aligned.
- IncompatibleScoringSchemeException() - Constructor for exception net.maizegenetics.analysis.gbs.neobio.IncompatibleScoringSchemeException
-
Constructs an IncompatibleScoringSchemeException with null as its error detail message.
- IncompatibleScoringSchemeException(message) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.IncompatibleScoringSchemeException
-
Constructs an IncompatibleScoringSchemeException with the specified detail message.
- IncompatibleScoringSchemeException(cause) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.IncompatibleScoringSchemeException
-
Constructs an IncompatibleScoringSchemeException with the specified cause (and a detail message that typically contains the class and detail message of cause).
- IncompatibleScoringSchemeException(message, cause) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.IncompatibleScoringSchemeException
-
Constructs an IncompatibleScoringSchemeException with the specified detail message and cause.
- incompleteGammaP(a, x) - Static method in class net.maizegenetics.stats.math.GammaFunction
-
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
- incompleteGammaP(a, x, lnGammaA) - Static method in class net.maizegenetics.stats.math.GammaFunction
-
Incomplete Gamma function P(a,x) = 1-Q(a,x) (a cleanroom implementation of Numerical Recipes gammp(a,x); in Mathematica this function is 1-GammaRegularized)
- incompleteGammaQ(a, x) - Static method in class net.maizegenetics.stats.math.GammaFunction
-
Incomplete Gamma function Q(a,x) (a cleanroom implementation of Numerical Recipes gammq(a,x); in Mathematica this function is called GammaRegularized)
- increment(taxaNum) - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Add the taxa to do the distribution, with an additional depth of 1
- increment(tissueNum, taxaNum) - Method in class net.maizegenetics.taxa.TaxaTissueDist
-
- incrementScore(val) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- inDegree(n) - Method in class net.maizegenetics.util.DirectedGraph
-
Gets the number of nodes with an edge coming into the query node
- indel(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set whether position is indel (default=false)
- INDEL_CHAR - Static variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
The character that indicates the row and column for insertion and deletion penalties in the matrix.
- indelInKnownVariant(knownVariants) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- indelMinusInKnownVariant(knownVariants) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- indelSize(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return size of indel at given site.
- indelSize(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- indelSize(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- indelSize(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return size of indel at given site.
- indelSize(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- indelSize(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- IndelsToUnknownPlugin - Class in net.maizegenetics.analysis.data
-
- IndelsToUnknownPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.IndelsToUnknownPlugin
-
- index - Variable in class net.maizegenetics.analysis.modelfitter.SNP
-
- index() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- index() - Method in enum net.maizegenetics.dna.WHICH_ALLELE
-
Sequential index that can be use for primitive arrays
- indexComparator() - Static method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- indexForAttrLabel(label) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- indexOf(o) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- indexOf(o) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- indexOf(o) - Method in class net.maizegenetics.dna.snp.FilterList
-
- indexOf(name) - Method in interface net.maizegenetics.taxa.TaxaList
-
Return a list of all matching taxa indices for a given name.
- indexOf(taxon) - Method in interface net.maizegenetics.taxa.TaxaList
-
Return a list of all matching taxa indices for a given name.
- indexOfAttribute(attribute) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- indexOfAttribute(attribute) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- indexOfAttribute(attribute) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- indexOfNthSetBit(n) - Method in interface net.maizegenetics.util.BitSet
-
Returns index of the nth set bit.
- indexOfNthSetBit(n) - Method in class net.maizegenetics.util.OpenBitSet
-
- indexOfNthSetBit(n) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- indicesOfSortByPosition - Variable in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- inDir() - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- inFile() - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
Name of file to split. It must have 1 and only 1 period in the name to separate dataset name from table name
- inFile(value) - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
Set Input FIle. Name of file to split. It must have 1 and only 1 period in the name to separate dataset name from table name
- inFile() - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- info - Variable in class net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition
-
- iniMatrix(tagLengthInLong, tagNum) - Method in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- iniMatrix(tagLengthInLong, tagNum) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Initialize the matrix of TOGM
- iniMatrix(tagLengthInLong, tagNum) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
Initialize the matrix of data structure extending AbstractPETags
- iniMatrix(tagLengthInLong, tagNum) - Method in class net.maizegenetics.dna.tag.PETagCounts
-
- init() - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- init(max_length, max_score) - Method in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
Initialised this OUT matrix interface. This method needs to be executed only once per alignment.
- init() - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition
-
- init() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- init(n) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- init(n, keepId) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Initialized node instance variables based on given Node. children are ignored.
- init(n, keepId, lm) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Initialized node instance variables based on given Node. children are ignored.
- init(dataSource) - Static method in class net.maizegenetics.util.db.LambdaTuplesContext
-
- init(schema, dataSource) - Static method in class net.maizegenetics.util.db.LambdaTuplesContext
-
- init() - Method in class net.maizegenetics.util.db.ResultSetIterator
-
- initialCutSiteRemnant - Static variable in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
- initialCutSiteRemnant() - Method in class net.maizegenetics.analysis.gbs.v2.GBSEnzyme
-
- initialGenotype - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- initialize() - Method in class net.maizegenetics.analysis.association.PhenotypeLM
-
- initialize() - Method in class net.maizegenetics.analysis.gbs.PolymorphismFinder
-
- initialize() - Method in class net.maizegenetics.analysis.gbs.UTagPairFinder
-
- initialize() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithm
-
- initialize() - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
-
- initializeBarcodeTrie(taxaList, masterTaxaList, myEnzyme) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Produces a trie for sorting the read
- initializeBarcodeTrie(taxaList, masterTaxaList, masterTissueList, myEnzyme) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
- initializeHDF5(tagGWASMapFileS) - Method in class net.maizegenetics.dna.map.TagGWASMap
-
- initializeHDF5(inputFileS) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Initialize a HDF5 file
- initializeMatrix(tagCount, tagLengthInLong) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Initialize tag matrix
- initializeReportBuilders() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- initializeReportBuilders() - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
Initializes builders for the site and allele reports. The report names and column headers for a specific analysis are created in this method.
- initialStateProbability(probs) - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- initialStateProbability(probs) - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- initiateAccuracy() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
-
- initMatrices(tagNum) - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- initMatrices(tagNum) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- initMatrices(taxaNum, tagNum) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Initializes the storage matrices for reading (unclear why in interface)
- initMatrices(taxaNum, tagNum) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- initMatrices(taxaNum, tagNum) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- initMatrices(taxaNum, tagNum) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- initMatrices(taxaNum, tagNum) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- initMatrices(taxaNum, tagNum) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- initMatrices(taxaNum, tagNum) - Method in class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- innerProduct(x, y) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- input() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Input file of matched tag pairs
- input(value) - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Set Input. Input file of matched tag pairs
- input_border - Variable in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
The input border of a block.
- inputDB() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Input Tags by Taxa File. Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
- inputDB() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
Input database file with tags and taxa distribution
- inputDB(value) - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
Set Input DB. Input database file with tags and taxa distribution
- inputDB() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Input Database file if using SQLite
- inputDB(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Set Input GBS Database. Input Database file if using SQLite
- inputDir(value) - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- inputDir() - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- inputDir() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Input directory containing fastq AND/OR qseq files.
- inputDir(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Set Input Directory. Input directory containing fastq AND/OR qseq files.
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
Input directory containing subdirectories with fastq AND/OR qseq files
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
Set Input Directory. Input directory containing subdirectories with fastq AND/OR qseq files
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
Input directory containing fastq AND/OR qseq files.
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
Set Input Directory. Input directory containing fastq AND/OR qseq files.
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Set Input Directory. Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Input directory containing fastq AND/OR qseq files.
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Set Input Directory. Input directory containing fastq AND/OR qseq files.
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Input directory containing .fastq files
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Set Input Directory. Input directory containing .fastq files
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Set Input Directory. Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.
- inputDirectory() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Input directory containing fastq AND/OR qseq files.
- inputDirectory(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Set Input Directory. Input directory containing fastq AND/OR qseq files.
- inputDirectory() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.
- inputDirectory(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
Set Input Directory. Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name.
- inputFile() - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
Input, unfinished HDF5 genotype (*.h5) file to be fininalized
- inputFile(value) - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
Set Input file. Input, unfinished HDF5 genotype (*.h5) file to be fininalized
- inputFile(filename) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- inputFile() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- inputFile() - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
Input file
- inputFile(value) - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
Set Input file. Input file
- inputFile() - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
Input File
- inputFile(value) - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
Set Input File. Input File
- inputFile() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- inputFile(value) - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- inputFile() - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- inputFile(value) - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- inputFile() - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
Input file of merged tag counts
- inputFile(value) - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
Set Input file. Input file of merged tag counts
- inputFile() - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
Tab-delimited Input File containing a header line and entries, or Directory containing Tab-delimited files of gwas data. If parameter is a directory, each file must contain a header line, and the files must end with .txt or .txt.gz
- inputFile(value) - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
Set Input File. Tab-delimited Input File containing a header line and entries, or Directory containing Tab-delimited files of gwas data. If parameter is a directory, each file must contain a header line, and the files must end with .txt or .txt.gz
- inputFile() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
hmp.txt file including, including the header line, which will be used to create marker related and dnarun related intermediary files for GOBII loading
- inputFile(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set inputFile. hmp.txt file including, including the header line, which will be used to create marker related and dnarun related intermediary files for GOBII loading
- inputFile() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
File or a Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!
- inputFile(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Input Directory. Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!
- inputFile() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
File or a Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!
- inputFile(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Input Directory. Directory containing Tab-delimited files with data to add to the database. Files must be named chr01.txt, chr02.txt etc!
- inputFile() - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
Input file or directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively
- inputFile(value) - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
Set Input Directory. Input file or directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively
- inputFileGlob - Static variable in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
- inputFileGlob - Static variable in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- inputGBSDatabase() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Input Database file if using SQLite
- inputGBSDatabase(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Set Input GBS Database. Input Database file if using SQLite
- inputGBSDatabase() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Input Database file if using SQLite
- inputGBSDatabase(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Set Input GBS Database. Input Database file if using SQLite
- inputHDF5GenotypeFile() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
Input HDF5 genotype (*.h5) file to be annotated with the reference allele
- inputHDF5GenotypeFile(value) - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
Set Input HDF5 Genotype File. Input HDF5 genotype (*.h5) file to be annotated with the reference allele
- inputHDF5GenotypeFile() - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
Input HDF5 genotype (*.h5) file to be split by chromosome. The output files will be named *_chr#.h5 (where # = chromosome number)
- inputHDF5GenotypeFile(value) - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
Set Input HDF5 Genotype File. Input HDF5 genotype (*.h5) file to be split by chromosome. The output files will be named *_chr#.h5 (where # = chromosome number)
- InputSource - Class in net.maizegenetics.util
-
convenience class to open input streams linked to files, stdin, and strings
- inputTagsByTaxaFile() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
- inputTagsByTaxaFile(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Input Tags by Taxa File. Input TagsByTaxa file (if hdf5 format, use .hdf or .h5 extension)
- inputTOPMFile() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
TagsOnPhysicalMap (TOPM) file containing genomic positions of tags
- inputTOPMFile(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Input TOPM File. TagsOnPhysicalMap (TOPM) file containing genomic positions of tags
- inputTOPMFile() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
Physical map file containing tags and corresponding variants (production TOPM)
- inputTOPMFile(value) - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
Set Input TOPM File. Physical map file containing tags and corresponding variants (production TOPM)
- inputVCFFile() - Method in class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
Input VCF file
- inputVCFFile(value) - Method in class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
Set Input VCF File. Input file
- INSERT_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- INSERT_ALLELE_STR - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- INSERT_DIPLOID_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- insertChild(c, pos) - Method in interface net.maizegenetics.taxa.tree.Node
-
add new child node (insertion at a specific position)
- insertChild(n, pos) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
add new child node (insertion at a specific position)
- insertionPosition(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set Insertion-position
- instance(name) - Static method in class net.maizegenetics.dna.map.Chromosome
-
Creates Chromosome instance with specified name. Returns single instance given same name multiple times.
- instance(name) - Static method in class net.maizegenetics.dna.map.Chromosome
-
Creates Chromosome instance with specified name. Returns single instance given same name multiple times.
- instance(name, length, features) - Static method in class net.maizegenetics.dna.map.Chromosome
-
- instance(fastaFileName) - Static method in class net.maizegenetics.dna.map.GenomeSequenceBuilder
-
Builds GenomeSequence from a fasta file.
- instance(fastaFileName, charConversion) - Static method in class net.maizegenetics.dna.map.GenomeSequenceBuilder
-
Builds GenomeSequence from a fasta file. The char conversion provide a mechanism to convert upper and lower case or convert one case to N. This is useful if a case if used to define a certain class of bases
- instance(chromosome, sequence) - Static method in class net.maizegenetics.dna.map.GenomeSequenceBuilder
-
Builds GenomeSequence from a String with one Chromosome.
- instance(fastaFileName, gvcfFileName) - Static method in class net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder
-
Builds GenomeSequence from a fasta file and a GVCF file.
- instance(fastaFileName, charConversion, gvcfFileName) - Static method in class net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder
-
Builds GenomeSequence from a fasta file. The char conversion provide a mechanism to convert upper and lower case or convert one case to N. This is useful if a case if used to define a certain class of bases
- instance(base, maskedBitSet, filteredBitSet) - Static method in class net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder
-
- instance(vcf) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
-
- instance(header, variants) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
-
- instance(header, variants) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
-
- instance(seq2Bit, length) - Static method in class net.maizegenetics.dna.tag.TagBuilder
-
- instance(seq2BitInBytes, length) - Static method in class net.maizegenetics.dna.tag.TagBuilder
-
- instance(sequence) - Static method in class net.maizegenetics.dna.tag.TagBuilder
-
- INSTANCE - Static variable in class net.maizegenetics.util.ChangeLog
-
This outputs the change logs messages in HTML for tassel-5-source since this last
"New Build Date" message. The results can be added to Tassel5ChangeHistory.html on
the website.
- INT_MISSING - Static variable in interface net.maizegenetics.dna.map.TOPMInterface
-
- intDeflation - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- intDeflation - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- intersect() - Method in class net.maizegenetics.phenotype.GenotypePhenotypeBuilder
-
Indicates that an intersect join should be performed. If necessary the GenotypeTable and Phenotype will be filtered before building the GenotypePhenotype. The filtered tables will have only the taxa common to both.
- intersect(other) - Method in interface net.maizegenetics.util.BitSet
-
this = this AND other
- intersect(other) - Method in class net.maizegenetics.util.OpenBitSet
-
this = this AND other
- intersect(other) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- IntersectionAlignmentPlugin - Class in net.maizegenetics.analysis.data
-
- IntersectionAlignmentPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
-
Creates a new instance of IntersectionAlignmentPlugin
- intersectionCount(a, b) - Static method in class net.maizegenetics.util.OpenBitSet
-
Returns the popcount or cardinality of the intersection of the two sets. Neither set is modified.
- intersectJoin() - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- intersects(other) - Method in interface net.maizegenetics.util.BitSet
-
Returns true if the sets have any elements in common
- intersects(other) - Method in class net.maizegenetics.util.OpenBitSet
-
returns true if the sets have any elements in common
- intersects(other) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- intValue(obs) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- InvalidScoringMatrixException - Exception in net.maizegenetics.analysis.gbs.neobio
-
Signals that the substitution matrix does not comply with the specification (see
class ScoringMatrix for details).
- InvalidScoringMatrixException() - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidScoringMatrixException
-
Constructs an InvalidScoringMatrixException with null as its error detail message.
- InvalidScoringMatrixException(message) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidScoringMatrixException
-
Constructs an InvalidScoringMatrixException with the specified detail message.
- InvalidScoringMatrixException(cause) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidScoringMatrixException
-
Constructs an InvalidScoringMatrixException with the specified cause (and a detail message that typically contains the class and detail message of cause).
- InvalidScoringMatrixException(message, cause) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidScoringMatrixException
-
Constructs an InvalidScoringMatrixException with the specified detail message and cause.
- InvalidSequenceException - Exception in net.maizegenetics.analysis.gbs.neobio
-
- InvalidSequenceException() - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidSequenceException
-
Constructs an InvalidSequenceException with null as its error detail message.
- InvalidSequenceException(message) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidSequenceException
-
Constructs an InvalidSequenceException with the specified detail message.
- InvalidSequenceException(cause) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidSequenceException
-
Constructs an InvalidSequenceException with the specified cause (and a detail message that typically contains the class and detail message of cause).
- InvalidSequenceException(message, cause) - Constructor for exception net.maizegenetics.analysis.gbs.neobio.InvalidSequenceException
-
Constructs an InvalidSequenceException with the specified detail message and cause.
- inverse() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- inverse() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- inverse() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
This returns the inverse or a square matrix, without modifying the original matrix.
- inverse() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- inverseErf(z) - Static method in class net.maizegenetics.stats.math.ErrorFunction
-
inverse error function
- invert() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- invert() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- invert() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
This returns the inverse or a square matrix, replacing the original with the inverse.
- invert() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- invH - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- invXHX - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- isACGT(diploidAllele) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Return whether a simple DNA state (i.e. no indels or N). Heterozygous resolves to true also.
- isAllPolymorphic() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- isAllPolymorphic() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- isAllPolymorphic() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns whether all sites are polymorphic.
- isAllPolymorphic() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns whether all sites are polymorphic.
- isAllPolymorphic() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- isAllPolymorphic() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isAncestor(possibleAncestor, node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
For two nodes in the tree true if the first node is the ancestor of the second
- isAnnotatedWithValue(annoName, annoValue) - Method in interface net.maizegenetics.util.GeneralAnnotation
-
Returns whether the entity contains the annotation with the specified value. If either the annotation or the value is missing false is return
- isAnnotatedWithValue(annoName, annoValue) - Method in class net.maizegenetics.util.GeneralAnnotationStorage
-
- isB73HaplotypeA(a) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- isBar() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- isBlockSchematic() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- isBoxWhisker() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- isCanceled() - Method in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- isCaseSensitive() - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Tells whether this scoring scheme ignores the case of characters when computing their score.
- isCellEditable(rowIndex, columnIndex) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
Always returns false.
- isCellEditable(rowIndex, columnIndex) - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
Always returns false.
- isChromosomalView() - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- isColumnInnerLoop() - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Returns true if the matrix stored for better performance when column loop inside row loop. False if matrix stored for better performance when row loop inside column loop.
- isColumnInnerLoop() - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- isColumnInnerLoop() - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- isColumnInnerLoop() - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- isColumnInnerLoop() - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- isDoSlidingHaps() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- isEmpty() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- isEmpty() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- isEmpty() - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- isEmpty() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- isEmpty() - Method in class net.maizegenetics.dna.snp.FilterList
-
- isEmpty() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- isEmpty() - Method in interface net.maizegenetics.util.BitSet
-
Returns true if there are no set bits
- isEmpty() - Method in class net.maizegenetics.util.OpenBitSet
-
Returns true if there are no set bits
- isEmpty() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- isEqual(alleles1, alleles2) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns whether two diploid allele values are equal ignoring order.
- isEqual(diploidAllele1, diploidAllele2) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns whether two diploid allele values are equal ignoring order.
- isEqualOrUnknown(alleles1, alleles2) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns whether two diploid allele values are equal ignoring order where unknown values equal anything.
- isEqualOrUnknown(diploidAllele1, diploidAllele2) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns whether two diploid allele values are equal ignoring order where unknown values equal anything.
- isErrBar() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- isExtractIndels() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- isFilterMinorSNPs() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- isFilterOutput() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- isFilterOutput() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- isFinal() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- isHDF5() - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
- isHDF5GenotypeLocked(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- isHDF5TagLocked(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- isHeader() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- isHeterozygous(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- isHeterozygous(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- isHeterozygous(taxon, site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns whether allele values at given taxon and site are heterozygous. If two values returned by genotype() are different, this will return false.
- isHeterozygous(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns whether allele values at given taxon and site are heterozygous. If two values returned by genotype() are different, this will return false.
- isHeterozygous(diploidAllele) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns whether diploid allele values are heterozygous. First 4 bits in byte is one allele value. Second 4 bits is other allele value.
- isHeterozygous(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- isHeterozygous(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isHeterozygous(obs, site) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- isHomozygous() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- isHomozygous(diploidAllele) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Returns whether diploid allele values are homozygous. Unknown values return false.
- isHomozygousACGT(diploidAllele) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Return whether a simple homozgyous DNA state (i.e. no indels or N).
- isInbred() - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- isInCurrentBlock(queryIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Return boolean value if an index belongs to current block
- isIndel() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- isIndel() - Method in interface net.maizegenetics.dna.map.Position
-
Whether the position includes indels, which would be defined in the variants
- isIndel(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Returns whether give site is an indel.
- isIndel(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- isIndel(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- isIndel(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns whether give site is an indel.
- isIndel(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- isIndel(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isInteractive() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
If interactive = true, the plugin will create dialogs and panels to interacts with the user
- isInteractive() - Method in interface net.maizegenetics.plugindef.Plugin
-
If interactive = true, the plugin will create dialogs and panels to interacts with the user
- isLeaf() - Method in interface net.maizegenetics.taxa.tree.Node
-
check whether this node is an external node
- isLeaf() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
check whether this node is an external node
- isMasked(taxon, site) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- isMasked(taxon, site) - Method in class net.maizegenetics.dna.snp.MaskGenotypeMatrix
-
- isMasked(taxon, site) - Method in class net.maizegenetics.dna.snp.MaskGenotypeStatsMatrix
-
- isMergePossible() - Method in class net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule
-
- isMergePossible() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule
-
Whether merge is even possible
- isMergePossible() - Method in class net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule
-
- isMergePossible() - Method in class net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule
-
- isMissing(obs) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- isMissing(obs, attrnum) - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- isMissing(obs, attrnum) - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- isMissing(obs) - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- isMissing(obs, attrnum) - Method in interface net.maizegenetics.phenotype.Phenotype
-
- isMissing(obs) - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- isMissing(obs) - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- isMonomorphic(probs) - Static method in class net.maizegenetics.analysis.association.AssociationUtils
-
- isNested(nested) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- isNested() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Should SNPs/markers be nested within a factor, such as family?
- isNested(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Is Nested. Should SNPs/markers be nested within a factor, such as family?
- isNucleotide() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- isNucleotide() - Method in interface net.maizegenetics.dna.map.Position
-
Whether the position is a nucleotide position or another marker type (SSR, AFLP, RAPD, CNV, which are recoded with text states)
- isNucleotideEncodings(alleleStates) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns whether given allele encodings are for Nucleotide Data.
- isOkayChecked() - Method in class net.maizegenetics.gui.ReportDestinationDialog
-
- isPartiallyEqual(genotype1, genotype2) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
Return true if either at least one allele agree
- isPartialMatchSupported() - Method in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
Tells whether this scoring scheme supports partial matches, which it does not.
- isPartialMatchSupported() - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Tells whether this scoring scheme supports partial matches, which it does, although a particular scoring matrix loaded by this instace might not. A partial match is a situation when two characters are not equal but, for any reason, are regarded as similar by this scoring scheme, which then returns a positive score value. This is common for amino acid scoring matrices.
- isPartialMatchSupported() - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Returns true if this scoring scheme supports partial matches, false otherwise. A partial match is a situation when two characters are not equal but, for any reason, are regarded as similar by this scoring scheme, which then returns a positive score. This is common when for scoring schemes that implement amino acid scoring matrices.
- isPAV(index) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Return if this tag is a PAV
- isPermutationNumber() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- isPhased() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- isPhased() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- isPhased() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns whether this alignment is phased.
- isPhased(isPhased) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- isPhased() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns whether this genotype table is phased.
- isPhased() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- isPhased() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isPhysicalPosition() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- isPlugin(className) - Static method in interface net.maizegenetics.plugindef.Plugin
-
Returns whether given class name is Plugin.
- isPluginParameter(key) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- isPolymorphic(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- isPolymorphic(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- isPolymorphic(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return whether given site is polymorphic.
- isPolymorphic(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return whether given site is polymorphic.
- isPolymorphic(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- isPolymorphic(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isPositiveStrand(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return whether is positive strand at given site.
- isPositiveStrand(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- isPositiveStrand(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- isPositiveStrand(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return whether is positive strand at given site.
- isPositiveStrand(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- isPositiveStrand(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isPowerOfTwo(v) - Static method in class net.maizegenetics.util.BitUtil
-
returns true if v is a power of two or zero
- isPowerOfTwo(v) - Static method in class net.maizegenetics.util.BitUtil
-
returns true if v is a power of two or zero
- isPresent() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- isRapidAnalysis() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- isReference() - Method in class net.maizegenetics.dna.tag.AbstractTag
-
- isReference() - Method in interface net.maizegenetics.dna.tag.Tag
-
- isReferenceBlock() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
Returns whether this line specifies a range of positions that match the reference.
- isRegression() - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- isRoot() - Method in interface net.maizegenetics.taxa.tree.Node
-
check whether this node is a root node
- isRoot() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
check whether this node is a root node
- isSame(s1, s2) - Static method in class net.maizegenetics.taxa.tree.CladeSystem
-
checks whether two clades are identical (assuming they are of the same length and use the same leaf order)
- isSame(s1, s2) - Static method in class net.maizegenetics.taxa.tree.SplitUtils
-
checks whether two splits are identical (assuming they are of the same length and use the same leaf order)
- isSingular(column) - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- isSiteMaskedHint(site) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- isSiteMaskedHint(site) - Method in interface net.maizegenetics.dna.snp.MaskMatrix
-
Returns false if specified site is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this site is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.
- isSiteMaskedHint(site) - Method in class net.maizegenetics.dna.snp.MaskSiteMatrix
-
Returns false if specified site is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this site is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.
- isSiteMaskedHint(site) - Method in class net.maizegenetics.dna.snp.MaskTaxaMatrix
-
Returns false if specified site is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this site is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- isSiteOptimized() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
This returns true if this Genotype performs better when processing whole sites at a time. Return false if performance is better when processing whole taxa.
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- isSiteOptimized() - Method in interface net.maizegenetics.dna.snp.MaskMatrix
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.MaskSiteMatrix
-
- isSiteOptimized() - Method in class net.maizegenetics.dna.snp.MaskTaxaMatrix
-
- isSlidingWindowAnalysis() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
Whether this is sliding window analysis
- isSlidingWindowAnalysis(value) - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
Set Sliding Window Analysis. Whether this is sliding window analysis
- isSNP(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- isSymmetric() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
test whether this matrix is a symmetric distance matrix
- isTASSEL4HDF5Format(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- isTaxaLocked(reader) - Static method in class net.maizegenetics.util.HDF5Utils
-
- isTaxonMaskedHint(taxon) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- isTaxonMaskedHint(taxon) - Method in interface net.maizegenetics.dna.snp.MaskMatrix
-
Returns false if specified taxon is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this taxon is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.
- isTaxonMaskedHint(taxon) - Method in class net.maizegenetics.dna.snp.MaskSiteMatrix
-
Returns false if specified taxon is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this taxon is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.
- isTaxonMaskedHint(taxon) - Method in class net.maizegenetics.dna.snp.MaskTaxaMatrix
-
Returns false if specified taxon is definitely not masked. Otherwise returns true. A true returned doesn't necessarily mean this taxon is masked. This can be used to optimize performance of masked genotype table components. If false returned, checking for masking can be skipped.
- isTypeCompatible(type) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- isTypeCompatible(type) - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- isTypeCompatible(type) - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- isTypeCompatible(type) - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- isUniqueRef() - Method in class net.maizegenetics.dna.map.TagGWASMapInfo
-
- isUseAllSiteTypes() - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- isUseGenotype() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- isUseGenotype() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- isUseP3D() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- isUseP3D() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- isUseRefProb() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- isUseRefProb() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- isWriteOutputToFile() - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- isWriteOutputToFile() - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- iterator() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- iterator() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- iterator() - Method in class net.maizegenetics.dna.snp.FilterList
-
- iterator() - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- maf - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- MAF - Variable in class net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
-
- maf(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set Minor Allele Frequency annotation (default=Float.NaN)
- MAF - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- MAF - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- MAFClass - Static variable in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- MAGIC_NUMBER - Static variable in class net.maizegenetics.dna.snp.io.LineIndexBuilder
-
- magicNumber() - Method in class net.maizegenetics.dna.snp.io.LineIndex
-
- main(args) - Static method in class net.maizegenetics.analysis.avro.ExportAvro
-
- main(args) - Static method in class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.ProductionPipelineMain
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.TagMatchFinder
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.TerryPipelines
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.v2.BarcodeTrie
-
- main(args) - Static method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gobii.BMSConnection
-
- main(args) - Static method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.gobii.UpdateMarkerAndDNA_idxes
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- main(args) - Static method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- main(args) - Static method in class net.maizegenetics.analysis.numericaltransform.TransformDataDialog
-
- main(args) - Static method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- main(args) - Static method in class net.maizegenetics.dna.map.UpdateTOPMWithGeneticMapping
-
- main(args) - Static method in class net.maizegenetics.dna.pd.FolderParser
-
- main(args) - Static method in class net.maizegenetics.dna.pd.PDAnnotation
-
- main(args) - Static method in class net.maizegenetics.dna.pd.PDReport
-
- main(args) - Static method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- main(args) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- main(args) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- main(args) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- main(args) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
- main(args) - Static method in class net.maizegenetics.gui.ReportDestinationDialog
-
- main(args) - Static method in class net.maizegenetics.pipeline.TasselPipeline
-
- main(args) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- main(args) - Static method in class net.maizegenetics.tassel.TASSELMainApp
-
- main(args) - Static method in class net.maizegenetics.util.ChangeLog
-
- main(args) - Static method in class net.maizegenetics.util.Sizeof
-
- MAJOR_ALLELE - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- majorAllele(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- majorAllele(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- majorAllele(alleles) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- majorAllele(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- majorAllele(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- majorAllele() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- majorAllele(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- majorAllele(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- majorAllele(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- majorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- majorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- majorAlleleAsString(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- majorAlleleAsString(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return most common allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- majorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- majorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- majorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- majorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- majorAlleleCount(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns the major allele count for given site.
- majorAlleleCount(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns the major allele count for given site.
- majorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- majorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- majorAlleleForAllSites() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns major allele for all sites.
- majorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- majorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- majorAlleleFrequency(alleles) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- majorAlleleFrequency(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return frequency for major allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- majorAlleleFrequency(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- majorAlleleFrequency() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- majorAlleleFrequency(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return frequency for major allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- majorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- majorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- majorMinorCounts() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- majorMinorCounts() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- majorMinorCounts() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns counts of all major/minor allele combinations from highest frequency to lowest for whole alignment. Resulting double dimension array holds major/minor allele (Strings) in result[0]. And the counts are in result[1] (Longs).
- majorMinorCounts() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns counts of all major/minor allele combinations from highest frequency to lowest for whole genotype table. Resulting double dimension array holds major/minor allele (Strings) in result[0]. And the counts are in result[1] (Longs).
- majorMinorCounts() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- majorMinorCounts() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- make(row, col) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- make(row, col, values) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- make(row, col, values, columnMajor) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- make(values) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- make(values) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- make(row, col, val) - Method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- makeClusters() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
Groups a list of Haplotypes into clusters. Clusters are created so that all Haplotypes in a cluster have 0 pairwise distance. Because of missing data a Haplotype can be assigned to more than one cluster.
- makeHetsConsistent(seqIn) - Method in class net.maizegenetics.analysis.clustering.Haplotype
-
- makePositionHashes(alignments) - Static method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
Takes an array of GenotypeTables and returns a matching array of HashMaps linking each Position to its index
- makeTaxaHashes(alignments) - Static method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
Takes an array of GenotypeTables and returns a matching array of HashMaps linking each Taxon to its index
- makeTree(theTree, isInteractive, frame) - Static method in class net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
-
- ManhattanDisplayPlugin - Class in net.maizegenetics.analysis.chart
-
- ManhattanDisplayPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
-
Creates a new instance of ManhattanDisplayPlugin
- ManhattanNumberFormat - Class in net.maizegenetics.analysis.chart
-
- ManhattanNumberFormat(base, actualPosition) - Constructor for class net.maizegenetics.analysis.chart.ManhattanNumberFormat
-
- MAPBASE - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- mapFile() - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Map File
- mapFile(value) - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Set Map File. Map File
- mapFilename() - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
Map File
- mapFilename(value) - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
Set Map File. Map File
- mapP - Variable in class net.maizegenetics.dna.map.TagMappingInfo
-
Genetic mapping probability Round(Log2(P)), unknown Byte.MIN_VALUE
- mapP - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Genetic mapping probability Round(Log2(P)), unknown= Byte.MIN_VALUE
- mappedTags() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- mappingApproach(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Set Mapper (one of 'Bowtie2', 'BWA', or 'bwaMem').
- mappingApproach() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Get Mapper (one of 'Bowtie2', 'BWA', or 'bwaMem').
- mappingDistribution() - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
Returns an array whose indices are the number of mappings and whose elements are the number of tags with that mapping.
- mappingFile() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
tab-delimited File containing columns for taxaname, name, MGID, libraryID, project_id, experiment_name, platform_name, reference_name and dataset_name
- mappingFile(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set mappingFile. tab-delimited File containing columns for taxaname, name, MGID, libraryID, project_id, experiment_name, platform_name, reference_name and dataset_name
- mappingFile() - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
tab-delimited File containing columns: taxaColumn, name, MGID, GID,libraryID, plate_code, well, species, type, project_id, experiment_name, platform_name, reference_name and dataset_name
- mappingFile(value) - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
Set mappingFile. tab-delimited File containing columns: taxaColumn, name, MGID, GID,libraryID, plate_code, well, species, type, project_id, experiment_name, platform_name, reference_name and dataset_name
- mappingNum - Variable in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Number of physical positions from different aligner or aligner with different parameters
- mappingRank - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
The rank of this mapping based on the scores from one aligner, starting from 0. If there are two 0, the rank of the third one is 1
- mappingResultToTagGWASMapPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- mappingScore - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
The mapping score of this mapping, unknown = Byte.MIN_VALUE
- mappingSource - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Code of mappingSource.0: Bowtie2; 1: BWA; 2: BLAST; 3: BWAMEM; 4: PE one end; 5: PE the other end; 6: Genetic Mapping; missing = Byte.MIN_VALUE
- mapset() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Name of the mapset to which these breakpoints refer. Must match an existing name in the mapset table, e.g AGPV3
- mapset(value) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Set mapset. Name of the mapset to which these breakpoints refer. Must match an existing name in the mapset table, e.g AGPV3
- mapsetName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Integer identifying the mapset_id from the linkage group table to use when mapping to marker_linkage_group.
- mapsetName(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set mapsetId
- Marker(pos, values, df) - Constructor for class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
-
- Marker(pos, additive, dominant, df) - Constructor for class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
-
- MarkerDNARun_IFLFilePlugin - Class in net.maizegenetics.analysis.gobii
-
BEWARE: Whenever you "pull" to update the GOBII projects, there could be changes that effect these plugins. Need to check if the .nmap or .dupmap files have changed, and make corresponding changes here as required. This class takes a hmp.txt file(s) or vcf file(s) with a mapping file and creates the intermediate files for the marker, marker_linkage_group, dataset_marker, dnarun, and dataset_dnarun tables. The inputFile variable can be a file or a directory. If it is a directory, the code will look for all files with format *(hmp.txt,hmp.txt.gz,vcf,vcf.gz) and process them. It is assumed all files use the same taxa. Because we assume it is all the same taxa, the dnarun and dataset_dnarun files are created from the first *.hmp.txt file processed. These are the intermediate files that map this dnarun to a dataset, and contain one entry for each taxa which contains the taxa name (in the name field), libraryPrepID (as the code field), and ids into experiment and dnasample tables. The "mapping file" needs to contain columnns for the following data: taxaname: as appears in the vcf/hmp file name: taxa name it maps to (do I need this?) MGID: MGID for this taxa name GID: GID for this dnarun libraryID: same as in dnasample file project_name: db will be queried to get project_id from project name. Needed by IFL get get dnasample_id experiment_name: name of experiment needed for dnarun table (IFL maps to id) platform_name: name of platform needed for marker table, (IFL maps to ID) reference_name: name of reference table (IFL maps to ID) dataset_name: needed for dataset_dnarun and dataset_marker tables (IFL Maps to ID) samplename: will be used for table dnasample.name field The mapping file needs an entry for all taxa that may appear in the data input file. It is ok if multiple taxa names appear with the same MGID/GID/etc. These are synonyms. We mostly aren't storing the names, just the MGID. It must be identified in the mapping file. THe dataset id must be gotten from the database. Check the dataset from the mapping file, query the database to get the dataset_id. GOBII creates the data_table and data_file names from the GUI when it creates the ID. It always names them DS_.h5 and DS_ for the table. We must do this by hand as we want to maintain consistency. The marker_linkage_group: Their mapping now requires both marker_name and platform_id. So Platform_name must also be a parameter. The software will query the db to get the platform_id from platform name. Both the marker and the marker_linkage_group intermediate files need the platform_name. This could be moved to the mapping file, but currently is an input parameter. VCF file headers have these fields: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT taxa1 taxa2 ... HMP.txt file headers have these fields: rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode taxa1 ... Class Gobii_IFLUtils is used to find chrom,pos, alt and strand values based on file type of hmp or vcf. THe type of file is determined by the file suffix (hmp.txt, hmp.txt.gz, vcf or vcf.gz) July 6, 2016: In addition, this method will create a file to be used with PostProcessMarkerPlugin(). This file will contain the marker name, platformid and alts array. It may be used at a future date to find existing markers in the DB and update the alts array. See PostProcessMarkerPlugin() for details. Currently any allele in A/C/G/T that is not the reference will appear on the alt list. This is per Ed who says given a large enough population, each allele will appear as an alternate. August 3: BEcause we continue to change the data that makes up the sample name (was GID:plate:well, now is extraction_id) I have added a column called "SampleName" to the mapping file. The software will take whatever is stored here and use it as the dnasample name. Biologists can then change at will without a need to change the software Problems with GOBII loaders: The GOBII dnarun.nmap file now takes "num" instead of "platename" EIther one can be a problem for BL as they are not required fields, and we often don't have values for these columns. The IFL scripts preprocessor_ifile.py does not check for IS NULL. It merely checks if the input file and exsiting db column match. You can't compare blank to null in postgres. BEcause of this, I changed our copy of the dnarun.nmap file and removed "num" as a mapping criteria. I have left it in this code to alert me if I do a "pull" on GOBII and move over new scripts. Uploading DS_X.dnarun should reulst in no entries, which will hopefully remind me to chaneg the mapping script again.
- MarkerDNARun_IFLFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- MarkerDNARun_IFLFilePlugin() - Constructor for class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- MarkerDNARun_IFLFilePlugin.HmpTaxaData - Class in net.maizegenetics.analysis.gobii
-
- markerEffectCIReportBuilder - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- markerEffectReportBuilder - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- markerpvalueColumn - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- markerSSdf - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- mask() - Method in class net.maizegenetics.dna.snp.score.MaskAlleleDepth
-
- mask() - Method in class net.maizegenetics.dna.snp.score.MaskAlleleProbability
-
- MaskAlleleDepth - Class in net.maizegenetics.dna.snp.score
-
- MaskAlleleDepth(depth, mask) - Constructor for class net.maizegenetics.dna.snp.score.MaskAlleleDepth
-
- MaskAlleleProbability - Class in net.maizegenetics.dna.snp.score
-
- MaskAlleleProbability(probability, mask) - Constructor for class net.maizegenetics.dna.snp.score.MaskAlleleProbability
-
- MaskDosage - Class in net.maizegenetics.dna.snp.score
-
- MaskedGenotypes - Class in net.maizegenetics.dna.snp.genotypecall
-
- MaskedGenotypes(numTaxa, numSites) - Constructor for class net.maizegenetics.dna.snp.genotypecall.MaskedGenotypes
-
- maskForSite(site) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- maskForSite(site) - Method in interface net.maizegenetics.dna.snp.MaskMatrix
-
Mask for specified site
- maskForSite(site) - Method in class net.maizegenetics.dna.snp.MaskSiteMatrix
-
Mask for specified site
- maskForSite(site) - Method in class net.maizegenetics.dna.snp.MaskTaxaMatrix
-
Mask for specified site
- maskForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- maskForTaxon(taxon) - Method in interface net.maizegenetics.dna.snp.MaskMatrix
-
Mask for specified taxon
- maskForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.MaskSiteMatrix
-
Mask for specified taxon
- maskForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.MaskTaxaMatrix
-
Mask for specified taxon
- MaskGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
-
- MaskGenotypeCallTable(base, mask) - Constructor for class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- MaskGenotypeMatrix - Class in net.maizegenetics.dna.snp
-
- MaskGenotypePlugin - Class in net.maizegenetics.analysis.data
-
The purpose of this class is to mask (make UNKNOWN) a portion of the genotypes of the given GenotypeTable. The resulting GenotypeTable will be the same except some genotypes will have been changed to Unknown.
- MaskGenotypePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
- MaskGenotypeStatsMatrix - Class in net.maizegenetics.dna.snp
-
- maskKeyAlign - Static variable in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- MaskMatrix - Interface in net.maizegenetics.dna.snp
-
- MaskMatrixBuilder - Class in net.maizegenetics.dna.snp
-
- MaskReferenceProbability - Class in net.maizegenetics.dna.snp.score
-
- MaskSiteMatrix - Class in net.maizegenetics.dna.snp
-
- MaskTaxaMatrix - Class in net.maizegenetics.dna.snp
-
- match(seq) - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash
-
Return the first unique kmer match found starting at the 5' end of the sequence.
- Match(mapIndex, quality) - Constructor for class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- Match() - Constructor for class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- match_reward - Variable in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
The reward for a match (a substitution of equal characters).
- match_reward() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
- match_reward(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Match Reward Amount. Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
- match_reward() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
- match_reward(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Match Reward Amount. Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
- match_reward() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
- match_reward(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Match Reward Amount. Parameter sent to Smith Waterman aligner for use in calculating reward when base pairs match.
- MATCH_TAG - Static variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Tag character that signals a match in the score tag line of an alignment. Its use is conditioned by the use_match_tag flag.
- matchCount(site1, site2, a) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- matchingType() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Approach used for matching the reads to the contigs
- matchingType(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Set Matching approach. Approach used for matching the reads to the contigs
- matchTagsToTaxa(fastqFileS, keyFileS, enzyme, theMasterTags, outputDir, minCount, useTBTByte, useTBTShort) - Static method in class net.maizegenetics.analysis.gbs.FastqToTBTPlugin
-
Uses an existing Tags object to create one TagsByTaxa file for each fastq file in the input directory. Output TBT files written to the outputDir, using fastq file names with extension changed to .tbt.bin (or .tbt.txt)
- matchTagsToTaxa(fastqFileS, theMasterTags, outputDir, minCount, useTBTByte, useTBTShort) - Static method in class net.maizegenetics.analysis.gbs.KmerToTBTPlugin
-
Uses an existing Tags object to create one TagsByTaxa file for each fastq file in the input directory. Output TBT files written to the outputDir, using fastq file names with extension changed to .tbt.bin (or .tbt.txt)
- matchTagsToTaxa(qseqFileS, keyFileS, enzyme, theMasterTags, outputDir, minCount, useTBTByte) - Static method in class net.maizegenetics.analysis.gbs.QseqToTBTPlugin
-
Uses an existing Tags object to create one TagsByTaxa file for each qseq file in the input directory. Output TBT files written to the outputDir, using qseq file names with extension changed to .tbt.bin (or .tbt.txt)
- matchTagsToTaxa(fastqFileS, keyFileS, enzyme, theMasterTags, outputTBT, outputLog) - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Uses an existing Tags object to create one TagsByTaxa file for each fastq file in the input directory. Output TBT files written to the outputDir, using fastq file names with extension changed to .tbt.bin (or .tbt.txt)
- matchType(matchType) - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Builder
-
- Matrix - Interface in net.maizegenetics.analysis.gbs.neobio
-
This interface defines a minimal set of operations that a matrix must implement. This interface is used by the
class Smawk class to provide a general services regardless of how the matrix is actually stored.
- matrix - Variable in class net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
-
The dynamic programming matrix. Each position (i, j) represents the best score between the firsts i characters of seq1 and j characters of seq2.
- matrix - Variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Stores values for each operation (substitution, insertion or deletion) defined by this matrix.
- matrix - Variable in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
A pointer to the matrix that is being manipulated.
- matrix - Variable in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
The dynamic programming matrix. Each position (i, j) represents the best score between a suffic of the firsts i characters of seq1 and a suffix of the first j characters of seq2.
- matrix - Variable in class net.maizegenetics.analysis.gbs.SmithWaterman
-
The dynamic programming matrix. Each position (i, j) represents the best score between a suffic of the firsts i characters of seq1 and a suffix of the first j characters of seq2.
- MATRIX_ALGORITHM_VARIATION - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- MATRIX_MULTIPLIER - Static variable in class net.maizegenetics.analysis.distance.Kinship
-
Deprecated.
- MATRIX_TYPE - Static variable in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- max(v1, v2) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Helper method to compute the the greater of two values.
- max(v1, v2, v3) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Helper method to compute the the greater of three values.
- max(v1, v2, v3, v4) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Helper method to compute the the greater of four values.
- max(v1, v2) - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Helper method to compute the the greater of two values.
- max(v1, v2, v3) - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Helper method to compute the the greater of three values.
- max(v1, v2, v3, v4) - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Helper method to compute the the greater of four values.
- max_absolute_score - Variable in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
The maximum absolute score that this scoring scheme can return, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.
- max_absolute_score - Variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
The maximum absolute score that this matrix can return for any substitution, deletion or insertion.
- max_col - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
The column index of a block (in the block table) where the high scoring local alignment ends.
- max_col - Variable in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
Indicate the column of where an optimal local alignment can be found in the matrix.
- max_col - Variable in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Indicate the column of where an optimal local alignment can be found in the matrix.
- max_length - Variable in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
The length of the longest sequence (number of characters) being aligned. It needs to be set only once per alignment.
- MAX_NUM_ALLELES - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- max_path_type - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
The type of the high scoring local alignment found.
- max_row - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
The row index of a block (in the block table) where the high scoring local alignment ends.
- max_row - Variable in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
Indicate the row of where an optimal local alignment can be found in the matrix..
- max_row - Variable in class net.maizegenetics.analysis.gbs.SmithWaterman
-
Indicate the row of where an optimal local alignment can be found in the matrix..
- max_score - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
The score of the high scoring local alignment found.
- max_score - Variable in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
The maximum absolute score that the current scoring scheme can return. It needs to be set only once per alignment.
- max_source_index - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
If the high scoring local alignment ends in an E-path at a block B, this field contains the index of the entry in the input border of B that where the E-path starts.
- maxAbsoluteScore() - Method in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.
- maxAbsoluteScore() - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion.
- maxAbsoluteScore() - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion.
- maxAlleles() - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
Max Alleles
- maxAlleles(value) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
Set Max Alleles. Max Alleles
- MAXARC - Variable in interface net.maizegenetics.taxa.tree.BranchLimits
-
maximum branch length
- maxCombinedErrorToImputeTwoDonors() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
The maximum genetic divergence allowable to cluster taxa
- maxCombinedErrorToImputeTwoDonors(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Max combined error to impute two donors. The maximum genetic divergence allowable to cluster taxa
- maxCombinedErrorToImputeTwoDonors() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Maximum error rate for applying Viterbi with to haplotypes to entire site window
- maxCombinedErrorToImputeTwoDonors(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Max combined error to impute two donors. Maximum error rate for applying Viterbi with to haplotypes to entire site window
- maxCores() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Maximum number of cores to be used for processing
- maxCores(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Set Maximum number of cores for processing. Maximum number of cores to be used for processing
- maxCores() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Maximum number of cores to be used for processing
- maxCores(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Set Maximum number of cores for processing. Maximum number of cores to be used for processing
- maxDiff() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
use to decide if two haplotypes are equivalent
- maxDiff(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Max Diff. use to decide if two haplotypes are equivalent
- maxDifferenceScore - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
Haplotypes with a difference score less than or equal to maxDifferenceScore will be assigned to the same cluster. The difference between two non-equal homozygotes is 2, between a homozygote and heterozygote is 1.
- maxDistance() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Maximum physical distance between sites to search for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
- maxDistance(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Set Max distance between site to find LD. Maximum physical distance between sites to search for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
- maxDistance() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Maximum physical distance between sites to search for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
- maxDistance(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Set Max distance between site to find LD. Maximum physical distance between sites to search for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
- maxDistance() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
Maximum physical distance between sites to look for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
- maxDistance(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
Set Max distance between site to find LD. Maximum physical distance between sites to look for LD (-1 for no distance cutoff - unlinked chromosomes will be tested)
- maxDistanceFromNN() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Maximum distance from Nearest Neighbor
- maxDistanceFromNN(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Set Maximum distance from Nearest Neighbor. Maximum distance from Nearest Neighbor
- maxDistanceFromNN() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Maximum distance from Nearest Neighbor
- maxDistanceFromNN(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Set Maximum distance from Nearest Neighbor. Maximum distance from Nearest Neighbor
- maxDivergence() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
- maxDivergence(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Set Max Divergence. Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
- maxDivergence - Static variable in class net.maizegenetics.analysis.gbs.TagMatchFinder
-
- maxDivergence() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
- maxDivergence(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Set Max Divergence. Maximum divergence (edit distance) between new read and previously mapped read (Default: 0 = perfect matches only)
- maxDivergenceFromFounder() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Maximum genetic divergence from founder haplotype to cluster sequences
- maxDivergenceFromFounder(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Max divergence from founder. Maximum genetic divergence from founder haplotype to cluster sequences
- maxDonorHypotheses() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Maximum number of donor hypotheses to be explored
- maxDonorHypotheses(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Max donor hypotheses. Maximum number of donor hypotheses to be explored
- maxErrorToImputeOneDonor() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Maximum error rate for applying one haplotype to entire site window
- maxErrorToImputeOneDonor(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Max error to impute one donor. Maximum error rate for applying one haplotype to entire site window
- maxFrequencyMissingPerHaplotype() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Maximum frequency of missing data in the output haplotype
- maxFrequencyMissingPerHaplotype(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Max frequency missing per haplotype. Maximum frequency of missing data in the output haplotype
- maxGoodReads(value) - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- maxGoodReads() - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- maxGoodReads() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Max good reads per lane.
- maxGoodReads(value) - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Set Max Good Reads. Max good reads per lane.
- maxHaplotypesPerSegment() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Maximum number of haplotypes per segment
- maxHaplotypesPerSegment(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Max haplotypes per segment. Maximum number of haplotypes per segment
- maxHetDeviation - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
Filter out sites more than maxHetDeviation * (standard deviation) different from the mean percent heterozygosity.;
- maxHeterozygosityOfOutputHaplotypes() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Maximum heterozygosity of output haplotype. Heterozygosity results from clustering sequences that either have residual heterozygosity or clustering sequences that do not share all minor alleles.
- maxHeterozygosityOfOutputHaplotypes(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Max heterozygosity of output haplotypes. Maximum heterozygosity of output haplotype. Heterozygosity results from clustering sequences that either have residual heterozygosity or clustering sequences that do not share all minor alleles.
- maxHeterozygous() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Max Heterozygous Proportion
- maxHeterozygous(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Max Heterozygous Proportion. Max Heterozygous Proportion
- maxHeterozygous() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Max Heterozygous Proportion
- maxHeterozygous(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Set Max Heterozygous Proportion. Max Heterozygous Proportion
- maxHeterozygous() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- maxHeterozygous() - Method in class net.maizegenetics.dna.snp.FilterTaxa
-
- maxHeterozygousProportion() - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Max Heterozygous Proportion
- maxHeterozygousProportion(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Set Max Heterozygous Proportion. Max Heterozygous Proportion
- maximumKmerNumber(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Set maximum number of kmers
- maximumKmerNumber(value) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Set maximum number of kmers
- maximumMismatchInBarcodeAndOverhang - Variable in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
- maximumNumberOfPCs() - Method in class net.maizegenetics.stats.PCA.ClassicMds
-
- maxiter - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- maxMajorAllelesTaxa(a, numMaxTaxa, alleleNumber) - Static method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- maxMajorAllelesTaxa(a, numMaxTaxa, alleleNumber) - Static method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- MAXMAPPING - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- maxMissing() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
filter out sites with proportion missing > maxMissing
- maxMissing(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Max Missing. filter out sites with proportion missing > maxMissing
- maxNumAlleles() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- maxNumAlleles() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- maxNumAlleles() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return max number of alleles defined for any given site.
- maxNumAlleles() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return max number of alleles defined for any given site.
- maxNumAlleles() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- maxNumAlleles() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- maxNumberOfMarkers() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
The maximum number of markers that will be fit, if the enter limit is not reached first
- maxNumberOfMarkers(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
Set Maximum markers. The maximum number of markers that will be fit, if the enter limit is not reached first
- maxP - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- maxP(maxP) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- maxp() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
The maximum p-value that will be output by the analysis.
- maxp(value) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Set MaxPValue. The maximum p-value that will be output by the analysis.
- maxP(maxP) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- maxPercentNaN() - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
Maximum percent of NaN allowed
- maxPercentNaN(value) - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
Set Maximum Percent NaN. Maximum percent of NaN allowed
- maxPValue() - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
The maximum p-value that will be output by the analysis.
- maxPValue(value) - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
Set MaxPValue. The maximum p-value that will be output by the analysis.
- maxPvalue() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Only results with p <= maxPvalue will be reported. Default = 1.0.
- maxPvalue(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set max P value. Only results with p <= maxPvalue will be reported. Default = 1.0.
- maxSitesInModel - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- maxSitesInModel(maxSites) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- maxSize() - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
Maximum size of each file after splitting.
- maxSize(value) - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
Set Maximum file size. Maximum size of each file after splitting.
- maxTagsPerCutSite() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Maximum number of tags per cut site (for alignment)
- maxTagsPerCutSite(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set maxTagsPerCutSite. This is the maximum number of tags allowed per cute site when performaing an alignment. Too many tags and biojava 4 getMultipleSequenceAlignment grinds to a halt.
- maxTaxa() - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Number of taxa that depth is being recorded for. Maximum taxa index = (maxTaxa-1)
- maxTerms() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
The maximum number of SNPs/markers that will be fit. If the model selection criterion is met first, then the fitting process will stop at that point.
- maxTerms(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Max SNPs/markers. The maximum number of SNPs/markers that will be fit. If the model selection criterion is met first, then the fitting process will stop at that point.
- maxThreads() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
the maximum number of threads to be used by this plugin.
- maxThreads(value) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Set Max Threads. the maximum number of threads to be used by this plugin.
- maxVariants - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- MAXVARIANTS - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- maxWordCopies(maxWordCopies) - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Builder
-
- maxWordRepeats() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Maximum repetitiveness of the word
- maxWordRepeats(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Set Maximum repeats of word. Maximum repetitiveness of the word
- mbic(RSS, N, modelDf, numberOfSites) - Static method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- mean(col, data) - Static method in class net.maizegenetics.analysis.numericaltransform.ImputationByMean
-
- mean(n) - Static method in class net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
-
mean of the chi-square distribution
- mean(n) - Static method in class net.maizegenetics.stats.statistics.ChiSquareDistribution
-
mean of the chi-square distribution
- mean(lambda) - Static method in class net.maizegenetics.stats.statistics.ExponentialDistribution
-
mean of the exponential distribution
- mean(shape, scale) - Static method in class net.maizegenetics.stats.statistics.GammaDistribution
-
mean of the Gamma distribution
- mean(m, sd) - Static method in class net.maizegenetics.stats.statistics.NormalDistribution
-
mean
- mean(k, m) - Static method in class net.maizegenetics.stats.statistics.ParetoDistribution
-
mean of the Pareto distribution
- MEAN_CLADE_HEIGHT - Variable in interface net.maizegenetics.taxa.tree.AttributeNode
-
attribute name for the mean height of this clade in a group of trees.
- meanDistance() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
Returns the mean pairwise distance of this matrix
- meanStdDev(data) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- members - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- MemoryByte2D - Class in net.maizegenetics.dna.snp.byte2d
-
- memorySize() - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Estimated memory footprint of this taxa distribution. Can be used to estimate the size of the Map containing these distributions.
- MemoryUsagePlugin - Class in net.maizegenetics.analysis.data
-
- MemoryUsagePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.MemoryUsagePlugin
-
- mendelErrorComparison(mjT, mnT, mj1, mn1, mj2, mn2) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
Determines the number of sites in which the target (T) sequence cannot be explained by the genotypes of either donor (1 & 2). Only sites where the genotype for all taxa can be tested.
- mendelianErrors - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- merge() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
merge families and chromosomes
- merge(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Merge. merge families and chromosomes
- merge(filenames) - Static method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
Merges several TOPM files into one, removing duplicate rows. Variants from matching tags are combined in the output file. If there are more variants in the input files than can fit in the output, extra variants are discarded with no particular order.
- merge(ifPrintAlignment) - Method in class net.maizegenetics.dna.read.PEFastqChunk
-
Merge PE to Pcontig
- merge(ifPrintAlignment) - Method in class net.maizegenetics.dna.read.PERead
-
- merge(base, translate) - Static method in class net.maizegenetics.dna.snp.TranslateIndexBuilder
-
- merge(second) - Method in interface net.maizegenetics.util.db.DBTuple
-
- MergeAlignmentsSameSitesPlugin - Class in net.maizegenetics.analysis.data
-
- MergeAlignmentsSameSitesPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
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- MergeBreakpointFilesPlugin - Class in net.maizegenetics.analysis.imputation
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- MergeBreakpointFilesPlugin() - Constructor for class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
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- MergeBreakpointFilesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
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- mergeCalls(calls) - Static method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
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Take an array of Byte genotype calls and merge TODO: Make this smarter; currently just uses the last call (to be same as in TASSEL4)
- mergeCalls(geno1, geno2) - Method in class net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule
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- mergeCalls(geno1, geno2) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule
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Merges diploid genotypic calls into one
- mergeCalls(geno1, geno2) - Method in class net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule
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- mergeCalls(geno1, geno2) - Method in class net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule
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- mergeChunks(chunkFileNames, outputFileName, minCount) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
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- mergeClusters(maxdiff) - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
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Merges clusters whose maximum pairwise difference is less than maxdiff. Clusters are tested sequentially. That is, if two clusters are merged, they become the new head cluster against which remaining clusters are tested for merging.
- MergedGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
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- MergedGenotypeTable - Class in net.maizegenetics.dna.snp
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- MergedGenotypeTable(genoTables, taxaList, positionList) - Constructor for class net.maizegenetics.dna.snp.MergedGenotypeTable
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- MergeDuplicateSNPsPlugin - Class in net.maizegenetics.analysis.gbs
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This class is intended to be run directly after DiscoverySNPCallerPlugin, using the HapMap file from that step as input. It finds duplicate SNPs in the HapMap file, and merges them if they have the same pair of alleles (not necessarily in the same maj/min order) and if there mismatch rate is no greater than the threshold (-maxMisMat). If -callHets is on, then genotypic disagreements will be called heterozygotes (otherwise set to 'N' = default). By default, any remaining unmerged duplicate SNPs (but not indels) will be deleted. They can be kept by invoking the -kpUnmergDups option. If the germplasm is not fully inbred, and still contains residual heterozygosity (like the maize NAM or IBM populations do) then -callHets should be on and -maxMisMat should be set fairly high (0.1 to 0.2, depending on the amount of heterozygosity). Todo the VCF support has been commented out, but this should all be merged into the main pipeline.
- MergeDuplicateSNPsPlugin() - Constructor for class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
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- MergeDuplicateSNPsPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
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- mergeFiles(mergeFiles, idcol, datacol, colOrder, outfile) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
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- mergeGenotypeTables(alignments) - Static method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
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Merge an array of GenotypeTables into a single GenotypeTable
- MergeGenotypeTablesPlugin - Class in net.maizegenetics.analysis.data
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Merge alignments into a single alignment containing all taxa and positions. TODO: Add capacity for depth
- MergeGenotypeTablesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
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- MergeGenotypeTablesPluginV2 - Class in net.maizegenetics.analysis.data
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- MergeGenotypeTablesPluginV2(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
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- MergeGenotypeTablesPluginV2.CALL_MERGE - Enum in net.maizegenetics.analysis.data
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- MergeGenotypeTablesPluginV2.DEPTH_MERGE - Enum in net.maizegenetics.analysis.data
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- MergeGenotypeTablesPluginV2.MERGE_TYPES - Enum in net.maizegenetics.analysis.data
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- mergeHDF5GenoTables() - Method in class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
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- MergeHDF5GenotypesSameSitesPlugin - Class in net.maizegenetics.analysis.data
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- MergeHDF5GenotypesSameSitesPlugin() - Constructor for class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
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- MergeHDF5GenotypesSameSitesPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
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- mergeMajorHaplotypes(clusterMaker, minClusterSize) - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
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- mergeMappingResultPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
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- MergeMultipleTagCountPlugin - Class in net.maizegenetics.analysis.gbs
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- MergeMultipleTagCountPlugin() - Constructor for class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
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- MergeMultipleTagCountPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
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- mergeMultipleTagCountPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
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- MergeMultipleTOPMPlugin - Class in net.maizegenetics.analysis.gbs
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- MergeMultipleTOPMPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
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- mergeNonconsensusFiles(dir, match, outfileName) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
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- mergePETagCount() - Method in class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
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Merge each individual PETagCounts file into one master PETagCounts file
- MergePETagCountPlugin - Class in net.maizegenetics.analysis.gbs
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Merge PETagCounts file of each taxon into one master PETagCounts file (collapsed and sorted)
- MergePETagCountPlugin() - Constructor for class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
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- MergePETagCountPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
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- mergePosition(a, b) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
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- MergeRenameDeleteTaxaPlugin - Class in net.maizegenetics.analysis.data
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- MergeRenameDeleteTaxaPlugin() - Constructor for class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
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- MergeRenameDeleteTaxaPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
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- MergeTagsByTaxaFilesByRowPlugin - Class in net.maizegenetics.analysis.gbs
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Merges multiple TagsByTaxa files that are too large to fit in memory when combined. Currently, the output file stores only presence or absence of a tag in a taxon, so the merged count is the boolean OR of the individual counts. The program loops over files to determine their size, creates a RandomAccessFile object large enough to hold the merged data, then loops over each file again to fill the RandomAccessFile.
- MergeTagsByTaxaFilesByRowPlugin() - Constructor for class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
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- MergeTagsByTaxaFilesByRowPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
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- MergeTagsByTaxaFilesPlugin - Class in net.maizegenetics.analysis.gbs
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Merges multiple TagsByTaxa files that are too large to fit in memory when combined. Currently, the output file stores only presence or absence of a tag in a taxon, so the merged count is the boolean OR of the individual counts. The program loops over files to determine their size, creates a RandomAccessFile object large enough to hold the merged data, then loops over each file again to fill the RandomAccessFile.
- MergeTagsByTaxaFilesPlugin() - Constructor for class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
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- MergeTagsByTaxaFilesPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
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- mergeTaxa() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
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- mergeTaxa(value) - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
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- mergeTaxaByName(inputFileName, outputFileName, format, caseSensitive) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
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Merge taxa with identical names (merge their (binary) tag counts into a single column). The input must be a TagsByTaxaBit file in either binary or text format. The output is written in binary TagsByTaxaBit format. Other TagsByTaxa formats (Byte, Short, etc) are not currently supported.
- mergeTaxaIncremental(existingHDF5File, mergeRule) - Static method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
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Merges taxa to an existing HDF5 file. The position list is derived from the positions already in the existing HDF5 file.
- mergeTaxon(a, b) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
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- mergeTOGM(another) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
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- mergeToMutableHDF5(infiles, newMerge) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromGenotypeHDF5
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This merge multiple alignment together into one ByteNucleotideHDF5 File. This is designed for putting multiple chromosomes together into one whole genome file.
- mergeTrees(trees) - Static method in class net.maizegenetics.taxa.tree.NewickUtils
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This merges two or more trees into one tree.
Nodes are merged when the names are the same.
- MergeTreesPlugin - Class in net.maizegenetics.analysis.tree
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- MergeTreesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.tree.MergeTreesPlugin
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- MergeTreesPlugin() - Constructor for class net.maizegenetics.analysis.tree.MergeTreesPlugin
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- MergeTreesPluginKt - Class in net.maizegenetics.analysis.tree
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- mergeTwoClusters(c0, c1) - Static method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
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Merges two clusters, c0 and c1.
- mergeWithDepth(geno1depths, geno2depths) - Method in class net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule
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- mergeWithDepth(geno1depths, geno2depths) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule
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Merges sequencing depths of two taxa
- mergeWithDepth(geno1depths, geno2depths) - Method in class net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule
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- mergeWithDepth(geno1depths, geno2depths) - Method in class net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule
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- MersenneTwisterFast - Class in net.maizegenetics.stats.math
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MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.
- MersenneTwisterFast() - Constructor for class net.maizegenetics.stats.math.MersenneTwisterFast
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Constructor using the time of day as default seed.
- MersenneTwisterFast(seed) - Constructor for class net.maizegenetics.stats.math.MersenneTwisterFast
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Constructor using a given seed. Though you pass this seed in as a long, it's best to make sure it's actually an integer.
- metaphone2(s1, ignoreCase, ignoreWhite, ignorePunc) - Static method in class net.maizegenetics.taxa.IdentifierSynonymizer
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- method() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
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Scan method
- method(value) - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
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Set Scan method. Scan method
- method() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
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Method used to created the breakpoints, e.g. FILLIN, beagle, etc
- method(value) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
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Set Breakpoint Method. Method used to created the breakpoints, e.g. FILLIN, beagle, etc
- methodIds() - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
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Name of GWAS method as it appears in the name field of the gwas_method table
- methodIds(value) - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
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Set Method Name. Name of GWAS method as it appears in the name field of the gwas_method table
- MigrateHDF5FromT4T5 - Class in net.maizegenetics.analysis.data
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Provides a migration tool from TASSEL4 HDF5 to TASSEL5 HDF5
- MIN_HETS - Static variable in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
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- minAlignLength() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
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Minimum length of bps aligning to store the SAM entry
- minAlignLength(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
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Set SAM Min Align Length. Minimum length of bps aligning to store the SAM entry
- minAlignProportion() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
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Minimum proportion of sequence that must align to store the SAM entry
- minAlignProportion(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
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Set SAM Min Align Proportion. Minimum proportion of sequence that must align to store the SAM entry
- MINARC - Variable in interface net.maizegenetics.taxa.tree.BranchLimits
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minimum branch length
- minCallBestGenoRatio() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
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Minimum ratio between best and second best genotype to make a call
- minCallBestGenoRatio(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
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Set Minimum support ratio for best genotype. Minimum ratio between best and second best genotype to make a call
- minCallBestGenoRatio() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
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Minimum ratio between best and second best genotype to make a call
- minCallBestGenoRatio(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
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Set Minimum support ratio for best genotype. Minimum ratio between best and second best genotype to make a call
- minClassSize - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
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- minClassSize() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
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The minimum acceptable genotype class size. Genotypes in a class with a smaller size will be set to missing.
- minClassSize(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
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Set Minimum Class Size. The minimum acceptable genotype class size. Genotypes in a class with a smaller size will be set to missing.
- minClusterSize - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
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Only use clusters with minClusterSize taxa as parent haplotypes
- minCount() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
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- minCount(value) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
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- minCount() - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
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- minCount(value) - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
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- minCount() - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
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Minimum count of reads for a tag to be output
- minCount(value) - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
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Set Min Count. Minimum count of reads for a tag to be output
- minCoverage - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
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Filter out sites with coverage less than minCoverage.
- minCoverageForDonors() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
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Minimum coverage for donor genotype and LD calculation
- minCoverageForDonors(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
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Set Minimum coverage for donors and LD. Minimum coverage for donor genotype and LD calculation
- minCoverageForDonors() - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
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Minimum coverage for donor genotype and LD calculation
- minCoverageForDonors(value) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
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Set Minimum coverage for donors and LD. Minimum coverage for donor genotype and LD calculation
- minDepth() - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
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Minimum depth required before masking.
- minDepth(value) - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
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Set Min Depth. Minimum depth required before masking.
- minDepth() - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
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Min Depth
- minDepth(value) - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
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Set Min Depth. Min Depth
- minDist() - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
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Minimum distance in bp between adjacent sites
- minDist(value) - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
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Set Minimum distance. Minimum distance in bp between adjacent sites
- minHap() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
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haplotype must be observed at least this often
- minHap(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
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Set Min Hap. haplotype must be observed at least this often
- minHeterozygous() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
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Min Heterozygous Proportion
- minHeterozygous(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
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Set Min Heterozygous Proportion. Min Heterozygous Proportion
- minHeterozygous() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
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Min Heterozygous Proportion
- minHeterozygous(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
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Set Min Heterozygous Proportion. Min Heterozygous Proportion
- minHeterozygous() - Method in class net.maizegenetics.dna.snp.FilterSite
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- minHeterozygous() - Method in class net.maizegenetics.dna.snp.FilterTaxa
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- minHeterozygousProportion() - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
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Min Heterozygous Proportion
- minHeterozygousProportion(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
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Set Min Heterozygous Proportion. Min Heterozygous Proportion
- minHets() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
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The minimum number of individuals that are heterozygous at a site for the dominance term to be included. If the number of hets is less than minHets at a site, an additive only model will be fit for that site.
- minHets(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
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Set Minimum number of heterozygotes. The minimum number of individuals that are heterozygous at a site for the dominance term to be included. If the number of hets is less than minHets at a site, an additive only model will be fit for that site.
- minHitCount() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
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Minimum count of hits in a cluster for a reference tag to be created for this cluster
- minHitCount(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
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Set Min Count. Minimum count of hits in a cluster for a reference tag to be created fro this cluster
- minimumClassSize(minsize) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
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- minimumClassSize(minsize) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
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- minimumEigenvalue() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
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All principal components with an eigenvalue greater than or equal to this value will be returned.
- minimumEigenvalue(value) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
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Set minimum eigenvalue. All principal components with an eigenvalue greater than or equal to this value will be returned.
- minimumF() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
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Minimum F (inbreeding coefficient)
- minimumF(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
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Set Minimum F. Minimum F (inbreeding coefficient)
- minimumKmerLength() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
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Minimum Tag Length
- minimumKmerLength(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
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Set Minimum Tag Length. Minimum Tag Length
- minimumKmerLength() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
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Minimum Tag Length
- minimumKmerLength(value) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
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Set Minimum Tag Length. Minimum Tag Length
- minimumKmerLength() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
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Minimum Tag Length
- minimumKmerLength(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
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Set Minimum Tag Length. Minimum Tag Length
- minimumQualityScore() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
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Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
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Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
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Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
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Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore(value) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
Minimum quality score within the barcode and read length to be accepted
- minimumQualityScore(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
- minKmerCount() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Minimum tag count
- minKmerCount(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Set Min Tag Count. Minimum tag count
- minKmerCount() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Minimum tag count
- minKmerCount(value) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
Set Min Tag Count. Minimum tag count
- minKmerCount() - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
Minimum tag count
- minKmerCount(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
Set Min Tag Count. Minimum tag count
- minLocusCoverage() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Minimum locus coverage (proportion of Taxa with a genotype)
- minLocusCoverage(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Min Locus Coverage. Minimum locus coverage (proportion of Taxa with a genotype)
- minLocusCoverage() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Minimum locus coverage (proportion of Taxa with a genotype)
- minLocusCoverage(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Min Locus Coverage. Minimum locus coverage (proportion of Taxa with a genotype)
- minMaf - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
Filter out sites with minimum allele frequency less than minMaf.
- minMaf() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
filter out sites with less than minimumMinorAlleleFrequency
- minMaf(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Min Maf. filter out sites with less than minimumMinorAlleleFrequency
- minMAPQ() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Minimum value of MAPQ to store the SAM entry
- minMAPQ(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Set SAM minimum MAPQ value. Minimum value of MAPQ to store the SAM entry
- minMinorAlleleCount() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Minimum minor allele count
- minMinorAlleleCount(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Min Minor Allele Count. Minimum minor allele count
- minMinorAlleleFreq() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Minimum minor allele frequency
- minMinorAlleleFreq(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Min Minor Allele Freq. Minimum minor allele frequency
- minMinorAlleleFreq() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Minimum minor allele frequency
- minMinorAlleleFreq(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Min Minor Allele Freq. Minimum minor allele frequency
- minNotMissing() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Min Proportion of Sites Present
- minNotMissing(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Set Min Proportion of Sites Present. Min Proportion of Sites Present
- minNotMissing() - Method in class net.maizegenetics.dna.snp.FilterTaxa
-
- minNotMissingProportion - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
Only cluster haplotypes with a minimum number of non missing values.
- minNumOfMinorAllelesToCompare() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Minimum number of informative minor alleles in the search window (or 10X major)
- minNumOfMinorAllelesToCompare(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Min num of minor alleles to compare. Minimum number of informative minor alleles in the search window (or 10X major)
- MINOR_ALLELE - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- minorAllele(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- minorAllele(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- minorAllele(alleles) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- minorAllele(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAllele(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- minorAllele() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- minorAllele(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAllele(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- minorAllele(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- minorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- minorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- minorAlleleAsString(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAlleleAsString(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- minorAlleleAsString(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- minorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- minorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- minorAlleleCount(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns the minor allele count for given site.
- minorAlleleCount(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns the minor allele count for given site.
- minorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- minorAlleleCount(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- minorAlleleForAllSites() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns minor allele for all sites.
- minorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- minorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- minorAlleleFrequency(alleles) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- minorAlleleFrequency(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return frequency for most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAlleleFrequency(index) - Method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- minorAlleleFrequency() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- minorAlleleFrequency(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return frequency for most common minor allele at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- minorAlleleFrequency(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- minorAlleles(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- minorAlleles(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- minorAlleles(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return all minor alleles at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAlleles(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return all minor alleles at given site. Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- minorAlleles(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- minorAlleles(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- minP - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- minProportionOfSitesPresent() - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Min Proportion of Sites Present
- minProportionOfSitesPresent(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Set Min Proportion of Sites Present. Min Proportion of Sites Present
- minQualScore() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Minimum quality score within the barcode and read length to be accepted
- minQualScore(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Set Minimum quality score. Minimum quality score within the barcode and read length to be accepted
- minR() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
filter out sites not correlated with neighboring sites
- minR(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Min R. filter out sites not correlated with neighboring sites
- minR2 - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
Filter out sites with less than minR2 average r-square with neighboring sites (window size = 50).
- minSitesToCluster() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
- minSitesToCluster(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Min sites to cluster. The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
- minSitesToTestMatch() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Minimum number of present sites within input sequence to do the search
- minSitesToTestMatch(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Min sites to test match. Minimum number of present sites within input sequence to do the search
- minSitesToTestMatch() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Minimum number of sites to test for IBS between haplotype and target in focus block
- minSitesToTestMatch(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Min sites to test match. Minimum number of sites to test for IBS between haplotype and target in focus block
- minTagCount(value) - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- minTagCount() - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- minTagCount() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Minimum count of reads for a tag to be aligned
- minTagCount(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Min Tag Count. Minimum count of reads for a tag to be aligned
- minTagCount() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Minimum count of reads for a tag to be output
- minTagCount(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Min Count. Minimum count of reads for a tag to be output
- minTagCount() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Minimum count of reads for a tag to be output
- minTagCount(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Min Count. Minimum count of reads for a tag to be output
- minTaxa() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
Minimum number of taxa that must be present for R-squared to be calculated.
- minTaxa(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
Set Min Taxa for RSquared. Minimum number of taxa that must be present for R-squared to be calculated.
- minTaxa() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Minimum taxa containing tag
- minTaxa(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
Set Min Taxa Count. Minimum Taxa count
- minTaxaToGenerateAHaplotype() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Minimum number of taxa to generate a haplotype
- minTaxaToGenerateAHaplotype(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Min taxa to generate a haplotype. Minimum number of taxa to generate a haplotype
- minus(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- minus(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- minus(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- minus(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- minus(parent, taxaToRemove) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
Returns a distance matrix with the specified taxa removed.
- minusEquals(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- minusEquals(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- minusEquals(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
This function subtracts dm, modifying the original matrix
- minusEquals(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- minusLog10P(p) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPM
-
Return -log10(p-value), if p-value doesn't exist(p < 0), reutrn Double.NEGATIVE_INFINITY
- mismatch_penalty - Variable in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
The penalty for a mismatch (a substitution of different characters).
- mismatch_penalty() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
- mismatch_penalty(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Mismatch Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
- mismatch_penalty() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
- mismatch_penalty(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Mismatch Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
- mismatch_penalty() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
- mismatch_penalty(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Mismatch Penalty Amount. Parameter sent to Smith Waterman aligner for use in calculating penalty when base pairs are mis-matched.
- MISMATCH_TAG - Static variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Character that signals a mismatch in the score tag line of an alignment.
- missing - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- missing() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- missing() - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- missing() - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- missing() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- missingObsForSite - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- missingValue - Static variable in class net.maizegenetics.phenotype.CategoricalAttribute
-
- missToZero() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
- missToZero(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Missing float values to zero?. Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
- missToZero() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
- missToZero(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Missing float values to zero?. Will set missing float denoted column values to zero (otherwise they are set to Float.MIN
- mkFastaFile(fFastaFileS, bFastaFileS) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
Write forword and backword fasta files of PE tag for Bowtie2 alignment, the sequence is in format of index_f/b_c/n, where f means forward, b means backword, c means contig, n means no contig When contig exist, the forward and backword tags are the contig and reverse complement of the contig, respectively.
- mkFastaFile(tagsFFastaFileS, tagsBFastaFileS, contigFastaFileS) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
Deprecated.
- MLMPlugin - Class in net.maizegenetics.analysis.association
-
- MLMPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.association.MLMPlugin
-
- MLMPlugin.CompressionType - Enum in net.maizegenetics.analysis.association
-
- model(missingObs, numberOfNonmissingObs) - Method in class net.maizegenetics.analysis.association.PhenotypeLM
-
- modelCriterion() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
The model selection criterion used to determine which terms enter the model and how many. Value must be one of pval, bic, mbic, or aic
- modelCriterion(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Model selection criterion. The model selection criterion used to determine which terms enter the model and how many. Value must be one of pval, bic, mbic, or aic
- ModelEffect - Interface in net.maizegenetics.stats.linearmodels
-
- ModelEffectUtils - Class in net.maizegenetics.stats.linearmodels
-
- modelSelectionCriterion - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- modelSelectionCriterion(criterion) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- modelTrainingPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- modelType() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
The model selection criteria used to determine which terms enter the model and how many. Value must be one of pvalue, bic, mbic, or aic
- modelType(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
Set Model type. The model selection criteria used to determine which terms enter the model and how many. Value must be one of pvalue, bic, mbic, or aic
- ModifyTBTHDF5Plugin - Class in net.maizegenetics.analysis.gbs
-
This pipeline modifies TagsByTaxa HDF5 file with data organized by taxa. It can: 1. Create an empty TBT. 2. Merge two TBT 3. Combined similarly named taxa 4. Pivot a taxa TBT to a tag TBT
- ModifyTBTHDF5Plugin() - Constructor for class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- ModifyTBTHDF5Plugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- moment(n, k, m) - Static method in class net.maizegenetics.stats.statistics.ParetoDistribution
-
moments E(X^n) of the Pareto distribution
- MonetDB_IFLFilePlugin - Class in net.maizegenetics.analysis.gobii
-
This class has methods to create GOBII intermediary files to be used when creating a GOBII monetdb dataset table. The GOBII IFL scripts require 3 files: a matrix of variants, a list of maker_ids, and a list of dnarun ids. The matrix of variants is created from the hmp.txt file at the same time the intermediary files for the postgres marker and dnarun related tables are created. (see MarkerDNARunFromHMP_IFLFilePlugin) Once the IFL scripts have been run to populate these postgres tables, the marker_id and dnarun_id values are created. This script pulls the id values from the postgres DB to create the final 2 intermediary files needed by the GOBII loadVariantMatrix.py script See this link for details: http://cbsugobii05.tc.cornell.edu:6084/display/TD/MonetDB+IFL The db config file should look like this: host=cbsudc01.tc.cornell.edu user= password= DB=gobii_maizeifltest (or other postgres db you want to query) The outputDir field should also contain the prefix for the file. Previously this was the dataset.name. But GOBII names their .h5 and monetdb table with DS_. We want to do the same to be consistent. THis will need to be queried from the db before running this plugin. If the dataset name is known, this is a simple query. AUgust2016 UPDATE: The list of markers in the marker_id, and dnarun_ids in dnarun_id file must be in proper order. They must be in the order the markers are stored in the monetdb table, ie in the order they are stored in the variant file. TO achieve this, the DB query orders the output by marker_idx (marker query) and dnarun_idx (dnarun query). These idx values were created sequentially when the marker and dnarun tables were created.
- MonetDB_IFLFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
- MonetDB_IFLFilePlugin() - Constructor for class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
- MONTHS - Variable in interface net.maizegenetics.taxa.tree.Units
-
- mostFrequentDonorsAcrossFocusBlocks(allDH, maxHypotheses) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
Produces a sort list of most prevalent donors across the donorAlignment. It looks at all focus blocks and weights blocks by rank
- MotherKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for the mother of the taxon
- mouseClicked(e) - Method in class net.maizegenetics.tassel.MyTableUI.MyMouseInputListener
-
- mouseDragged(e) - Method in class net.maizegenetics.tassel.MyTableUI.MyMouseInputListener
-
- mousePressed(e) - Method in class net.maizegenetics.tassel.MyTableUI.MyMouseInputListener
-
- moveAllHaplotypesToBiggestCluster(maxdiff) - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
For each cluster, from largest to smallest, move all consistent haplotypes from other clusters to that cluster
- moveAllPossibleHaplotypesToCluster(clusterIndex, fromClustersWithHigherIndexOnly, maxdiff) - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
For the indexed cluster, move all haplotypes consistent with the cluster haplotype to this cluster from any other cluster
- MTMapping(outfileS) - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
MT genetic mapping
- MTMapping() - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
-
MT genetic mapping
- mult(dm, transpose, transposedm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- mult(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- mult(dm, transpose, transposedm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- mult(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- mult(dm, transpose, transposedm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Multiply this matrix times another.
- mult(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- mult(dm, transpose, transposedm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- mult(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- multadd(A, B, alpha, beta, transpose, transposeA) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- multadd(A, B, alpha, beta, transpose, transposeA) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- multadd(A, B, alpha, beta, transpose, transposeA) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Using this function for combining multiplication and addition allows the implementing library to optimize the operations. Performs: alpha * XA + beta*B, where X is this matrix
- multadd(A, B, alpha, beta, transpose, transposeA) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- multbc() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
use the multiple backcross algorithm
- multbc(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Multbc. use the multiple backcross algorithm
- MultiDimensionalScalingPlugin - Class in net.maizegenetics.analysis.distance
-
- MultiDimensionalScalingPlugin(parent, interactive) - Constructor for class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- multimaps - Variable in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- MULTIMAPS - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- MultiMemberGZIPInputStream - Class in net.maizegenetics.util
-
- MultiMemberGZIPInputStream(in, size) - Constructor for class net.maizegenetics.util.MultiMemberGZIPInputStream
-
- MultiMemberGZIPInputStream(in) - Constructor for class net.maizegenetics.util.MultiMemberGZIPInputStream
-
- MultiParameterized - Class in net.maizegenetics.taxa.tree
-
Title: MultiParameterized
- MultiParameterized(bases) - Constructor for class net.maizegenetics.taxa.tree.MultiParameterized
-
- MultiParameterized(bases, watcher) - Constructor for class net.maizegenetics.taxa.tree.MultiParameterized
-
- MultiParameterized.ParameterAccessWatcher - Interface in net.maizegenetics.taxa.tree
-
An interface for classes that wish to find out about particular parameter access
- multiplePrint(out, c, num) - Method in class net.maizegenetics.util.FormattedOutput
-
repeatedly print a character
- multMatrices(A, nrowsA, ncolsA, B, nrowsB, ncolsB, C, alpha, beta, transA, transB) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- myAlignmentTableModel - Variable in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- myAttributeList - Variable in class net.maizegenetics.phenotype.CorePhenotype
-
- myAttributeNameMap - Variable in class net.maizegenetics.phenotype.CorePhenotype
-
- myAttributeTypeList - Variable in class net.maizegenetics.phenotype.CorePhenotype
-
- myAttributeTypeMap - Variable in class net.maizegenetics.phenotype.CorePhenotype
-
- myAvailableListModel - Variable in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- myBaseModel - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myBaseModel - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- myBaseModel - Variable in class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- myBlues - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myChromosomes - Variable in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- myCovariateAttributes - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myCovariateAttributes - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myCurrentSite - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myCurrentSiteMinimumClassSize - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myDataAttributes - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myDataAttributes - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myDatum - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myDatum - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myFactorAttributes - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myFactorAttributes - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myFittedVariants - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- myGenoPheno - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myGenoPheno - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- myGenotype - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- myGenotype - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- myGenotype - Variable in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- myGenotypePhenotype - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- myIndexRedirect - Variable in class net.maizegenetics.dna.snp.TranslateIndexRedirect
-
- myIsCanceled - Variable in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- myIsCaptureSelected - Variable in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- myLogger - Static variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myLogger - Static variable in interface net.maizegenetics.plugindef.Plugin
-
- myMatrix - Variable in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- myMatrix - Variable in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- myMaxVariants - Variable in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- myModel - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myModel - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- myModel - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- myNumBlocksRead - Static variable in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- myNumCacheMisses - Static variable in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- myNumProcesses - Static variable in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- myNumSites - Variable in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- myNumTags - Variable in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- myNumTaxa - Variable in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- myParentPlugin - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- myPermutedData - Variable in class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- myPhenotype - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myPhenotype - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- myPhenotype - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- myPopulationData - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- myPosition - Variable in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
-
- myProgenyIDs - Variable in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- mySelectedListModel - Variable in class net.maizegenetics.gui.SelectFromAvailableDialog
-
- mySites - Variable in class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- mySites - Variable in class net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
-
- mySites - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- mySweepFast - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- MyTableUI.MyMouseInputListener - Class in net.maizegenetics.tassel
-
- myTaxa - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myTaxaAttribute - Variable in class net.maizegenetics.phenotype.CorePhenotype
-
- myTaxaList - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- myTimeReading - Static variable in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- myUniquePositions - Variable in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- myWasCancelled - Variable in class net.maizegenetics.plugindef.AbstractPlugin
-
- p(value) - Method in class net.maizegenetics.analysis.popgen.LDResult.Builder
-
- p() - Method in class net.maizegenetics.analysis.popgen.LDResult
-
- p - Variable in class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
P-value from binomial test
- P_VALUE - Static variable in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- paddedSequence - Variable in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
Processed sequence padded with polyA
- paddedSequence - Variable in class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
- padDistance() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Distance to pad between each tag pair
- padDistance(value) - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Set Pad distance. Distance to pad between each tag pair
- paint(g) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- paint(g) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
-
- paint(g, c) - Method in class net.maizegenetics.gui.VerticalLabelUI
-
- paintComponent(g) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- paintComponent(g) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
-
- Pair<T,K> - Class in net.maizegenetics.util.db
-
Pair utility type User: julian3 Date: 2013/11/10 Time: 7:06 PM PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- Pair(car, cdr) - Constructor for class net.maizegenetics.util.db.Pair
-
- PairwiseAlignment - Class in net.maizegenetics.analysis.gbs.neobio
-
This class is the product of a pairwise alignment, generated by one subclasses of
class PairwiseAlignmentAlgorithm. It contains the two sequences strings with gaps, a score tag line, and a score value. It is typically displayed in three rows as in the following example of an alignment between parts of two protein sequences:
MDEIHQLEDMFTVDSETLRKVVKHFILPHD-----MRTTKHQEELWSFIAELDSLKDFMVEQE // sequence 1
M +I E +FTV +ETL+ V KHFILP D MRTT++ +ELW FIA DSLK F+ EQ // score tag line
MQQIENFEKIFTVPTETLQAVTKHFILP-DATETLMRTTQNPDELWEFIA--DSLKAFIDEQF // sequence 2
- PairwiseAlignment(gapped_seq1, score_tag_line, gapped_seq2, score) - Constructor for class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Creates a PairwiseAlignment instance with the specified gapped sequences, score tag line and score value.
- PairwiseAlignment(gapped_seq1, score_tag_line, gapped_seq2, score, row, col) - Constructor for class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Creates a PairwiseAlignment instance with the specified gapped sequences, score tag line and score value.
- PairwiseAlignmentAlgorithm - Class in net.maizegenetics.analysis.gbs.neobio
-
This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms. Subclasses are required to provide methods to build a high scoring alignment between two sequences and compute its score with a given scoring scheme.
- PanAAddPosToTagMapPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Add alignment information from Bowtie2 to tagMap. Used to identify unique ref tags for model training
- PanAAddPosToTagMapPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- PanAAddPosToTagMapPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- PanABuildPivotTBTPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
- PanABuildPivotTBTPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- PanABuildPivotTBTPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- PanABuildTagBlockPosPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Build blocked physical position of tags. The blocked physical position of tag is used to block the corresponding marker in genetic mapping if the tag is mapping to the marker coming from itself Positions come from TOPM alignment hypothesis or the best position from machine learning prediction
- PanABuildTagBlockPosPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- PanABuildTagBlockPosPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- PanABuildTagGWASMapPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
- PanABuildTagGWASMapPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- PanABuildTagGWASMapPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- PanABuildTrainingSetPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Build training data set from tagMap, including boxcox transformation and converting to ARFF format
- PanABuildTrainingSetPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- PanABuildTrainingSetPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- PanAFilteringTagMapPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Filtering high quality mapped tag and write them into a file, based on the predicted distance
- PanAFilteringTagMapPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- PanAFilteringTagMapPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- PanAH5ToAnchorPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
- PanAH5ToAnchorPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- PanAH5ToAnchorPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- PanAMergeMappingResultPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
- PanAMergeMappingResultPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- PanAMergeMappingResultPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- PanAModelTrainingPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Training data with M5Rules model, generate model file and training report files
- PanAModelTrainingPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- PanAModelTrainingPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- PanAPredictionPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Make predictions based on trained machine learning model. Write predicted values into tagMap file
- PanAPredictionPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- PanAPredictionPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- PanAReadDigestPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Digest Fastq/Qseq data with recognition sequence Do not use underscore in taxa name in keyfile
- PanAReadDigestPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- PanAReadDigestPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- PanAReadToKmerPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Generate Kmers from Fastq/Qseq data Do not use underscore in taxa name in keyfile
- PanAReadToKmerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- PanAReadToKmerPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- PanASamToMultiPositionTOPMPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
- PanASamToMultiPositionTOPMPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- PanASamToMultiPositionTOPMPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- PanASplitTagBlockPosPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Split TagBlockPos
class TagBlockPosition file into subsets. Designed to submit genetic mapping jobs in cluster
- PanASplitTagBlockPosPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- PanASplitTagBlockPosPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- PanASplitTBTPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Split large TagsByTaxaByteHDF5TagGroup file into small sub TBTs. Designed to submit genetic mapping jobs in cluster
- PanASplitTBTPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- PanASplitTBTPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- PanATagGWASMappingPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Genetic mapping (GWAS) tags
- PanATagGWASMappingPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- PanATagGWASMappingPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- PanATagMapToFastaPlugin - Class in net.maizegenetics.analysis.gbs.pana
-
Output sequence in tagMap (e.g.
class TagGWASMap) file in Fasta format, which is used in Bowtie2 alignment
- PanATagMapToFastaPlugin() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- PanATagMapToFastaPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- PanAUsageExample - Class in net.maizegenetics.analysis.gbs.pana
-
- PanAUsageExample() - Constructor for class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- ParameterCache - Class in net.maizegenetics.plugindef
-
This class is for storing a cache of parameters retrieved from a java.util.Properties file that is available to all plugins on the command line. This is used when run_pipeline.pl -configParameters config.txt... is used. config.txt example entries as follow... First five are using by GetDBConnectionPlugin -config config.txt but that should be refactored to individual PluginParameters. Then entry example would be GetDBConnectionPlugin.DBType=sqlite KinshipPlugin.method=TYPE is the standard. PLUGIN_NAME.COMMAND_LINE_NAME=VALUE host=localHost user=sqlite password=sqlite DB=/tempFileDir/outputDir/phgTestDB.db DBtype=sqlite KinshipPlugin.method=Normalized_IBS
- Parameterized - Interface in net.maizegenetics.taxa.tree
-
interface for class with (optimizable) parameters
- Parameterized.Null - Class in net.maizegenetics.taxa.tree
-
NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters
- Parameterized.ParameterizedBase - Class in net.maizegenetics.taxa.tree
-
A Utility class for using as the superclass to subclasses which are based on double arrays
- Parameterized.ParameterizedUser - Class in net.maizegenetics.taxa.tree
-
A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)
- Parameterized.Utils - Class in net.maizegenetics.taxa.tree
-
- ParameterizedBase(parameters, lowerLimits, upperLimits, defaultValues) - Constructor for class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays
- ParameterizedBase(parameters, lowerLimits, upperLimits, defaultValues, parametersSE) - Constructor for class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays
- ParameterizedBase() - Constructor for class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
Builds a parameterized objects around a set of double arrays. The user needs to call setSource() at some point to correctly set things up
- ParameterizedUser(base) - Constructor for class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- ParameterizedUser() - Constructor for class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
Sub class should call setParameterizedBase() at some point if using this constructor... otherwise many explosions and the flashing of lights.
- parameterSet(baseParameterized, param, localParameter) - Method in interface net.maizegenetics.taxa.tree.MultiParameterized.ParameterAccessWatcher
-
- parameterType() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- parent1 - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- parent2 - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- parentA() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
The full name of parent to be encoded as A
- parentA(value) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
Set Parent A. The full name of parent to be encoded as A
- parentageFile() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
The input file containing the parentage which lists the parents of each progeny and whether they were derived by self or outcross.
- parentageFile(value) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
Set Parentage Input File. The input file containing the parentage which lists the parents of each progeny and whether they were derived by self or outcross.
- parentB() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
The full name of parent to be encoded as B
- parentB(value) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
Set Parent B. The full name of parent to be encoded as B
- parentHaplotypeFilename() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
The input file containing the parent haplotypes expressed as nucleotides.
- parentHaplotypeFilename(value) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
Set Parent Haplotypes Input File. The input file containing the parent haplotypes expressed as nucleotides.
- parentId() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- parentId(parentId) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- ParentPhasingPlugin - Class in net.maizegenetics.analysis.imputation
-
- ParentPhasingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- parents(mom, dad) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Set text definition of parents (default=null)
- ParetoDistribution - Class in net.maizegenetics.stats.statistics
-
Pareto distribution (scale-free distribution without characteristic length scale). Parameters: shape parameter k>0, scale parameter m>0 ("minimum income")
- parse(source, parsePosition) - Method in class net.maizegenetics.analysis.chart.ManhattanNumberFormat
-
- parse(filename) - Static method in class net.maizegenetics.analysis.phg.ParseGVCF
-
- parse(args) - Method in class net.maizegenetics.util.ArgsEngine
-
Parses the input command line arguments. The result of parsing will be stored in the current instance of ArgsEngine.
- parseArgs(input) - Method in class net.maizegenetics.pipeline.TasselPipeline
-
- ParseBarcodeRead - Class in net.maizegenetics.analysis.gbs
-
Takes a key file and then sets up the methods to decode a read from the sequencer. The key file decribes how barcodes are related to their taxon. Generally, a keyfile with all flowcells is included, and then the flowcell and lane to be processed are indicated in the constructor.
- ParseBarcodeRead(keyFile, enzyme, flowcell, lane) - Constructor for class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
Create the barcode parsing object
- parseByteWMissing(s) - Static method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- parseCharWMissing(s) - Static method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- parseCIGAR(cigarString, tagSequence) - Static method in class net.maizegenetics.dna.tag.SAMUtils
-
Searches a CIGAR string for insertions in the reference sequence.
- parseGffLine(line) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
Create a GenomeFeature from a line of GFF file. This method is modified from the BioJava source code for the same purpose, in biojava3-genome/src/main/java/org/biojava3/genome/GFF3Reader.java
- ParseGVCF - Class in net.maizegenetics.analysis.phg
-
- ParseGVCF.GVCFLine - Class in net.maizegenetics.analysis.phg
-
- ParseGVCF.ProcessLines - Class in net.maizegenetics.analysis.phg
-
- parseIntWMissing(s) - Static method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- parseJsonObject(featureData) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- parseKeyfileIntoMap(fileName) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Parses a tab-delimited keyFile storing the flow cell and lane values into a multimap. The flow cell is the key, which may have multiple associated lanes.
- parseMDField(mdField, tagSequence) - Static method in class net.maizegenetics.dna.tag.SAMUtils
-
Decodes the MD: field in a SAM file to determine the location of polymorphisms and whether they are mismatches or deletions from the reference sequence.
- parseNucleotideDiploidByte(value) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Returns Optional diploid byte value for given nucleotide value. First four bits contain first allele value. And second four bits contain second allele value. Optional empty if not present in the Hash.
- parseReadIntoTagAndTaxa(seqS, qualS, fastq, minQual) - Method in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
- parseReadIntoTagAndTaxa(seqSF, qualSF, seqSB, qualSB, fastq, minQual, tagLengthInLong) - Method in class net.maizegenetics.analysis.gbs.PEParseBarcodeRead
-
Parse sequence pair to a PE tag and taxon.
- parseVCFHeadersIntoMap(s) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Parses a VCF header with the taxa names and annotations into a multimap. The taxa name is return as the "ID" key, as used by the VCF format.
- PartitionedLinearModel - Class in net.maizegenetics.stats.linearmodels
-
- PartitionedLinearModel(baseModel, lm) - Constructor for class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- PartitionedLinearModel(baseModel, lm) - Constructor for class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- PassThroughPlugin - Class in net.maizegenetics.analysis.data
-
- PassThroughPlugin() - Constructor for class net.maizegenetics.analysis.data.PassThroughPlugin
-
Creates a new instance of PassThroughPlugin
- password(value) - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
Set Password. Password
- password() - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- path_type - Variable in class net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
-
The type of the highest scoring path ending at a given position of the output border of a block.
- pChr - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Physical chromosome of tag, unknown = Integer.MIN_VALUE
- PDAnnotation - Class in net.maizegenetics.dna.pd
-
- PDAnnotation(hapMapPath, pathGwas, annoPath, outputFile, startChr, endChr) - Constructor for class net.maizegenetics.dna.pd.PDAnnotation
-
- pdf(x, n) - Static method in class net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
-
probability density function of the chi-square distribution
- pdf(x, n) - Static method in class net.maizegenetics.stats.statistics.ChiSquareDistribution
-
probability density function of the chi-square distribution
- pdf(x, lambda) - Static method in class net.maizegenetics.stats.statistics.ExponentialDistribution
-
probability density function of the exponential distribution (mean = 1/lambda)
- pdf(x, shape, scale) - Static method in class net.maizegenetics.stats.statistics.GammaDistribution
-
probability density function of the Gamma distribution
- pdf(x, m, sd) - Static method in class net.maizegenetics.stats.statistics.NormalDistribution
-
probability density function
- pdf(x, k, m) - Static method in class net.maizegenetics.stats.statistics.ParetoDistribution
-
probability density function of the Pareto distribution
- PDReport - Class in net.maizegenetics.dna.pd
-
User: dkroon Date: 6/25/13
- PDReport(polymorphismDescriptorFile) - Constructor for class net.maizegenetics.dna.pd.PDReport
-
- pedFile() - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Ped File
- pedFile(value) - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Set Ped File. Ped File
- pedFilename() - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
Create A Matrix
- pedFilename(value) - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
Set Ped Filename. Create A Matrix
- pedigree(val) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Set text definition of pedigree (default=null)
- pedigreeFile() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Pedigree file containing full sample names (or expected names after merging) & expected inbreeding coefficient (F) for each. Only taxa with expected F >= mnF used to calculate F = 1-Ho/He. (default: use ALL taxa to calculate F
- pedigreeFile(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Pedigree File. Pedigree file containing full sample names (or expected names after merging) & expected inbreeding coefficient (F) for each. Only taxa with expected F >= mnF used to calculate F = 1-Ho/He. (default: use ALL taxa to calculate F
- PedigreeKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for the pedigree of the taxon
- pedigrees() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
the pedigree file name
- pedigrees(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Pedigrees. the pedigree file name
- pedMatrix(pedigree) - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- peek() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- peek() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- PEFastqChunk - Class in net.maizegenetics.dna.read
-
Hold PE Fastq file. Providing merging function
- PEFastqChunk(fastqR1FileS, fastqR2FileS, format, startIndex, readNum) - Constructor for class net.maizegenetics.dna.read.PEFastqChunk
-
Constructor to sample PE Fastq files, ignore those bad sequence at the beginning
- PEFastqChunk(fastqR1FileS, fastqR2FileS, format) - Constructor for class net.maizegenetics.dna.read.PEFastqChunk
-
Constructor to read in whole PE Fastq files, fastq file should be small for test
- PenalizedLikelihood - Class in net.maizegenetics.stats.statistics
-
Penalized likelihood criteria
- PEParseBarcodeRead - Class in net.maizegenetics.analysis.gbs
-
- PEParseBarcodeRead(keyFile, enzyme, flowcell, lane) - Constructor for class net.maizegenetics.analysis.gbs.PEParseBarcodeRead
-
Construct empty object from key file, enzyme and Illumina data from a lane. Set up likely end and barcode for parsing data
- percentageMasked() - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
Percentage of genotypes to mask.
- percentageMasked(value) - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
Set Percentage Masked. Percentage of genotypes to mask.
- percentNotMissing() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- PERead - Class in net.maizegenetics.dna.read
-
Holding paired end read. Providing merging function
- PERead(rf, rb) - Constructor for class net.maizegenetics.dna.read.PERead
-
- PEReadBarcodeResult - Class in net.maizegenetics.analysis.gbs
-
Container class for returning the results of parsed barcoded sequencing read.
- PEReadBarcodeResult(rF, rB) - Constructor for class net.maizegenetics.analysis.gbs.PEReadBarcodeResult
-
Construct object from forward and backward sequence
- perfectMatch - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
If the alignment is a perfect match to the reference, y = 1, n = 0, unknown = Byte.MIN_VALUE
- performCrossValidation() - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
Perform cross-validation: True or False
- performCrossValidation(value) - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
Set Perform cross-validation. Perform cross-validation: True or False
- performFunction(input) - Method in class net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.chart.QQDisplayPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
- performFunction(dataSet) - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
Returns combined data set if all inputs have been received.
- performFunction(input) - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.HetsToUnknownPlugin
-
Returns Homozygous version of input Genotype Table.
- performFunction(input) - Method in class net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
-
- performFunction(dataSet) - Method in class net.maizegenetics.analysis.data.PassThroughPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.SeparatePlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.data.UnionAlignmentPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.filter.FilterDataSetPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- performFunction(input) - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.FastqToTBTPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.KmerToTBTPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.QseqToTBTPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- performFunction(input) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
Workhorse function to actually run LD on a dataset
- performFunction(input) - Method in class net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
-
- performFunction(input) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- performFunction(input) - Method in interface net.maizegenetics.plugindef.Plugin
-
Performs function of this plugin.
- performFunction(input) - Method in class net.maizegenetics.tassel.TasselLogging
-
- performFunctionForAlignment(inputAlignment) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForDistanceMatrix(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForFilter(filter) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForPhenotype(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForPositionList(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForSimpleTree(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForTableReport(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- performFunctionForTaxaList(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- permpvalueColumn - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- permutationAlpha - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- permutationAlpha(alpha) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- permutationAlpha() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Type I errors will be controlled at this level.
- permutationAlpha(value) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
Set Alpha for permutations. Type I errors will be controlled at this level.
- permutationReportBuilder - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- permutationTest(permute, nperm) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- permutationTest(permute, nperm) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- permute - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- permute() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Should a permutation analysis be run? The permutation analysis controls the experiment-wise error rate for individual phenotypes.
- permute(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Run Permutations. Should a permutation analysis be run? The permutation analysis controls the experiment-wise error rate for individual phenotypes.
- permuteData(data) - Method in class net.maizegenetics.stats.linearmodels.WithinPopulationPermuter
-
- permutedData - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- pError - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- PETagCounts - Class in net.maizegenetics.dna.tag
-
Hold PE tags and their counts, also including contigs
- PETagCounts(inFile, format) - Constructor for class net.maizegenetics.dna.tag.PETagCounts
-
Construct PETagCounts from a file
- PETagCounts(tagLengthInLong, tagNum) - Constructor for class net.maizegenetics.dna.tag.PETagCounts
-
Initialize PETagCounts with empty matrix
- PETags - Interface in net.maizegenetics.dna.tag
-
Basic interface for holding sets of sequence tag (these are compressed into 2-bit codings of tags). The length of tag in good sequence is also tracked.
- PETagsOnPhysicalMap - Class in net.maizegenetics.dna.map
-
- PETagsOnPhysicalMap(infileS, format) - Constructor for class net.maizegenetics.dna.map.PETagsOnPhysicalMap
-
- PETagsOnPhysicalMap(ptc, fSamFileS, bSamFileS, contigSamFileS) - Constructor for class net.maizegenetics.dna.map.PETagsOnPhysicalMap
-
- PETagsOnPhysicalMapV3 - Class in net.maizegenetics.dna.map
-
This class hold the multiple mapping positions of PE tags, including forward and backward PE tags. Data in this class are used to annotate HDF5TOPM When contig exist, the forward and backword tags are the contig and reverse complement of the contig, respectively. The PE tags were first aligned with bowtie2 (-k N), any number of mapping position can be imported PE tags of both end are stored in one long array with variable length, then they were truncated to 2 longs. This is easy for searching Using a pairIndex, each 64 bp tag has a index pointing to the other end of PE. It is worth noting that, the 64 bp tags are not unique. Rarely, there are multiple identical 64 bp tags, although the full length PE tags are unique. When multiple identical 64 bp tags exist, the one with longest full length PE is used to annotate HDF5TOPM.
- PETagsOnPhysicalMapV3(PETOPMFileS) - Constructor for class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Constructor from a file
- PETagsOnPhysicalMapV3(fFastaFileS, bFastaFileS, fSamFileS, bSamFileS) - Constructor for class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Constructor using fasta files and sam files
- pev - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- phased() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- phasedResults - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- PhaseHighCoverage - Class in net.maizegenetics.analysis.imputation
-
- PhaseHighCoverage(genotype) - Constructor for class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- phaseParentsUsingAllAvailableProgeny(minEigenRatio, savepath) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- phaseParentsUsingAllAvailableProgeny(minEigenRatio) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- phaseParentUsingOneProgeny(parent, otherParent, progeny, gt) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- phaseParentUsingSelfAndCrossProgeny(parent, myGeno, minEigenRatio, plotInfo) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- phaseSelfedParents(parentpath, savepath) - Method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- phenotype() - Method in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- phenotype() - Method in interface net.maizegenetics.analysis.modelfitter.ForwardRegression
-
- phenotype() - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- phenotype(thePhenotype) - Method in class net.maizegenetics.phenotype.GenotypePhenotypeBuilder
-
- Phenotype - Interface in net.maizegenetics.phenotype
-
Phenotype represents phenotype data as a two dimensional matrix. Rows are observations. Columns are attributes.
- Phenotype.ATTRIBUTE_TYPE - Enum in net.maizegenetics.phenotype
-
- PhenotypeAttribute - Interface in net.maizegenetics.phenotype
-
- PhenotypeBuilder - Class in net.maizegenetics.phenotype
-
- PhenotypeBuilder() - Constructor for class net.maizegenetics.phenotype.PhenotypeBuilder
-
- phenotypeFile() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
Phenotype File
- phenotypeFile(value) - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
Set Phenotype File. Phenotype File
- PhenotypeLM - Class in net.maizegenetics.analysis.association
-
- PhenotypeLM(phenotypeOnly) - Constructor for class net.maizegenetics.analysis.association.PhenotypeLM
-
- phenotypeOnly() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Should the phenotype be analyzed with no markers and BLUEs generated? (BLUE = best linear unbiased estimate)
- phenotypeOnly(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Analyze Phenotype Only. Should the phenotype be analyzed with no markers and BLUEs generated? (BLUE = best linear unbiased estimate)
- PhenotypeUtils - Class in net.maizegenetics.phenotype
-
- phet() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
proportion of sites that are heterozygous
- phet(value) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Set Phet. proportion of sites that are heterozygous
- pHeterozygous - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- pHomoD1 - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- pHomoD2 - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- physicalMapFile() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Physical map file containing alignments. (Only -t or -m allowed)
- physicalMapFile(value) - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Set Physical Map File. Physical map file containing alignments. (Only -t or -m allowed)
- physicalPositions() - Method in interface net.maizegenetics.dna.map.PositionList
-
Returns all physical positions.
- physicalPositions() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- physicalPositions() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- physicalPositions() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns all physical positions.
- physicalPositions() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- physicalPositions() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- PieChartPanel - Class in net.maizegenetics.analysis.chart
-
Title: PieChartPanel
- PieChartPanel(theTable) - Constructor for class net.maizegenetics.analysis.chart.PieChartPanel
-
- pivotOn(factors) - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- pivotTBTHDF5File() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- pivotTBTHDF5File(value) - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- platformName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
THe platform on which this data set was run, e.g. GBSv27. Must match a platform name from the platform db table
- platformName(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set Platform Name. THe platform on which this data set was run, e.g. GBSv27. Must match a platform name from the platform db table
- PlinkLoadPlugin - Class in net.maizegenetics.analysis.data
-
- PlinkLoadPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Creates a new instance of PlinkLoadPlugin
- plinkToPed(ped) - Static method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
Takes a filepath to a PLINK formatted file(see below). Converts to a String[][] format where each row contains 3 columns: Individual Identifier, Paternal Identifier, Maternal Identifier This format is convenient in calculating an pedigree-based kinship (A) matrix Expected PLINK pedigree file format (.ped) Family ID Individual ID Paternal ID Maternal ID and several more fields These fields are separated by one or more whitespace characters, and each row is on its own line. For our purposes, we expect every Individual ID in the file to be unique
- plm - Variable in class net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
-
- ploidy() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- Plugin - Interface in net.maizegenetics.plugindef
-
- Plugin.PARAMETER_PROPERTIES - Enum in net.maizegenetics.plugindef
-
- PluginAction - Interface in net.maizegenetics.plugindef
-
- pluginDescription() - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
- pluginDescription() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- pluginDescription() - Method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- pluginDescription() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- pluginDescription() - Method in interface net.maizegenetics.plugindef.Plugin
-
Returns description of the plugin.
- PluginEvent - Class in net.maizegenetics.plugindef
-
- PluginEvent(source) - Constructor for class net.maizegenetics.plugindef.PluginEvent
-
Creates a new instance of PluginEvent
- PluginEvent(source, metaData) - Constructor for class net.maizegenetics.plugindef.PluginEvent
-
Creates a new instance of PluginEvent
- PluginListener - Interface in net.maizegenetics.plugindef
-
- PluginParameter<T> - Class in net.maizegenetics.plugindef
-
Defines the attributes of parameters to be used in the plugins
- PluginParameter(oldParameter, newValue) - Constructor for class net.maizegenetics.plugindef.PluginParameter
-
Use these to change the value of an existing parameter, e.g. after a user changes the value. Otherwise use the Builder to create the parameter
- PluginParameter(oldParameter, possibleValues) - Constructor for class net.maizegenetics.plugindef.PluginParameter
-
Use this to change the possible values of a PluginParameter built as objectListSingleSelect().
- PluginParameter.Builder<T> - Class in net.maizegenetics.plugindef
-
- PluginParameter.PARAMETER_TYPE - Enum in net.maizegenetics.plugindef
-
- pluginParameters() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- pluginParameters() - Method in interface net.maizegenetics.plugindef.Plugin
-
Get map of plugin parameters. Key is command line name and value is current value.
- PluginProgressUnit - Class in net.maizegenetics.progress
-
- PluginProgressUnit(plugin, level) - Constructor for class net.maizegenetics.progress.PluginProgressUnit
-
- PluginProgressUnit(plugin, level, cancelButton) - Constructor for class net.maizegenetics.progress.PluginProgressUnit
-
- PluginProgressUnit(plugin, level, cancelButton, cancelPlugin) - Constructor for class net.maizegenetics.progress.PluginProgressUnit
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- pluginUserManualURL() - Method in interface net.maizegenetics.plugindef.Plugin
-
Returns URL to User Manual.
- plus(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- plus(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- plus(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- plus(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- plusEquals(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- plusEquals(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- plusEquals(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
This function adds dm, modifying the original matrix
- plusEquals(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- PolymorphismDistribution - Class in net.maizegenetics.analysis.popgen
-
This class provides the distribution of polymorphisms
- PolymorphismDistribution() - Constructor for class net.maizegenetics.analysis.popgen.PolymorphismDistribution
-
- PolymorphismFinder - Class in net.maizegenetics.analysis.gbs
-
- PolymorphismFinder(rbt) - Constructor for class net.maizegenetics.analysis.gbs.PolymorphismFinder
-
- pop(x) - Static method in class net.maizegenetics.util.BitUtil
-
Returns the number of bits set in the long
- pop_andnot(A, B, wordOffset, numWords) - Static method in class net.maizegenetics.util.BitUtil
-
Returns the popcount or cardinality of A & ~B Neither array is modified.
- pop_array(A, wordOffset, numWords) - Static method in class net.maizegenetics.util.BitUtil
-
* Returns the number of set bits in an array of longs.
- pop_array_to_index(A, index) - Static method in class net.maizegenetics.util.BitUtil
-
- POP_GEN - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- pop_intersect(A, B, wordOffset, numWords) - Static method in class net.maizegenetics.util.BitUtil
-
Returns the popcount or cardinality of the two sets after an intersection. Neither array is modified.
- pop_union(A, B, wordOffset, numWords) - Static method in class net.maizegenetics.util.BitUtil
-
Returns the popcount or cardinality of the union of two sets. Neither array is modified.
- pop_xor(A, B, wordOffset, numWords) - Static method in class net.maizegenetics.util.BitUtil
-
- populateBlock(blockIndex) - Method in class net.maizegenetics.dna.map.TagGWASMap
-
- populateBlock(blockIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Populate a block in memory with default values, update current block index at the same time
- populateChrAndVarPositions() - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
Creates the arrays for the all the positions for each chromosome as defined by the variants. Call this method after remapping or after loading the file, and it will be used for SNP calling.
- populateTableFromFile(conn, table, sourceFile, header) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- PopulationData - Class in net.maizegenetics.analysis.imputation
-
- posEndB - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- posEndContig - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- posEndF - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- position() - Method in class net.maizegenetics.analysis.gbs.repgen.RefTagData
-
- position - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- position - Variable in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- position() - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- position() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- position - Variable in class net.maizegenetics.analysis.modelfitter.SNP
-
- position(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set Position in Chromosome
- position(position) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- position(position) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- Position - Interface in net.maizegenetics.dna.map
-
Defines a genomic positions and its known variants. Includes attributes of chromosome, position, sub-position, strand, name (or SNP ID), whether this position is a nucleotide, or includes an indel.
- position - Variable in class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
Position of the most significant site
- position() - Method in interface net.maizegenetics.dna.snp.Allele
-
- position() - Method in class net.maizegenetics.dna.snp.SimpleAllele
-
- position() - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
-
- POSITION_ALLELE_VALUE - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_ATTRIBUTES_PATH - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- POSITION_CM - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_GENOME_VERSION - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- POSITION_HAS_REFEFERENCE - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- POSITION_IS_INDEL - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_IS_NUCLEOTIDE - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_LIST_NONE - Static variable in class net.maizegenetics.plugindef.AbstractPlugin
-
- POSITION_MAF - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_MODULE - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- POSITION_NUM_SITES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- POSITION_SCHEMA - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_SITE_COVERAGE - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- POSITION_STRAND - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- positionList() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Position List
- positionList(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Position List.
- positionList(connection, datasetName) - Static method in class net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
-
- PositionList - Interface in net.maizegenetics.dna.map
-
List of positions in the genome. This type is used by every
interface GenotypeTable, but it can also be used list of GWAS results and other genomic annotations.
- positionList() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- PositionList.PositionListCollector - Class in net.maizegenetics.dna.map
-
- PositionListBuilder - Class in net.maizegenetics.dna.map
-
A builder for creating immutable PositionList. Can be used for either an in memory or HDF5 list.
- PositionListBuilder() - Constructor for class net.maizegenetics.dna.map.PositionListBuilder
-
Creates a new builder. The returned builder is equivalent to the builder generated by .
- PositionListBuilder(numberOfPositions) - Constructor for class net.maizegenetics.dna.map.PositionListBuilder
-
Creates a new builder with a given number of Positions. This is most useful when the number of sites is known from the beginning and the set method will be used to set positions perhaps out of order. Useful in multithreaded builders.
- PositionListBuilder(h5w, a) - Constructor for class net.maizegenetics.dna.map.PositionListBuilder
-
Creates a positionList in a new HDF5 file.
- PositionListCollector(validateOrder) - Constructor for class net.maizegenetics.dna.map.PositionList.PositionListCollector
-
- PositionListIOUtils - Class in net.maizegenetics.dna.map
-
Utilities for reading and writing Position Lists
- PositionListTableReport - Class in net.maizegenetics.dna.map
-
- PositionListTableReport(positionList) - Constructor for class net.maizegenetics.dna.map.PositionListTableReport
-
- positionMergeSelection() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Selection for Position Merge Rule
- positionMergeSelection(value) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Set Position Merge Rule. Selection for Position Merge Rule
- positionQualityScore() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Minimum Position Quality Score
- positionQualityScore(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Set Minimum quality score for position: This value is used to pull SNPs out of the snpposition table. Only snps with quality scores meeting or exceeding the specified value will be processed.
- positionQualityScore() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Minimum Position Quality Score
- positionQualityScore(value) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Set Minimum quality score for position: This value is used to pull SNPs out of the snpposition table. Only snps with quality scores meeting or exceeding the specified value will be processed.
- positions(positions) - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- positions(positions) - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- positions - Variable in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- positions() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- positions() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- positions() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return the position list for the genotype table.
- POSITIONS - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- positions() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- positions() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- positions(inputFileName, format, topm, taxa) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Prints the physical coordinates of the supplied taxa, as stored in the supplied TOPM file.
- POSITIONS - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- POSITIONS_SCHEMA - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- positionSourceHDF5GenoFile() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Finished (built) HDF5 (*.h5) file to be used as a PositionList source (containing a small number of [ignored] taxa)
- positionSourceHDF5GenoFile(value) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Set Position Source HDF5 Geno File. Finished (built) HDF5 (*.h5) file to be used as a PositionList source (containing a small number of [ignored] taxa)
- positionType() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
SNP Position
- positionType(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Set SNP position.
- PositionVectors(chromosomes, startPos, strand, refAllele, altAllele) - Constructor for class net.maizegenetics.plugindef.GenerateRCode.PositionVectors
-
- possibleValues(possibleValues) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- possibleValues() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- possibleValuesString(friendly) - Method in class net.maizegenetics.plugindef.PluginParameter
-
- posStartB - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- posStartContig - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- posStartF - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- postgreSQLCopyFromReader(conn, table, reader) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- postorderSuccessor(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
determine postorder successor of a node
- postProcessParameters() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- powerTransform(original) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- powerTransformation() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataDialog
-
- pPos - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Physical position of tag, unknown = Integer.MIN_VALUE
- pred - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- predecessors(n) - Method in class net.maizegenetics.util.DirectedGraph
-
Gets the predecessors of the node n
- predictedDistance - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Predicted distance (log10 value) between mapping position and true position.
- prediction - Variable in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
- predictionPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- PreferencesDialog - Class in net.maizegenetics.tassel
-
- PreferencesDialog(parentFrame, isInteractive) - Constructor for class net.maizegenetics.tassel.PreferencesDialog
-
- preferredHaplotypeSize() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Preferred haplotype block size in sites (minimum 64); will use the closest multiple of 64 at or below the supplied value
- preferredHaplotypeSize(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Preferred haplotype size. Preferred haplotype block size in sites (minimum 64); will use the closest multiple of 64 at or below the supplied value
- preferredHaplotypeSize() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Preferred haplotype block size in sites (use same as in FILLINFindHaplotypesPlugin)
- preferredHaplotypeSize(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Preferred haplotype size. Preferred haplotype block size in sites (use same as in FILLINFindHaplotypesPlugin)
- preferredHaplotypeSize() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Preferred haplotype block size in sites (use same as in FILLINFindHaplotypesPlugin)
- preferredHaplotypeSize(value) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Set Preferred haplotype size. Preferred haplotype block size in sites (use same as in FILLINFindHaplotypesPlugin)
- preFilterSites() - Method in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- preorderSuccessor(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
determine preorder successor of this node
- PreProcessGOBIIMappingFilePlugin - Class in net.maizegenetics.analysis.gobii
-
This plugin should be run prior to creating the intermediate files for marker and dnarun. There are 3 purposes to this plugin's. Using the mapping file created for the dataset: 1. Identify duplicate/missing germplasm/dnasample entries, create intermediate file for germplasm and dnasmple tables, load any missing entries. Duplicates are skipped. 2. Identify duplicate libraryPrepIds. Write a list of duplicate libraryPrepIds, write to a file. 3. Provide mapping data to load new marker/dnarun related tables. Create intermediate files, load via GOBII IFL scripts For the first 2 purposes, the database must be queried. Missing entries entries are defined as below: germplasm table: From the db,Get list of distinct MGIDs (they should all be distinct). use this list to compare to MGIDs in the file. For any MGIDs that don't appear, create a line in the *.germplasm intermediate file used to add values. dnasample table: From the db, Get a list of dnasample names. These names are a string comprised of these components: GID:plate:well. From the input file, for each entry, create a concatenanted string of GID:plate:well. compare to list from db. For any names that don't appear, create a line in the *.dnasample intermediate file for loading. This file needs the "name" field to be a concatenation of GID:plate:well as this will be unique and GOBII dnasample.dupmap looks at only the name field. Code can be MGID if we need that stored (which I think we do). It takes "external code" column instead of germplasm_id as that maps to the external_code field in the germplasm table when GOBII IFL looks to find the germplasm_id from DB. This file also needs project_name, which comes from the mapping file. dnarun table: From the db, Get a list of all dnasample.name fields. These should be distinct library prep id. Compare to libraryPrepIds from the mapping file. IF there are duplicate, write to a file to show the biologist. NOTES: GOBII uses dnasample.name and dnasample.num to determine duplicates BL is not populating dnasample.num. "num" has been removed from the dnasample.dupmap file when running this. For some reason, with it present, but all values "null", the script believed the values were different and I ended up duplicating all dnasamples when sending the file through the GOBII scripts. When I removed this line, the scripts only checked the "name" field and project id and it worked. For step 3: The intermediate files are created by the MarkerDNARunMGID_fromHMPIFIFIlePLugin.java. Note the dnasample and germplasm entries must be loaded to the db before loading the marker/ dnarun intermediate files or the necssary db ids will not be found..
- PreProcessGOBIIMappingFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
- PreProcessGOBIIMappingFilePlugin() - Constructor for class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
- preProcessParameters(data) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.SubtractGenotypesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.tassel.PreferencesDialog
-
- pres_abs_pearson() - Method in class net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
-
- previousSetBit(index) - Method in interface net.maizegenetics.util.BitSet
-
Returns the index of the previous set bit starting at the index specified. If the bit at index is set, index is returned, otherwise the next lower numbered set bit is returned. -1 is returned if there are no more set bits.
- previousSetBit(index) - Method in interface net.maizegenetics.util.BitSet
-
Returns the index of the previous set bit starting at the index specified. If the bit at index is set, index is returned, otherwise the next lower numbered set bit is returned. -1 is returned if there are no more set bits.
- previousSetBit(index) - Method in class net.maizegenetics.util.OpenBitSet
-
- previousSetBit(index) - Method in class net.maizegenetics.util.OpenBitSet
-
- previousSetBit(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- previousSetBit(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- primers() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Tab delimited file that contains the column headers chrom,forward,reverse. The values in each column are the chromosone name, the forward primer sequence and the reverse primer sequence for the specified chromosome.
- primers(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Primers. Tab delimited file that contains the column headers chrom,forward,reverse. The values in each column are the chromosone name, the forward primer sequence and the reverse primer sequence for the specified chromosome.
- prin() - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- PrincipalComponentsPlugin - Class in net.maizegenetics.analysis.data
-
- PrincipalComponentsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
- PrincipalComponentsPlugin.PCA_LIMIT - Enum in net.maizegenetics.analysis.data
-
- PrinComp - Class in net.maizegenetics.stats.PCA
-
- PrinComp(data, type) - Constructor for class net.maizegenetics.stats.PCA.PrinComp
-
The class uses singular value decomposition to find the eigenvalues, eigenvectors and principal components of either the covariance or correlation matrix of the data. If covariance, then the result is the equivalent of finding the eighvalue decomposition of XX'/(n-1) where X is the data matrix with the column means subtracted from the columns. If correlation, the column values are also scaled. That is, after the mean is subtracted, the values are divided by the standard deviation.
- PrinComp.PC_TYPE - Enum in net.maizegenetics.stats.PCA
-
- printAll(value) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- printAll() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- printAlleleStats(gt, name) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- printAvailableDatasets(connection) - Static method in class net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
-
- printBitLong(A) - Static method in class net.maizegenetics.util.BitUtil
-
- printBitMatrix(A) - Static method in class net.maizegenetics.util.BitUtil
-
- printCLUSTALW(a, out) - Static method in class net.maizegenetics.dna.snp.ExportUtils
-
Print alignment (in CLUSTAL W format)
- printCoverage(inputFileName, format, itemized) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Prints tag coverage of each taxon in the file, and taxon coverage of each tag in the file. If itemized=true, prints one record for each tag and for each taxon. Otherwise prints a summary of how many tags/taxa are in each coverage "bin" (0-10% coverage, 10-20% coverage, etc.)
- printFactors() - Method in class net.maizegenetics.analysis.gbs.neobio.FactorSequence
-
Returns a string representation of the actual list of factors produced by the LZ78 parsing of the text. Each factor is printed out in a separate line, in the order they appear in the text, with its serial number, its ancestor's serial number, its new character, length and a string representation of the factor itself.
- PrintHeapAction - Class in net.maizegenetics.gui
-
- printInterleaved(a, out) - Static method in class net.maizegenetics.dna.snp.ExportUtils
-
print alignment (in PHYLIP 3.4 INTERLEAVED format)
- printMatrix() - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
Prints the current state of the matrix (reflecting deleted rows and columns) in the standard output. It can be used internally for debugging.
- printMatrix(matrix) - Static method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
Prints the contents of an object implementing the matrix interface in the standard output. It can be used for debugging.
- printMemoryUse() - Static method in class net.maizegenetics.util.Sizeof
-
- printNH(out, node, printLengths, printInternalLabels) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
prints node in New Hamshire format.
- printNH(out, node, printLengths, printInternalLabels, column, breakLines) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
- printNH(tree, out) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
print a this tree in New Hampshire format (including distances and internal labels)
- printNH(tree, out, printLengths, printInternalLabels) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
print this tree in New Hampshire format
- printParameterValues() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- printPHYLIP(out) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
print alignment (PHYLIP format)
- printPostgreSQLResultSet(rs) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- printPostgreSQLResultSet(rs, stride) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- printPostgreSQLResultSetToFile(rs, outFile) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- printRow(row) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- printRow(row, byPosition) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- printRows(numRows) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- printRows(numRows, requirePhysPosition, byPosition) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- printRows(numRows, requirePhysPosition, printChr) - Method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- printRows(numRows) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- printSequential(a, out) - Static method in class net.maizegenetics.dna.snp.ExportUtils
-
print alignment (in PHYLIP SEQUENTIAL format)
- printSimpleSummary(input) - Static method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- printSimpleSummary(current) - Static method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- printSimpleSummary(alignment, name) - Static method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- printSumCounts(inputFileName, format, progressIndication) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Prints a list of taxa in the specified TagsByTaxa file, along with the total count of all tags found in that taxon.
- printSumCountsOfAll(directoryName, format) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Calls printSumCounts once for every file in the specified directory.
- PrintTextArea - Class in net.maizegenetics.gui
-
- PrintTextArea(frame) - Constructor for class net.maizegenetics.gui.PrintTextArea
-
- printThis(s) - Method in class net.maizegenetics.gui.PrintTextArea
-
- printTotalTagsAndTaxa(directoryName, format) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Prints a count of the total number of tags and taxa in the files contained in the specified directory.
- printWithMissing(b) - Static method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- printWithMissing(i) - Static method in class net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
-
- probabilityOfATransition - Variable in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- process(resultSet, currentRow) - Method in interface net.maizegenetics.util.db.ResultSetProcessor
-
- processData(input) - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
- processData(data) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- processData(dataset) - Method in class net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.AdjustPhasingPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
Reads a PostgreSQL query file and a genomeAnnosDB connection config file, checks that the query is a SELECT query for chr, position, etc.., executes the query and turns the results into a PositionList with any result fields other that chr & position added as annotations.
- processData(input) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
The main method. Plugin to convert genotypes to parental comparisons and store them in an output file. The user can get outputs as A/H/B, 0/1/2, or 0/0.5/1 for a genotype matching parent A's genotype, heterozygous, or parent B's genotype respectively. If the genotype is neither A or B or a het combination of A/B (B/A) then it is coded as "NA".
- processData(input) - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.GetPositionListPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.GetTaxaListPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.IdentityRecognitionPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.IndelsToUnknownPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.KmerCountingPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.LIXPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.MemoryUsagePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
- processData(input) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
Main method for this plugin.
- processData(input) - Method in class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.SubtractGenotypesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- processData(input, isUnion) - Method in class net.maizegenetics.analysis.data.UnionAlignmentPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.AMatrixPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.HMatrixPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.BinaryToTextPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.GOBIIPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.ParentPhasingPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.ListPluginParameters
-
- processData(input) - Method in class net.maizegenetics.analysis.ListPlugins
-
- processData(input) - Method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.numericaltransform.ImputationPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.tree.MergeTreesPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- processData(input) - Method in class net.maizegenetics.analysis.workflow.WorkflowPlugin
-
- processData(input) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- processData(input) - Method in interface net.maizegenetics.plugindef.Plugin
-
For the new Generic Plugin Parameter design, performFunction() will automatically call this. Therefore, coders of Plugins should override this instead of performFunction().
- processData(input) - Method in class net.maizegenetics.tassel.PreferencesDialog
-
- processData(input) - Method in class net.maizegenetics.tassel.ShowParameterCachePlugin
-
- processData(input) - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- processDataforCrossValidation(reducedPheno, kinshipOriginal, inputPhenotypeName) - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- processDataforPrediction(myPhenotype, kinshipMatrix, inputPhenotypeName) - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
- processDatum(input) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- processedLines() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- processedSequence - Variable in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
Processed sequence with barcode removed
- processedSequence - Variable in class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
- processFastQFile(keyPath, fastQPath, enzymeName, masterTaxaList, taxaFileMap, outputDir, projectName, keyFormatIsNew) - Static method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- ProcessLines(headerLines) - Constructor for class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- ProcessLines(lineNum, lines) - Constructor for class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- ProcessLines() - Constructor for class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- processWindowEvent(e) - Method in class net.maizegenetics.tassel.AboutBox
-
- ProductionPipeline - Class in net.maizegenetics.analysis.gbs
-
- ProductionPipeline(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.ProductionPipeline
-
- ProductionPipelineMain - Class in net.maizegenetics.analysis.gbs
-
This class is for running the GBS Production Pipeline. It is to be run from within the sTASSEL.jar. The cron job should be set up to run the run_pipeline.pl which has been modified to make this class the main() to be run. The JVM memory settings within run_pipeline.pl should also be adjusted upwards. cron example 20 3 * * * cd /workdir/tassel/tassel4-src && /usr/local/bin/perl /workdir/tassel/tassel4-src/run_prod_cron.pl >> /workdir/tassel/tassel4-src/20130808_cron.log 2>&1 20130718 Note from Jeff Glaubitz: A minor detail: ProductionSNPCallerPlugin needs the key file name to end with "_key.txt". All the output files are named after the key file but replacing "_key.txt" with the appropriate extension. User: dkroon Date: 4/8/13
- ProductionPipelineMain(appPropertiesFile, runCheckSum, runImputation, testingCheckSum) - Constructor for class net.maizegenetics.analysis.gbs.ProductionPipelineMain
-
- ProductionSNPCallerPlugin - Class in net.maizegenetics.analysis.gbs
-
This plugin converts all of the fastq (and/or qseq) files in the input folder and keyfile to genotypes and adds these to a genotype file in HDF5 format. We refer to this step as the "Production Pipeline". The output format is HDF5 genotypes with allelic depth stored. SNP calling is quantitative with the option of using either the Glaubitz/Buckler binomial method (pHet/pErr > 1 = het) (=default), or the Stacks method. Merging of samples with the same LibraryPrepID is handled by GenotypeTableBuilder.addTaxon(), with the genotypes re-called based upon the new depths. Therefore, if you want to keep adding genotypes to the same target HDF5 file in subsequent runs, use the -ko (keep open) option so that the output GenotypeTableBuilder will be mutable, using closeUnfinished() rather than build(). If the target output HDF5 GenotypeTable file doesn't exist, it will be created. Each taxon in the HDF5 file is named "ShortName:LibraryPrepID" and is annotated with "Flowcell_Lanes" (=source seq data for current genotype). Requires a TOPM with variants added from a previous "Discovery Pipeline" run. In binary topm or HDF5 format (TOPMInterface). TODO add the Stacks likelihood method to BasicGenotypeMergeRule
- ProductionSNPCallerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- ProductionSNPCallerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- ProductionSNPCallerPluginV2 - Class in net.maizegenetics.analysis.gbs.v2
-
This plugin converts all of the fastq (and/or qseq) files in the input folder and keyfile to genotypes and adds these to a genotype file in HDF5 format. We refer to this step as the "Production Pipeline". The output format is either HDF5 or VCF genotypes with allelic depth stored. Output file type is determined by presence of the ".h5" suffix. SNP calling is quantitative with the option of using either the Glaubitz/Buckler binomial method (pHet/pErr > 1 = het) (=default), or the Stacks method. Merging of samples with the same LibraryPrepID is handled by GenotypeTableBuilder.addTaxon(), with the genotypes re-called based upon the new depths. Therefore, if you want to keep adding genotypes to the same target HDF5 file in subsequent runs, use the -ko (keep open) option so that the output GenotypeTableBuilder will be mutable, using closeUnfinished() rather than build(). If the target output is HDF5, and that GenotypeTable file doesn't exist, it will be created. Each taxon in the output file is named "ShortName:LibraryPrepID" and is annotated with "Flowcell_Lanes" (=source seq data for current genotype). Requires a database with variants added from a previous "Discovery Pipeline" run. References to "tag" are being replaced by references to "kmer" as the pipeline is really a kmer alignment process. TODO add the Stacks likelihood method to BasicGenotypeMergeRule
- ProductionSNPCallerPluginV2() - Constructor for class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- ProductionSNPCallerPluginV2(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- productionTOPM() - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
Physical map file containing tags and corresponding variants (production TOPM)
- productionTOPM(value) - Method in class net.maizegenetics.analysis.gbs.ProductionPipeline
-
Set Production T O P M. Physical map file containing tags and corresponding variants (production TOPM)
- progenyFile() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
The input file containing the progeny states (parentcalls). Needed for rephasing using haplotype probabilities or for writing breakpoints.
- progenyFile(value) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
Set Progeny States Input File. The input file containing the progeny states (parentcalls). Needed for rephasing using haplotype probabilities or for writing breakpoints.
- progenyStates(gt) - Static method in class net.maizegenetics.analysis.imputation.RephaseParents
-
- progress(event) - Method in class net.maizegenetics.pipeline.TasselPipeline
-
Returns progress of execution.
- progress(event) - Method in class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- progress(event) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
No operation for this abstract class.
- progress(percent, meta) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- progress(event) - Method in class net.maizegenetics.plugindef.DefaultPluginListener
-
- progress(event) - Method in interface net.maizegenetics.plugindef.PluginListener
-
Returns progress of execution.
- progress(event) - Method in class net.maizegenetics.progress.PluginProgressUnit
-
- progress(event) - Method in class net.maizegenetics.tassel.DataTreePanel
-
Returns progress of execution.
- progress(percent, meta) - Method in interface net.maizegenetics.util.ProgressListener
-
Returns progress of execution.
- progressListener(listener) - Method in class net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
-
- ProgressListener - Interface in net.maizegenetics.util
-
- ProgressPanel - Class in net.maizegenetics.progress
-
- ProjectionBuilder - Class in net.maizegenetics.dna.snp
-
Builder for a projection alignment. Projection alignments use defined haplotypes and breakpoints that point to high density genotypes (base GenotypeTable). These are used to efficiently store and connect low density maps with imputed high density genotypes.
- ProjectionBuilder(myBaseAlignment) - Constructor for class net.maizegenetics.dna.snp.ProjectionBuilder
-
- ProjectionGenotypeCallTable - Class in net.maizegenetics.dna.snp.genotypecall
-
Projection genotype use defined haplotypes and breakpoints that point to a high density genotypes (base GenotypeTable). These are used to efficiently store and connect low density maps with imputed high density genotypes.
- ProjectionGenotypeCallTable(hdAlign, allBreakPoints) - Constructor for class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- ProjectionGenotypeIO - Class in net.maizegenetics.dna.snp.io
-
Methods for reading and writing ProjectionGenotypes to files. ProjectionGenotypes have two parts - one is the Projection file that has the names of high density genotyped taxa and the recombination breakpoints for each of the low density taxa that point to the high density taxa.
- ProjectionLoadPlugin - Class in net.maizegenetics.analysis.data
-
- ProjectionLoadPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Creates a new instance of ProjectionLoadPlugin
- projectName() - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
Name for this project. Project name becomes part of the newly created fastq file name
- projectName(value) - Method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
Set Project File. Name for this project. Project name becomes part of the newly created fastq file name
- ProjectPcsAndRunModelSelectionPlugin - Class in net.maizegenetics.analysis.data
-
- ProjectPcsAndRunModelSelectionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Creates a new instance of ProjectPcsAndRunModelSelectionLPlugin
- projectPCsOntoNAMFounders(theAlignmentForGenotype, PCResults, chrVector, posVector, theGenotypesForCalculatingPCs, chr) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
- proportionHeterozygous(counts, totalCount) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- proportionHeterozygous(data) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- proportionHeterozygous() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- proportionOfDepthGenotypesToMask() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Proportion of genotypes of given depth to mask for accuracy calculation if depth available
- proportionOfDepthGenotypesToMask(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Proportion of depth genotypes to mask. Proportion of genotypes of given depth to mask for accuracy calculation if depth available
- proportionOfGenotypesToMaskIfNoDepth() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Proportion of genotypes to mask for accuracy calculation if depth not available
- proportionOfGenotypesToMaskIfNoDepth(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Proportion of genotypes to mask if no depth. Proportion of genotypes to mask for accuracy calculation if depth not available
- put(key, value) - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordChromosome
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordChromosome
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotype
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordPosition
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordPosition
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordTaxon
-
- put(arg0, arg1) - Method in class net.maizegenetics.analysis.avro.GenericRecordTaxon
-
- putAlignmentRetainRareAlleles(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putAll(m) - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- putAllelePairs(tagTagAlignMap) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Adds entries to the allelepair table
- putAllelePairs(tagTagAlignMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putAllNamesTag(tagNameMap) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Add a tag to list of known tags with their associated names (good for named contigs)
- putAllNamesTag(tagNameMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putAllNamesTag(tagNameMap) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putAllNamesTag(tagNameMap) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Add a tag to list of known tags with their associated names (good for named contigs)
- putAllRefTag(refTagPositionMap, refGenome) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Add a reference tag to list of known reference tags
- putAllRefTag(refTagPositionMap, refGenome) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putAllTag(tags, tagInstanceAverageQS) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Add a tag to list of known tags
- putAllTag(tags, tagInstanceAverageQS) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putAllTag(tags) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putAllTag(tags) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Add a tag to list of known tags
- putAllTissue(tissues) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putAllTissue(masterTissueList) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Adds list of tissues to the tissue table
- putBMSDB(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putBMSHost(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putBMSUser(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putBooleanPref(path, key, value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putConfigFile(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putDoublePref(path, key, value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putExportPluginExportDiploids(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putExportPluginIncludeTaxaAnnotations(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putFilterAlignPluginMaxFreq(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putFilterAlignPluginMinCount(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putFilterAlignPluginMinFreq(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putFilterTaxaPropsMaxHetFreq(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putFilterTaxaPropsMinHetFreq(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putFilterTaxaPropsMinNotMissingFreq(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putGOBIIDB(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putGOBIIUser(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putIntPref(path, key, value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putLocale(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putLogDebug(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putLogSendToConsole(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putLogXDim(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putLogYDim(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putMaxThreads(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putOpenDir(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putPref(path, key, value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putRefRefAlignments(tagAlignInfoMap, refGenome) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Adds entries to the tagAlignments table for ref-ref alignments
- putRefRefAlignments(tagAlignInfoMap, refGenome) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putRefTagMapping(tagAnnotatedPositionMap, refGenome) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Associates the specified Reference Tag with the specified site Position (value).
- putRefTagMapping(refTagPositionMap, refGenome) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putSaveDir(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putSNPPositionQS(qsPosL) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Stores a quality position in the snpposition table for each chromosome/position
- putSNPPositionQS(qsPL) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putSNPPositionQS(qsPL) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putSNPPositionQS(qsPosL) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Stores a quality position in the snpposition table for each chromosome/position
- putSNPQualityProfile(tagAnnotatedPositionMap, taxaSubset) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putSNPQualityProfile(tagAnnotatedPositionMap, taxaSubset, counter) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putSNPQualityProfile(tagAnnotatedPositionMap, taxaSubset) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putSNPQualityProfile(tagAnnotatedPositionMap, taxaSubset, counter) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTagAlignmentApproach(tagAlignmentName, protocol) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
- putTagAlignmentApproach(tagAlignmentName, protocol) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTagAlignmentApproach(tagAlignmentName, protocol) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTagAlignmentApproach(tagAlignmentName, protocol) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
- putTagAlignments(tagAnnotatedPositionMap) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTagAlignments(tagAnnotatedPositionMap) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Associates the specified Tag (key) with the specified cut site Position (value). Multiple associations are allowed, as Tags can map to multiple locations. Each tag should only have one best annotation.
- putTagAlleles(tagAlleleMap) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
- putTagAlleles(tagAlleleMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTagAlleles(tagAlleleMap) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTagAlleles(tagAlleleMap) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
- putTagRefTagAlignments(tagAlignInfoMap, refGenome) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Stores the Smith Waterman score from2 tag alignments. tag2 chrom/pos comes from the AlignmentInfo object. tag1 chrom/pos are separate parameters
- putTagRefTagAlignments(tagAlignInfoMap, refGenome) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTagTagAlignments(tagAlignInfoMap) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Stores the Smith Waterman score from2 tag alignments. tag2 chrom/pos comes from the AlignmentInfo object. tag1 chrom/pos are separate parameters
- putTagTagAlignments(tagAlignInfoMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTagTagCorrelationMatrix(tagCorrelationMap) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Adds entries to the tagCorrelations table for tag-tag correlation data
- putTagTagCorrelationMatrix(tagCorrelationMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTaxaDistribution(tagTaxaDistributionMap) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
Associates a map full of the specified Tag (key) with the specified TaxaDistribution (value). If there was a prior association is it replaced, as all pairs are unique.
- putTaxaDistribution(tagTaxaDistributionMap) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTaxaDistribution(tagTaxaDistributionMap) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTaxaDistribution(tagTaxaDistributionMap) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Associates a map full of the specified Tag (key) with the specified TaxaDistribution (value). If there was a prior association is it replaced, as all pairs are unique.
- putTaxaList(taxaList) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
- putTaxaList(taxaList) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- putTaxaList(taxaList) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTaxaList(taxaList) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
- putTaxaTissueDistribution(taxon, tissue, tags, counts) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- putTaxaTissueDistribution(taxon, tissue, tags, counts) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
Set distribution of taxa/tissue for each tag
- putXDim(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- putYDim(value) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
- r2() - Method in class net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
-
- r2(value) - Method in class net.maizegenetics.analysis.popgen.LDResult.Builder
-
- r2() - Method in class net.maizegenetics.analysis.popgen.LDResult
-
- RampSeqAlignFromBlastTags - Class in net.maizegenetics.analysis.gbs.repgen
-
This class takes a rAmpSeq database populated with tags,a reference Genome, a filtered BLAST file output and primers, then: (1) creates reference tags using the blast alignment output (2) runs tag/tag alignment for each tag in the DB, (3) runs tag/refTag alignment for each tag against each ref tag (4) runs refTag/refTag alignment for each refTag in the DB> (5) all alignments are stored in the db tagAlignments table. Alignments are performed and stored in groups to prevent overwhelming the DB with massive load commands. Blast was run on CBSU using these parameters: Make the reference files: makeblastdb -dbtype nucl -in -parse_seqids -out maizeAGPV4.db Run blast using maizeAGPV4.db from command above: blastn -num_threads 24 -db maizeAGPV4.db -query anp68R1Tags.fasta -evalue 1e-60 -max_target_seqs 5 -max_hsps 1 -outfmt 6 -out anp68TagsR1Result/blastANP68_R1.txt The blast output file was filtered using the 3 commands below. The first filters identity down to 98 %, the second gets alignment lengths that were at least 148, the 3rd filters it down to just the chrom, start, end positions: awk '$3 >= 98.000 {print $0}' blastANP68_R1.txt > blastANP68_R1_98per.txt awk '$4 >= 148 {print $0}' blastANP68_R1_98per.txt > blastANP68_R1_98per_148align.txt awk {'printf ("%s\t%s\t%s\n", $2, $9, $10)'} blastANP68_R1_98per_148align.txt > blastANP68_R1_98per_148align_3cols.txt It is the last file from awk, blastANP68_R1_98per_148align_3cols.txt, that is given as a parameter here.
- RampSeqAlignFromBlastTags() - Constructor for class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- RampSeqAlignFromBlastTags(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- RampSeqAlignFromBlastTags(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
- rand - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- randomComparator() - Static method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- RandomGenotypeImputationPlugin - Class in net.maizegenetics.analysis.imputation
-
- RandomGenotypeImputationPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
-
- randomiseParameters() - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- randomSeed - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- randomSeed() - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
Random Seed
- randomSeed(value) - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
Set Random Seed. Random Seed
- randomSeed() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Random Seed
- randomSeed(value) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Set Random Seed. Random Seed
- range() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'
- range(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set Range information?. Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'
- range() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'
- range(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set Range information?. Columns for range data. If true, will look for 'start' and 'end' (inclusive exclusive) or 'first' 'last' (inclusive inclusive) instead of 'Pos'
- range(start, end, base, numBaseIndices) - Static method in class net.maizegenetics.dna.snp.TranslateIndexBuilder
-
Keeps a range of indices from start (inclusive) to end (inclusive)
- range(range) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- range(values) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- rangeToString() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- rangeToString(friendly) - Method in class net.maizegenetics.plugindef.PluginParameter
-
- RARE_ALLELE - Static variable in interface net.maizegenetics.dna.snp.GenotypeTable
-
This encoding is used to lump together allele values with frequencies too low to be retained as one of the maximum number of alleles.
- RARE_ALLELE_STR - Static variable in interface net.maizegenetics.dna.snp.GenotypeTable
-
- RARE_DIPLOID_ALLELE - Static variable in interface net.maizegenetics.dna.snp.GenotypeTable
-
- rawData(value) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- rawData() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- rawHDF5GenotypeFile() - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Input, unfinished HDF5 (*.h5) file containing raw (unimputed) genotypes
- rawHDF5GenotypeFile(value) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Set Raw HDF5 Genotype File. Input, unfinished HDF5 (*.h5) file containing raw (unimputed) genotypes
- rawSeqFileNameRegex - Static variable in class net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
-
- Read - Class in net.maizegenetics.dna.read
-
Class holding reads of Fastq format.
- Read(ID, seq, des, qual) - Constructor for class net.maizegenetics.dna.read.Read
-
- read(filename) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a Genotype Table.
- read(filename, keepDepth, sortPositions) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a Genotype Table.
- read(vcf) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
-
- read(header, variants) - Static method in class net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
-
- read(filename, keepDepth, sortPositions) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
- read(filename) - Static method in class net.maizegenetics.taxa.tree.NewickUtils
-
Creates a Tree from the given newick formatted file
- read(inputBuffer, inputBufferOffset, inputBufferLen) - Method in class net.maizegenetics.util.MultiMemberGZIPInputStream
-
- readAllFastQBlock(bw, currentRead) - Static method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- ReadBarcodeResult - Class in net.maizegenetics.analysis.gbs
-
Container class for returning the results of parsed barcoded sequencing read.
- ReadBarcodeResult(read, length, taxon, taxonIndex) - Constructor for class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
- ReadBarcodeResult(sequence) - Constructor for class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
- readBasicAlignments(input, maxLabelLength) - Static method in class net.maizegenetics.dna.snp.ReadSequenceAlignmentUtils
-
read from stream, while letting the user set the maximum label (taxa) label length as non-standard phylip formats now exist
- readBasicAlignments(file, maxLabelLength) - Static method in class net.maizegenetics.dna.snp.ReadSequenceAlignmentUtils
-
read from file, while letting the user set the maximum label (taxa) label length as non-standard phylip formats now exist
- ReadBedfile - Class in net.maizegenetics.dna.snp.io
-
- ReadBedfile.BedFileRange - Class in net.maizegenetics.dna.snp.io
-
- readBinaryFile(inputFileS) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- readBinaryFile(infileS) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
read from a file
- readBinaryFile(currentFile) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- readBinaryTagCountFile(inFile) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- readBinMultiBlupCounts(filename, builder) - Static method in class net.maizegenetics.taxa.distance.ReadDistanceMatrix
-
- readBinMultiBlupID(filename) - Static method in class net.maizegenetics.taxa.distance.ReadDistanceMatrix
-
- readBinMultiBlupMatrix(filename) - Static method in class net.maizegenetics.taxa.distance.ReadDistanceMatrix
-
- readBlock(blockIndex) - Method in class net.maizegenetics.dna.map.TagGWASMap
-
- readBlock(blockIndex) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Read in a block from HDF5 file
- readChannel(inFile) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- readCluster(infileS, binary) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- readCount - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Tag count in master tagCount file, unknown = Integer.MIN_VALUE
- readDataSet(filename) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a DataSet.
- readDelimitedTableReport(saveFile, delimit) - Static method in class net.maizegenetics.util.TableReportUtils
-
- readDeMultiPlexFastQBlock(bw, currentRead) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Method for reading FastQ four line structure, and returning a string array with [sequence, qualityScore]
- readDigestPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- readDirectory(path) - Static method in class net.maizegenetics.util.Utils
-
- ReadDistanceMatrix - Class in net.maizegenetics.taxa.distance
-
- readDistanceMatrix(filename) - Static method in class net.maizegenetics.taxa.distance.ReadDistanceMatrix
-
- readDistFile(infileS, format) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMap
-
- readDistFile(infileS, format) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Read tagsOnGeneticMap file
- readDistFile(inFile, numberType) - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- readDistFile(infileS, format) - Method in class net.maizegenetics.dna.tag.PETagCounts
-
Read PETagCounts file
- readDistFile(infile, binary) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- readDistFile(inFile, binary) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- readDistFile(inFile, binary) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- readDouble(in) - Method in class net.maizegenetics.util.FormattedInput
-
read next number from stream and convert it to a double (newline/cr are treated as separators)
- readDouble(in, ignoreNewlineCR) - Method in class net.maizegenetics.util.FormattedInput
-
read next number from stream and convert it to a double
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- readEndCutSiteRemnantLength() - Method in class net.maizegenetics.analysis.gbs.v2.GBSEnzyme
-
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- readEndCutSiteRemnantLength - Static variable in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- readFasta(filename) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readFastQBlock(bw, currentRead) - Static method in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
Method for reading FastQ four line structure, and returning a string array with [sequence, qualityScore]
- readFromHapmap(filename) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
Read GenotypeTable from HapMap file
- readFromHapmap(filename, listener) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
Read GenotypeTable from HapMap file
- readFromHapmap(filename, listener, sortPositions) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
Read GenotypeTable from HapMap file
- readFromPLink(pedFilename, mapFilename, listener) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readFromPLink(pedFilename, mapFilename, listener, sortPositions) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readFromVCF(filename, listener, keepDepth, sortPositions) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readFromVCF(filename, listener, keepDepth) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readFromVCF(filename, listener) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readFromVCF(filename) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
- readGuessFormat(fileName) - Static method in class net.maizegenetics.dna.snp.ImportUtils
-
Deprecated.
- readH5File(inputFileS) - Method in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- readHDF5(hdf5FileS) - Method in class net.maizegenetics.dna.map.TagGWASMap
-
- readHDF5(hdf5FileS) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
Read in HDF5 file
- readHDF5Annotation(reader, path) - Static method in class net.maizegenetics.util.HDF5Utils
-
- readHDF5Annotation(reader, path, annotationKeys) - Static method in class net.maizegenetics.util.HDF5Utils
-
- readIndex(idxFilename) - Static method in class net.maizegenetics.dna.snp.io.LineIndexBuilder
-
- readInt(in) - Method in class net.maizegenetics.util.FormattedInput
-
read next number from stream and convert it to a int (newline/cr are treated as separators)
- readInt(in, ignoreNewlineCR) - Method in class net.maizegenetics.util.FormattedInput
-
read next number from stream and convert it to a int
- readLabel(in, maxLength) - Method in class net.maizegenetics.util.FormattedInput
-
read sequence label from stream A sequence label is not allowed to contain whitespace and either of :,;()[]{}. Note that newline/cr is NOT counted as white space!!
- readLine(in, keepWhiteSpace) - Method in class net.maizegenetics.util.FormattedInput
-
read a whole line
- readLineSkipComments(br) - Static method in class net.maizegenetics.util.Utils
-
- readNextChar(input) - Method in class net.maizegenetics.util.FormattedInput
-
read next character from stream (EOF does not count as character but will throw exception)
- readNextLine(reader, inFile) - Static method in class net.maizegenetics.analysis.gobii.GOBIIDbUtils
-
- readNumber(in, ignoreNewlineCR) - Method in class net.maizegenetics.util.FormattedInput
-
- readNumericMarkerFile(inputFile) - Static method in class net.maizegenetics.dna.snp.io.ReadNumericMarkerUtils
-
- ReadNumericMarkerUtils - Class in net.maizegenetics.dna.snp.io
-
- readOldFormatKeyFile(fileName, filters, mergeSameNames) - Static method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- readOldTaxaAnnotationFile(fileName, filters, mergeSameNames) - Static method in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- readPedigreeFile(popFilename) - Static method in class net.maizegenetics.analysis.imputation.PopulationData
-
- readPedigreeFile(popFilename, chrname, includeParents) - Static method in class net.maizegenetics.analysis.imputation.PopulationData
-
- readQualityScoreFile(fileName) - Static method in class net.maizegenetics.dna.map.PositionListIOUtils
-
Returns a PositionList from a tab-delimited text SNP Quality Score file. The input file has 3 tab-delimited fields indicating Chromosome Number and Quality Score Position A header row is the first line and looks like this: CHROM POS QUALITYSCORE The remaining rows contains integer values as below: 9 18234 15.5 NOTE: the CHROM field is a string.
- readReferenceGenomeChr(fastaFileName, charConversion) - Static method in class net.maizegenetics.dna.map.GenomeSequenceBuilder
-
- Reads - Interface in net.maizegenetics.dna.tag
-
Basic methods for working with nextgen reads
- readSAMFile(topm, inputFileName, tagLengthInLong) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
Reads SAM files output from bowtie2
- readSAMFile(inputFileName, tagLengthInLong) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
Reads SAM files output from BWA or bowtie2
- ReadsByTaxa - Class in net.maizegenetics.dna.tag
-
- ReadsByTaxa() - Constructor for class net.maizegenetics.dna.tag.ReadsByTaxa
-
- ReadsByTaxa(infile, binary) - Constructor for class net.maizegenetics.dna.tag.ReadsByTaxa
-
- ReadsByTaxa(taxaNames, theDistinctReads) - Constructor for class net.maizegenetics.dna.tag.ReadsByTaxa
-
- ReadsByTaxa(reads, readDist, namesForTaxa) - Constructor for class net.maizegenetics.dna.tag.ReadsByTaxa
-
- ReadSequenceAlignmentUtils - Class in net.maizegenetics.dna.snp
-
reads aligned sequence data from plain text files.
- readSiteStore(filename) - Static method in class net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
-
- readSNPConserveFile(fileName) - Static method in class net.maizegenetics.dna.map.PositionListIOUtils
-
Returns a PositionList from a tab-delimited text SNP Conserve file. The input file has 2 tab-delimited fields indicating Chromosome Number and Position A header row is the first line and looks like this: #CHROM POS The remaining rows contains integer values as below: 9 18234
- readTableReport(saveFile) - Static method in class net.maizegenetics.util.TableReportBuilder
-
- readTagBlockPostition(blockFileS) - Method in class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- readTagPair(infileS) - Method in class net.maizegenetics.dna.tag.UTagPairs
-
- readTaxaAnnotationFile(fileName, taxaNameField, filters, mergeSameNames) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Returns an annotated TaxaList from a text annotation file in matrix format. This is a tab delimited file. First row in the file with the field taxaNameField is the header row. taxaNameField indicated the taxon name, all other fields are user defined. The fields become the keys for the taxa annotation. Quantitative fields should be tagged with "#" sign, e.g. <#INBREEDF>. Multiple values are supported per key, and additional values can be either described with an additional column or ";" to delimit values with the same key.
- readTaxaAnnotationFile(fileName, taxaNameField) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Returns an annotated TaxaList from a text annotation file in matrix format. This is a tab delimited file. First row in the file with the field taxaNameField is the header row. taxaNameField indicated the taxon name, all other fields are user defined. The fields become the keys for the taxa annotation. Quantitative fields should be tagged with "#" sign, e.g. <#INBREEDF>. Multiple values are supported per key, and additional values can be either described with an additional column or ";" to delimit values with the same key.
- readTaxaAnnotationFileAL(fileName, taxaNameField, filters) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
- readTaxaFsFromFile(pedigreeFile) - Static method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- readTBTFile(inFile) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
Converts a TBT Bit file to a ReadsByTaxa object (for compatibility only).
- readTextFile(inFile) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- readTissueAnnotationFile(fileName, tissueNameField) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
This method takes a key file and creates a SortedSet that contains a set of the tissue values. The set will be null if no tissues are present
- readTOPM(filename) - Static method in class net.maizegenetics.dna.map.TOPMUtils
-
This reads in a TOPM file. It can be .topm.txt, .topm.bin, or .topm.h5.
- ReadUtils - Class in net.maizegenetics.dna.read
-
- ReadUtils.ReadFormat - Enum in net.maizegenetics.dna.read
-
- readWord(in) - Method in class net.maizegenetics.util.FormattedInput
-
read word from stream
- readXMLAsArgs(filename) - Static method in class net.maizegenetics.pipeline.TasselPipelineXMLUtil
-
- readXMLAsArgsFromResource(filename) - Static method in class net.maizegenetics.pipeline.TasselPipelineXMLUtil
-
- readZipFile(path) - Static method in class net.maizegenetics.util.Utils
-
- recalculateScores() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
Recalculates the scores of the clusters in the cluster list. Removes any clusters with a score of 0.
- receiveDataSetFrom(plugin) - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
Add given plugin as source to receive data sets iteratively.
- receiveDataSetOnceFrom(plugin) - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
Add given plugin as source to receive data sets only once and use that data set in every resulting output.
- receiveInput(input) - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
Sets up this plugin to receive input from another plugin.
- receiveInput(input) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
Sets up this plugin to receive input from another plugin.
- receiveInput(input) - Method in interface net.maizegenetics.plugindef.Plugin
-
Sets up this plugin to receive input from another plugin.
- reciprocate() - Method in class net.maizegenetics.analysis.gbs.UNetworkFilter
-
- recombinationBreakpoints() - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Recombination Breakpoints
- recombinationBreakpoints(value) - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Set Recombination Breakpoints. Recombination Breakpoints
- recombinationBreakpoints() - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Recombination Breakpoints
- recombinationBreakpoints(value) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Set Recombination Breakpoints. Recombination Breakpoints
- recursiveRead(file, startIndex, packages) - Static method in class net.maizegenetics.util.Utils
-
- reduce() - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
This method is the key component of the SMAWK algorithm. It reduces an n x m matrix (n rows and m columns), where n >= m, to an n x n matrix by deleting m - n rows that are guaranteed to have no maximum value for any column. The result is an squared submatrix matrix that contains, for each column c, the row that has the maximum value of c in the original matrix. The rows are deleted with the deleteRowmethod.
- reduce(suffix) - Method in interface net.maizegenetics.util.db.DBTuple
-
- reduceMaskTo(percent) - Method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- REF_ALLELE - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- REF_ALLELES - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- ref_genome() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- ref_strand() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- refAllele - Variable in class net.maizegenetics.plugindef.GenerateRCode.PositionVectors
-
- refAlleleFromChromPos(refChromBytes, allelePos) - Static method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryUtils
-
- refDir() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Directory holding files that contain all the SNP physical positions, separated by chr
- refDir(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
-
Set refDir. Directory holding files that contain all the SNP physical positions, separated by chr
- reference() - Method in class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
Input Reference Fasta
- reference(value) - Method in class net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
-
Set Reference. Input Reference Fasta
- reference() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- reference() - Method in class net.maizegenetics.dna.tag.TagBuilder
-
- referenceAllele(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- referenceAllele(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- referenceAllele(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return (haploid) reference allele value at given site.
- referenceAllele(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- referenceAllele(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- referenceAlleleForAllSites() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- referenceAlleleForAllSites() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- referenceAlleleForAllSites() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns (haploid) reference alleles for all sites.
- referenceAlleleForAllSites() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- referenceAlleleForAllSites() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- referenceAlleles(startSite, endSite) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- referenceAlleles(startSite, endSite) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- referenceAlleles(startSite, endSite) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns (haploid) reference alleles in specified range. End site not included.
- referenceAlleles(startSite, endSite) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- referenceAlleles(startSite, endSite) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- referenceGenomeFile() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
Reference genome file in fasta format
- referenceGenomeFile(value) - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
Set Reference Genome File. Reference genome file in fasta format
- referenceGenomeFile() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
- referenceGenomeFile(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Reference Genome File. Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
- referenceGenomeFile() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
- referenceGenomeFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Reference Genome File. Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
- referenceGenomeVersion() - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
Version of the reference genome
- referenceGenomeVersion(value) - Method in class net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
-
Set Reference Genome Version. Version of the reference genome
- referenceProb(site) - Method in class net.maizegenetics.phenotype.GenotypePhenotype
-
- referenceProbability() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- referenceProbability(taxon, site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- referenceProbability() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- referenceProbability(taxon, site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- referenceProbability() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns reference probability object (null if not present)
- referenceProbability(taxon, site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
- referenceProbability() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- referenceProbability(taxon, site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- ReferenceProbability - Class in net.maizegenetics.dna.snp.score
-
- referenceProbability() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- referenceProbability(taxon, site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- ReferenceProbabilityBuilder - Class in net.maizegenetics.dna.snp.score
-
- ReferenceProbabilityFELM - Class in net.maizegenetics.analysis.association
-
- ReferenceProbabilityFELM(data, parentPlugin) - Constructor for class net.maizegenetics.analysis.association.ReferenceProbabilityFELM
-
- refFile() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Species reference file used to determine ref allele at marker position
- refFile(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set Reference File. Species reference file used to determine ref allele at marker position
- refFile() - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Link to maize reference file.
- refFile(value) - Method in class net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
-
Set refFile.
- refGenome() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Referemce Genome File for aligning against
- refGenome(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Reference Genome File. Referemce Genome File for aligning against
- refGenome() - Method in class net.maizegenetics.analysis.gbs.repgen.RefTagData
-
- refGenome() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Output fastq file to use as input for BWA or bowtie2
- refGenome(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Output File. Output fastq file to use as input for BWA or bowtie2
- refGenome() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Output fastq file to use as input for BWA or bowtie2
- refGenome(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Output File. Output fastq file to use as input for BWA or bowtie2
- refKmerLen() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Length of kmers as tag sequences in the db
- refKmerLen(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Kmer length. Length of kmers to be stored as tag sequences in the db
- refKmerLen() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Length of kmers as tag sequences in the db
- refKmerLen(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Kmer length. Length of kmers to be stored as tag sequences in the db
- refName() - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Name of referenece, e.g agpv2. Must match name from entry in reference table in db.
- refName(value) - Method in class net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
-
Set Reference Name. Name of referenece, e.g agpv2. Must match name from entry in reference table in db.
- RefProbAdditiveSite - Class in net.maizegenetics.analysis.modelfitter
-
An AdditiveSite that takes a float[] valued covariate as an argument. The covariate should equal the probability that a given allele (major or minor, for example) would be selected at random from that site. It also stores the value of a statistic determined by selectionCriteria which results from fitting a linear model.
- RefProbAdditiveSite(site, chr, pos, id, selectionCriteria, covariate) - Constructor for class net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
-
- RefTagData - Class in net.maizegenetics.analysis.gbs.repgen
-
Class needed for storing reference tags into RepGen SQLite tables
- RefTagData(myTag, chromosome, position, refGenome) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RefTagData
-
- registerConversion(source, target, transformer) - Static method in class net.maizegenetics.util.db.TransformerService
-
- RegRidgeEmmaDoubleMatrix - Class in net.maizegenetics.analysis.association
-
- RegRidgeEmmaDoubleMatrix(phenotype, fixedEffects, genotypes, type) - Constructor for class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
Constructor using native double arrays. Need to specify DoubleMatrix FactoryType
- RegRidgeEmmaDoubleMatrix(phenotype, fixedEffects, genotypes) - Constructor for class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
Constructor using Tassel DoubleMatrix.
- RegRidgeEmmaDoubleMatrix(phenotype, fixedEffects, genotypes, kinship) - Constructor for class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
Constructor using Tassel DoubleMatrix. Use when kinship matrix from markers has already been calculated (XXt).
- ReImputeUpdatedTaxaByFILLINPlugin - Class in net.maizegenetics.analysis.imputation
-
Compares an unfinished HDF5 file containing raw genotypes to a corresponding unfinished HDF5 file containing FILLIN-imputed genotypes to find new taxa (or taxa with additional depth) in the raw geno file, then imputes (or reimputes) these with FILLIN and adds them to (or replaces them in) the imputed geno file. This is part of the Automated Production Pipeline.
- ReImputeUpdatedTaxaByFILLINPlugin() - Constructor for class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- ReImputeUpdatedTaxaByFILLINPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
- reindexTaxa(taxaIndex, uniqueTaxa) - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
This method re-indexes the taxa in the additive site so that the returned covariate will match the taxon order in the target phenotype
- reindexTaxa(taxaIndex, uniqueTaxa) - Method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- reindexTaxa(taxaIndex, uniqueTaxa) - Method in class net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
-
- remove(o) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- remove(index) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- remove(o) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- remove(index) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- remove(key) - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- remove(hap) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- remove(o) - Method in class net.maizegenetics.dna.snp.FilterList
-
- remove(index) - Method in class net.maizegenetics.dna.snp.FilterList
-
- remove(index) - Method in class net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
-
- remove(other) - Method in interface net.maizegenetics.util.BitSet
-
Remove all elements set in other. this = this AND_NOT other
- remove(other) - Method in class net.maizegenetics.util.OpenBitSet
-
Remove all elements set in other. this = this AND_NOT other
- remove() - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedIterator
-
- remove(o) - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- remove(other) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- removeAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- removeAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- removeAll(cluster) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
All haplotypes in cluster that are also in this cluster will be removed from this cluster
- removeAll(c) - Method in class net.maizegenetics.dna.snp.FilterList
-
- removeAll(c) - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- removeBranch(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
remove internal branch (collapse node with its parent)
- removeBranchLengths(tree) - Static method in class net.maizegenetics.taxa.tree.NewickUtils
-
This removes the branch lengths from
the given tree
- RemoveBranchLengthsPlugin - Class in net.maizegenetics.analysis.tree
-
- RemoveBranchLengthsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
-
- RemoveBranchLengthsPlugin() - Constructor for class net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
-
- RemoveBranchLengthsPluginKt - Class in net.maizegenetics.analysis.tree
-
- removeChild(n) - Method in interface net.maizegenetics.taxa.tree.Node
-
remove child
- removeChild(parent, child) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
remove child
- removeChild(n) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
remove child
- removeClusterHaplotypesFromOtherClusters(clusterIndex) - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
For this cluster, remove all of its haplotypes from other clusters, adjust the cluster scores, and re-sort the clusters. As a result, cluster size will equal cluster score for this cluster.
- removeCollinearMarkers(removeCollinearMarker) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- removeFirstHaplotypes(maxdistance) - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
Removes all haplotypes within maxdistance of the haplotype of the first cluster. After the haplotypes have been removed clusters are remade and sorted.
- removeHeterozygousClusters(maxHetSites) - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
- removeIndelsForBeagle() - Method in class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- RemoveIndelsForBeaglePlugin - Class in net.maizegenetics.analysis.imputation
-
- RemoveIndelsForBeaglePlugin() - Constructor for class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- RemoveIndelsForBeaglePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
-
- removeInstance(alignment) - Static method in class net.maizegenetics.tassel.SeqViewerPanel
-
- removeMinorSNPStates() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Remove Minor SNP States
- removeMinorSNPStates(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Remove Minor SNP States. Remove Minor S N P States
- removeMinorSNPStates() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- removeMissingObservations() - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- removeNaN() - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
Remove NaNs from matrix before performing MDS
- removeNaN(value) - Method in class net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
-
Set Remove NaNs. Remove NaNs from matrix before performing MDS
- RemoveNaNFromDistanceMatrixPlugin - Class in net.maizegenetics.analysis.distance
-
- RemoveNaNFromDistanceMatrixPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- removeParent() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
removes parent.
- removePolyAFromEnd(s) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Trim the poly-A off the sequence string
- removeProgressUnit(unit) - Method in class net.maizegenetics.progress.ProgressPanel
-
- removeRareTag(minCutoff) - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- removeSeqAfterSecondCutSite(seq, maxLength) - Static method in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
The barcode libraries used for this study can include two types of extraneous sequence at the end of reads. The first are chimeras created with the free ends. These will recreate the restriction site. The second are short regions (less than 64bp), so that will they will contain a portion of site and the universal adapter. This finds the first of site in likelyReadEnd, keeps the restriction site overhang and then sets everything to polyA afterwards
- removeSeqAfterSecondCutSite(seq, maxLength, tagLengthInLong, taxaName, ifForward) - Method in class net.maizegenetics.analysis.gbs.PEParseBarcodeRead
-
Remove the sequence of the second cutsite
- removeSitesBasedOnFreqIgnoreMissing(aa, minimumProportion, maximumProportion, minimumCount) - Static method in class net.maizegenetics.dna.snp.GenotypeTableUtils
-
remove sites based on minimum frequency (the count of good bases, INCLUDING GAPS) and based on the proportion of good alleles (including gaps) different from consensus
- RemoveSitesThatDoNotMatchMinMaj(donorFile, unimp, verboseOutput) - Static method in class net.maizegenetics.analysis.imputation.FILLINDonorGenotypeUtils
-
Remove sites in Donor and Unimp that don't match minMaj. Assumes same coordinate system. Designed to match sites between GBS and hapmap. Removes sites where minMaj is indel. Keeps sites with same minMaj even if third allele differs.
- removeSitesWithIndels() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Removes sites containing an indel (+ or -)
- removeSitesWithIndels(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Remove Sites With Indels. Removes sites containing an indel (+ or -)
- removeSitesWithIndels() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- removeSpecificAnnotations(baseTaxaList, annotationsToRemove) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Creates a new taxa list with the taxa retaining annotations EXCEPT those specified by the list. All taxa are retained, only the annotations are changed.
- removeSynonyms(rowNumber) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- removeTagByCount(minCnt) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap
-
- removeTaxa(taxaToRemove) - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- removeTerm(termNumber) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- reorderColumns(newIndices) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Reorders columns of this matrix based on the given indices.
- reorderColumns(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- reorderColumns(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- reorderColumns(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- reorderColumns(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- reorderPositions(newIndices) - Method in class net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
-
- reorderPositions(newIndices) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- reorderPositions(newIndices) - Method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
- reorderRows(newIndices) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Reorders rows of this matrix based on the given indices.
- reorderRows(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- reorderRows(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- reorderRows(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- reorderRows(newIndices) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- reorderTaxa(newIndices) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- repeatFilter(rbt, ratio) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- repeatLibraryFilter(rbt, TagSeqS, repeatlibS) - Method in class net.maizegenetics.analysis.gbs.Clusters
-
- RepGenAlignerPlugin - Class in net.maizegenetics.analysis.gbs.repgen
-
This plugin takes an existing repGen db, grabs the tags whose depth meets that specified in the minCount parameter, makes kmer seeds from these tags. Window for kmer seeds is default 20. The ref genome is walked with a sliding window of 1. Reference tags are created based on peaks within clusters where kmer seeds align. The kmerLen field should match the length of the kmers stored as tags during the RepGenLoadSeqToDBPlugin step. The default is 150. The refKmerLen() should minimally be the length of the db kmer tags, but can be longer. Our defaults are 150 for kmer tags, and twice this length (300) for the refKmerLen. There are 2 count parameters: minTagCount specifies the minimum depth of a tag for it to be used when creating seed kmers. minHitCount specifies the number of "hits" that must occur within a sliding window (window size = refKmerLen) for the window to remain part of a cluser. When sliding, if the hit count drops below the minhitCount threshold, the cluster ends. A new cluster does not begin until the hit count is back up to threshold. See createRefTagsForAlignment() and storeRefTagPositions() for specifics. This plugin creates and stores the reference tags in the refTag table in the database. Both the tagMapping and the physicalMapPosition table will we populated with the reference tag information. Once the tables have been populated with the reference information, Smith Waterman is run to align all the nonreference tags in the db against each other; each non-reference tag against the reference tags; finally each refTag against all other refTags. ALignment data is stored in the tagAlignments table. Smith Waterman from SourceForge neobio project is used to determine alignment score. Settings for match rewards, mismatch penalty and gap penalty may be changed by user via plugin parameters.
- RepGenAlignerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- RepGenAlignerPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- RepGenAlignerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
- RepGenData - Interface in net.maizegenetics.dna.tag
-
- RepGenDataWriter - Interface in net.maizegenetics.dna.tag
-
- RepGenLDAnalysisPlugin - Class in net.maizegenetics.analysis.gbs.repgen
-
This class takes a rAmpSeq (formerly RepGen) database and for each tag in the tag table, performs the following tag-tag correlations based on the taxa distribution for each tag (1) tag-tag Pearson's correlation (2) tag-tag Spearman's correlation (3) tag-tag presence/absence correlations (4) r-squared The vectors presented to the analysis methods represent a list of taxa and the number of times the tag was seen in that taxa. The presence/absence vectors have a 1 or 0 as values in each slot.
- RepGenLDAnalysisPlugin() - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- RepGenLDAnalysisPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- RepGenLDAnalysisPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
-
- RepGenLoadSeqToDBPlugin - Class in net.maizegenetics.analysis.gbs.repgen
-
Develops a discovery rGBS database based on a folder of sequencing files Keeps only good reads having no N's in the useful part of the sequence. Trims off the barcodes and truncates sequences that (1) have a second cut site, or (2) read into the common adapter. Originally the reference throughout was to "tag". This is being changed to "kmer" as the pipeline is a kmer alignment process.
- RepGenLoadSeqToDBPlugin() - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- RepGenLoadSeqToDBPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap - Class in net.maizegenetics.analysis.gbs.repgen
-
- RepGenPhase2AlignerPlugin - Class in net.maizegenetics.analysis.gbs.repgen
-
This plugin takes an existing repGen db, grabs the tags whose depth meets that specified in the minCount parameter, makes kmer seeds from these tags. Forward and reverse primer sequences are added as an input parameter. When a kmer seed is found on a reference chromosome, a ref sequence is created from 300bp before the hit, to 300 bp after the hit. This value is half the refKmerLen parameter passed by user. Default refKmerLen is 600. From the ref sequence created, a search is made for the primer pairs within this sequence. IF either both forward primer and the reverse complement of the reverse primer; or reverse primer and the reverse complement of the forward primer are found, a reference tag is created starting at the start of the first occurring primer from the primer pair found in the sequence. If both forward and reverse pairs are found, the ref tag is created based on the best match, defaulting to the forward primer if both are found. Search for additional kmer matches on the chromosome begins at the position on the ref chrom following the end of the second primer in the matched pair. The kmerLen field should match the length of the kmers stored as tags during the RepGenLoadSeqToDBPlugin step. The default is 150. The refKmerLen() should minimally be the length of the db kmer tags, but can be longer. Our defaults are 150 for kmer tags, and twice this length (300) for the refKmerLen. There are 2 count parameters: minTagCount specifies the minimum depth of a tag for it to be used when creating seed kmers. This plugin creates and stores the reference tags in the refTag table in the database. Both the tagMapping and the physicalMapPosition table will we populated with the reference tag information. Once the tables have been populated with the reference information, Smith Waterman is run to align all the nonreference tags in the db against each other; each non-reference tag against the reference tags; finally each refTag against all other refTags. ALignment data is stored in the tagAlignments table. Smith Waterman from SourceForge neobio project is used to determine alignment score. Settings for match rewards, mismatch penalty and gap penalty may be changed by user via plugin parameters.
- RepGenPhase2AlignerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- RepGenPhase2AlignerPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- RepGenPhase2AlignerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
- RepGenPhase2AlignerPlugin.BestScore - Enum in net.maizegenetics.analysis.gbs.repgen
-
- RepGenSQLite - Class in net.maizegenetics.dna.tag
-
- RepGenSQLite(filename) - Constructor for class net.maizegenetics.dna.tag.RepGenSQLite
-
- rephase() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
If true, rephase parents before imputing. If false, input haplotypes from file.
- rephase(value) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
Set Rephase Parents First. If true, rephase parents before imputing. If false, input haplotypes from file.
- RephaseParents - Class in net.maizegenetics.analysis.imputation
-
- RephaseParents() - Constructor for class net.maizegenetics.analysis.imputation.RephaseParents
-
- RephaseParents(originalGenotypes, phasedProgeny, plotList, parentHapmap) - Constructor for class net.maizegenetics.analysis.imputation.RephaseParents
-
- RephaseParents(originalGenotypes, phasedProgeny, parentage, parentHaps) - Constructor for class net.maizegenetics.analysis.imputation.RephaseParents
-
- replaceFeature(feature) - Method in class net.maizegenetics.dna.map.GenomeFeatureMapBuilder
-
Replaces the GenomeFeature with a specified ID with a new one. If unique ID isn't already in the map, it throws an UnsupportedOperationException.
- replaceHDF5GenotypesCalls(h5w, taxon, calls) - Static method in class net.maizegenetics.util.HDF5Utils
-
- replaceHDF5GenotypesCalls(h5w, taxon, startSite, calls) - Static method in class net.maizegenetics.util.HDF5Utils
-
- replaceHDF5GenotypesDepth(h5w, taxon, depth) - Static method in class net.maizegenetics.util.HDF5Utils
-
- replaceInNames(regex, replacement, inputFileName, format, outputFileName) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Replaces the supplied regex with the supplied string in taxon names.
- replaceTaxonAnnotations(h5w, modifiedTaxon) - Static method in class net.maizegenetics.util.HDF5Utils
-
- report() - Method in class net.maizegenetics.analysis.association.PhenotypeLM
-
- report(out) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- report(out) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
- report(tree, out) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
- reportAllSitesGWASStatus(outFile, minAlleleFreq, maxAlleleFreq, delimiter) - Method in class net.maizegenetics.dna.pd.PDReport
-
- reportBuilder - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- reportBuilder - Variable in class net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
-
- ReportDestinationDialog - Class in net.maizegenetics.gui
-
- ReportDestinationDialog() - Constructor for class net.maizegenetics.gui.ReportDestinationDialog
-
Creates a dialog that allows the user to send results to a file rather than to save them to memory. Very large output sets can fill up memory and cause TASSEL to crash otherwise.
- reportFilename() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
The name of the file to which these results will be saved.
- reportFilename(value) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Set Output File. The name of the file to which these results will be saved.
- required(required) - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- required() - Method in class net.maizegenetics.plugindef.PluginParameter
-
- reroot(num) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
make node with number num to root node
- reroot(node) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
make provided node the root node
- reroot(tree, node) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
a tree that has been re-rooted at the given internal node. The original root of the tree must have had at least 3 children.
- res - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- resampleProportion() - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
The size of the sample is resample proportion times the number of observations in the complete data. For bootstrap, set this value to 1 and with replacement to true. (Default = 0.8)
- resampleProportion(value) - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
Set Resample Proportion. The size of the sample is resample proportion times the number of observations in the complete data. For bootstrap, set this value to 1 and with replacement to true. (Default = 0.8)
- ResamplingGWASPlugin - Class in net.maizegenetics.analysis.modelfitter
-
- ResamplingGWASPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
- rescanAlpha - Variable in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- reset() - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
- reset() - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- reset() - Method in interface net.maizegenetics.stats.math.OrderEnumerator
-
Reset back to starting state, may have a differnet number of values, and a different ordering after a reset!
- reset() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- resetCounters() - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- resetModel(phenotypeIndex, enterLimit, maxVariants) - Method in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- resetModel(phenotypeIndex, enterLimit, maxVariants) - Method in interface net.maizegenetics.analysis.modelfitter.ForwardRegression
-
This method resets the fitted model to the base model and sets the index of the trait to be fit.
- resetTable() - Method in class net.maizegenetics.gui.AlignmentTableModel
-
Resets the table backing this matrix table model to an empty table.
- resetTable() - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
Resets the table backing this matrix table model to an empty table.
- resetTempTaxaList() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- resolveRefSorted(sortedAlleles, refAllele) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- resolveSortedAndKnownVariantsExport(sortedAllelesInput, knownVariantsInput) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- resolveVCFGeno(alleles, allelesInTaxa, tx) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- resolveVCFGeno(alleles, alleleDepth) - Static method in class net.maizegenetics.dna.snp.io.VCFUtil
-
- restoreBranch(node) - Static method in class net.maizegenetics.taxa.tree.NodeUtils
-
restore internal branch
- restoreOddColumns(original_numcols) - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
Restores the col array of indexes to the state it was before the deleteOddColumns method was called. It only needs to know how many columns there was originally. The indexes that were moved to the end of the array are restored to their original position.
- restorePhasedHaplotypes(restorePath) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- restorePhasedHaplotypes(restorePath) - Static method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- restoreRows(original_numrows) - Method in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
Restores the row array of indexes to the state it was before the reduce method was called. It only needs to know how many rows there was originally. The indexes that were moved to the end of the array are restored to their original position.
- ResultSetIterator - Class in net.maizegenetics.util.db
-
Result Set Iterator User: julian3 Date: Time: PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- ResultSetIterator(connection, sql) - Constructor for class net.maizegenetics.util.db.ResultSetIterator
-
- ResultSetProcessor - Interface in net.maizegenetics.util.db
-
Result Set Processor User: julian3 Date: Time: PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- RETAIN_RARE_ALLELES - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- retainAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- retainAll(c) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- retainAll(c) - Method in class net.maizegenetics.dna.snp.FilterList
-
- retainAll(c) - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- retainRareAlleles() - Method in class net.maizegenetics.tassel.PreferencesDialog
-
Retain Rare Alleles
- retainRareAlleles(value) - Method in class net.maizegenetics.tassel.PreferencesDialog
-
Set Retain Rare Alleles. Retain Rare Alleles
- retainSpecificAnnotations(baseTaxaList, annotationsToKeep) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Creates a new taxa list with the taxa only retaining annotations within a specified list. All taxa are retained, only the annotations are changed.
- retainsRareAlleles() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- retainsRareAlleles() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- retainsRareAlleles() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns true if this Alignment retains rare alleles. If false, rare alleles are recorded as unknown.
- retainsRareAlleles() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns true if this genotype table retains rare alleles. If false, rare alleles are recorded as unknown.
- retainsRareAlleles() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- retainsRareAlleles() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- returnAverageQuality(phredScale) - Method in class net.maizegenetics.dna.read.Read
-
Return average quality value of read
- returnEigenvalues() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Returns a list of eigenvalues sorted high to low.
- returnEigenvalues(value) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Set Return Eigenvalues. Returns a list of eigenvalues sorted high to low.
- returnEigenvectors() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Returns the eigenvectors calculated from a Singular Value Decomposition of the data. The resulting table can be quite large if the number of variants and taxa are big.
- returnEigenvectors(value) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Set Return Eigenvectors. Returns the eigenvectors calculated from a Singular Value Decomposition of the data. The resulting table can be quite large if the number of variants and taxa are big.
- ReturnHaplotype - Static variable in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
The TYPE used to represent all HaplotypeClusters
- revComplement(seq) - Static method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
- reverse() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- reverse() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- reverseComplement(tag) - Static method in class net.maizegenetics.dna.tag.TagBuilder
-
- reverseComplementAlleleByteArray(alleles) - Static method in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
Convert a haploid (allele) string (e.g. {0,1,2,3,0}) to its reverse complement (e.g. {3,0,1,2,3})
- reverseOrder(array) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- reversep() - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
String containing the reverse primer sequence.
- reversep(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
-
Set Reverse Primer. String containing the reverse primer sequence.
- reverseTrace(indent) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- reverseTranslateIndex(index) - Method in class net.maizegenetics.dna.snp.TranslateIndex
-
Translates base index to this index. This class has no translation.
- reverseTranslateIndex(index) - Method in class net.maizegenetics.dna.snp.TranslateIndexRange
-
- reverseTranslateIndex(index) - Method in class net.maizegenetics.dna.snp.TranslateIndexRedirect
-
Translates base index to this index. Uses binary search algorithm since indices are ordered.
- reverseTranslateIndex(index) - Method in class net.maizegenetics.dna.snp.TranslateIndexRedirectUnordered
-
Translates base index to this index. Searches all indices since not ordered.
- revg2sweep(column) - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- RGBSProductionSNPCallerPlugin - Class in net.maizegenetics.analysis.gbs.repgen
-
This plugin converts all of the fastq (and/or qseq) files in the input folder and keyfile to genotypes and adds these to a genotype file in HDF5 format. We refer to this step as the "Production Pipeline". The output format is either HDF5 or VCF genotypes with allelic depth stored. Output file type is determined by presence of the ".h5" suffix. SNP calling is quantitative with the option of using either the Glaubitz/Buckler binomial method (pHet/pErr > 1 = het) (=default), or the Stacks method. Merging of samples with the same LibraryPrepID is handled by GenotypeTableBuilder.addTaxon(), with the genotypes re-called based upon the new depths. Therefore, if you want to keep adding genotypes to the same target HDF5 file in subsequent runs, use the -ko (keep open) option so that the output GenotypeTableBuilder will be mutable, using closeUnfinished() rather than build(). If the target output is HDF5, and that GenotypeTable file doesn't exist, it will be created. Each taxon in the output file is named "ShortName:LibraryPrepID" and is annotated with "Flowcell_Lanes" (=source seq data for current genotype). Requires a database with variants added from a previous "Discovery Pipeline" run. References to "tag" are being replaced by references to "kmer" as the pipeline is really a kmer alignment process. TODO add the Stacks likelihood method to BasicGenotypeMergeRule
- RGBSProductionSNPCallerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- RGBSProductionSNPCallerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- RidgeRegressionEmmaPlugin - Class in net.maizegenetics.analysis.association
-
- RidgeRegressionEmmaPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
-
- RNADeMultiplexProductionPlugin - Class in net.maizegenetics.analysis.rna
-
- RNADeMultiplexProductionPlugin() - Constructor for class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- RNADeMultiplexProductionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- RNADeMultiPlexSeqToDBPlugin - Class in net.maizegenetics.analysis.rna
-
- RNADeMultiPlexSeqToDBPlugin() - Constructor for class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- RNADeMultiPlexSeqToDBPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- RNADeMultiPlexSeqToDBPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- ROOT - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- ROOT - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- ROOT - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- root_factor - Variable in class net.maizegenetics.analysis.gbs.neobio.FactorSequence
-
A pointer to the root factor, the one that starts the list of factors.
- RootedTreeUtils - Class in net.maizegenetics.taxa.tree
-
This class contains utility methods. These include:
1. gathering information about subtrees from a set of trees
2. comparing subtrees and clades.
All these methods assume rooted trees!
- rotateByLeafCount(tree) - Static method in class net.maizegenetics.taxa.tree.TreeUtils
-
Rotates branches by leaf count. WARNING: assumes binary tree!
- row - Variable in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
An array of row indexes reflecting the current state of the matrix. When rows are deleted, the corresponding indexes are simply moved to the end of the vector.
- row(i) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- row(i) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- row(i) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- row(i) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- row_codes - Variable in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Stores matrix row headers in the order they were found.
- row_position - Variable in class net.maizegenetics.analysis.gbs.neobio.Smawk
-
This array is used to store for each row of the original matrix, its index in the current state of the matrix, i.e. its index in the row array.
- rowAsTuple(sql, rs) - Static method in class net.maizegenetics.util.db.SQL
-
- RowHeaderRenderer - Class in net.maizegenetics.gui
-
- RowHeaderRenderer(table) - Constructor for class net.maizegenetics.gui.RowHeaderRenderer
-
- rowStart - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Basically, the longer sequence is stored in rows, the shorter on is stored in the columns. The beginning ROW of matrix that was aligned. If seq1 is the same length or shorter then seq2, this correlates to the position on seq2 where alignment started. If seq2 is shorter than seq1, this correlates to the position on seq1 where alignment started.
- rowSum(row) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- rowSum(row) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- rowSum(row) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- rowSum(row) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- Rsq - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- RSQUARE - Static variable in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- run() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
starts the thread to calculate LD
- run() - Method in class net.maizegenetics.gui.PrintHeapAction
-
Method executed when this thread starts that removes all items from the associated tree.
- run() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- run() - Method in class net.maizegenetics.plugindef.ThreadedPluginListener
-
- runAnalysis() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
-
- runAnalysis() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
This is called to run the analysis
- runAnalysis() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- runDiscoverySNPCallerPlugin() - Static method in class net.maizegenetics.analysis.gbs.TerryPipelines
-
- runFindMergeHaplotypes(inFile, exportFile, errorExportFile, maxDistance, minSites, appoxSitesPerHaplotype) - Method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
Produces donor haplotypes that can be used for imputation.
- runPermutationTest() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
-
- runPermutationTest() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- runPermutationTestNoMissingData() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- runPlugin(input) - Method in class net.maizegenetics.analysis.association.EqtlAssociationPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.association.GenomicSelectionPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(filename) - Static method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.GenosToABHPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(genotype) - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(genotype) - Method in class net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
-
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.MaskGenotypePlugin
-
Convenience method to run plugin with one return object.
- runPlugin(inputGenos) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Convenience method to run plugin with input and output GenotypeTable objects (rather than DataSets)
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Convenience method to run plugin.
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.ProjectionLoadPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(inputGenos) - Method in class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
Convenience method to run plugin with input and output GenotypeTable objects (rather than DataSets)
- runPlugin(input) - Method in class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(matrix) - Static method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- runPlugin(input) - Static method in class net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
-
- runPlugin() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- runPlugin(input) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
- runPlugin() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- runPlugin(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- runPlugin(input) - Method in class net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Convenience method to run plugin with one return object.
- runPluginDataSet(filename) - Static method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- runStep1(data, datumArray, fileOptions) - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
- runStep2(currentData, end2end) - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
- runStep3(data, step1Result, fileOptions) - Method in class net.maizegenetics.analysis.data.SynonymizerPlugin
-
- S_direction - Variable in class net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
-
The direction to the source of the S-path of the new vertex of this block.
- S_path_score - Variable in class net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
-
The value of the highest scoring path which starts inside the block and ends at its output border.
- SAMConverterPlugin - Class in net.maizegenetics.analysis.gbs
-
This class can read in a CBSU TagMapFile into the gbs.TagsOnPhysicalMap data structure.
- SAMConverterPlugin() - Constructor for class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- SAMConverterPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- sameTaxa(node1, node2) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- sAMInputFile() - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Name of input file in SAM text format
- sAMInputFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
Set SAM Input File. Name of input file in SAM text format
- sampleNameField - Static variable in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
- sampleNameField - Static variable in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- SAMToGBSdbPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
Reads SAM file formats to determine the potential positions of Tags against the reference genome.
- SAMToGBSdbPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
- SAMToGBSdbPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
-
- samToMultiPositionTOPMPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- SAMUtils - Class in net.maizegenetics.dna.tag
-
- SAMWGMapConverterPlugin - Class in net.maizegenetics.analysis.gbs
-
This class reads in SAM mapping results tests them against an anchor map and creates a update HDF5 TOPM file
- SAMWGMapConverterPlugin() - Constructor for class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- SAMWGMapConverterPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- saveAsFile() - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.
- saveAsFile(value) - Method in class net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
-
Set Write to file. Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.
- saveAsFile() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.
- saveAsFile(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Save to file. Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results will NOT be saved to the data tree. Default = false.
- saveBinMultiBlupCounts(filename, matrix) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveBinMultiBlupMatrix(matrix, filename) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveBinMultiBlupMatrix(matrix, taxaFile, matrixFile, countFile) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveDARwinIDs(filename, taxa) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveDARwinMatrix(matrix, saveFile) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveDARwinMatrix(matrix, donFile, disFile) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveDataToFile(img, format, saveFile) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- saveDataToFile(comp) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- saveDataToFile(comp, saveFile) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- saveDataToFile(tr, delimit, fileExtensions) - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
- saveDataToFile(tr, delimit) - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
- saveDelimitedAlignment(theAlignment, delimit, saveFile) - Static method in class net.maizegenetics.dna.snp.ExportUtils
-
- saveDelimitedDistanceMatrix(matrix, saveFile) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveDelimitedTableReport(theTableReport, saveFile) - Static method in class net.maizegenetics.util.TableReportUtils
-
Saves Table Report to file delimited by tabs.
- saveDelimitedTableReport(theTableSource, delimit, saveFile) - Static method in class net.maizegenetics.util.TableReportUtils
-
Saves Table Report to file delimited by specified delimiter.
- saveDelimitedTableReport(theTableSource, delimit, bw, includeHeader) - Static method in class net.maizegenetics.util.TableReportUtils
-
Saves Table Report to file delimited by specified delimiter.
- saveDistanceMatrix() - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Save Distance Matrix
- saveDistanceMatrix(value) - Method in class net.maizegenetics.analysis.tree.CreateTreePlugin
-
Set Save Distance Matrix. Save Distance Matrix
- saveFile() - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Save file as...
- saveFile(value) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Save file as...
- saveMultiBlupIDs(filename, taxa) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveRawMultiBlupMatrix(matrix, filename) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveRawMultiBlupMatrix(matrix, taxaFile, matrixFile) - Static method in class net.maizegenetics.taxa.distance.WriteDistanceMatrix
-
- saveSiteStats(siteStats) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- saveSiteStats(siteStats) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- saveTempTaxaList() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- saveToFile - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- SBIT - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- scalarAdd(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- scalarAdd(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- scalarAdd(s) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Adds a scalar to this matrix and returns a new matrix. The original is not modified.
- scalarAdd(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- scalarAddEquals(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- scalarAddEquals(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- scalarAddEquals(s) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Adds a scalar s to this matrix, replacing the original matrix with the result.
- scalarAddEquals(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- scalarMult(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- scalarMult(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- scalarMult(s) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Multiplies this matrix times a scalar and returns a new matrix. The original is not modified.
- scalarMult(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- scalarMultEquals(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- scalarMultEquals(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- scalarMultEquals(s) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Multiplies this matrix times a scalar s, replacing the original matrix with the result.
- scalarMultEquals(s) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- scale(values) - Static method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- scanAndFindCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- scanToFindCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
-
- scanToFindCI() - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- SCHEMA - Static variable in class net.maizegenetics.util.db.LambdaTuplesContext
-
- score - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
The overall score value for this alignment.
- score - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
This field stores just the score of the last pairwise alignment performed (if the score_computed flag is set to true). It is useful when just the score is needed (and not the alignment itselft). Its value is set after a successful execution of both computePairwiseAlignment or computeScore methods that subclasses must implement. If new sequences are loaded or a new scoring scheme is set, the score_computed flag is set to false, and this field's value becomes undefined.
- score() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- score_computed - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Flags whether the score of the alignment between the last two loaded sequences has already been computed. It is set to true after a successful execution of both computePairwiseAlignment or computeScore methods that subclasses must implement. It is set to falsef if new sequences are loaded or a new scoring scheme is set.
- score_tag_line - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
The score tag line.
- scoreDeletion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
Always returns gap_cost for the deletion of any character.
- scoreDeletion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Helper method to invoke the scoreDeletion method of the scoring scheme set to this algorithm.
- scoreDeletion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Returns the score of a deletion of character a according to this scoring matrix.
- scoreDeletion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Returns the score of a deletion of character a according to this scoring scheme. If this character is not recognised, an exception is raised.
- scoreDeletion(a) - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
- scoreInsertion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
Always returns gap_cost for the insertion of any character.
- scoreInsertion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Helper method to invoke the scoreInsertion method of the scoring scheme set to this algorithm.
- scoreInsertion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Returns the score of an insertion of character a according to this scoring matrix.
- scoreInsertion(a) - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Returns the score of an insertion of character a according to this scoring scheme. If this character is not recognised, an exception is raised.
- scoreInsertion(a) - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
- scoreMatch(s1, s2, ignoreCase, ignoreWhite, ignorePunc) - Static method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- scoreSubstitution(a, b) - Method in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
Returns the score of a substitution of character a for character b according to this scoring scheme. It is match_reward if a equals b, mismatch_penalty otherwise.
- scoreSubstitution(a, b) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Helper method to invoke the scoreSubstitution method of the scoring scheme set to this algorithm.
- scoreSubstitution(a, b) - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Returns the score of a substitution of character a for character b according to this scoring matrix.
- scoreSubstitution(a, b) - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Returns the score of a substitution of character a for character b according to this scoring scheme. If this substitution is not defined, an exception is raised.
- scoreSubstitution(a, b) - Method in class net.maizegenetics.analysis.gbs.SmithWaterman
-
- scoring - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
The scoring scheme used to compute a pairwise sequence alignment. It must be set before performing the alignment, and if a new scoring scheme is set, any alignment or score already computed is lost.
- ScoringMatrix - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implements a scoring scheme based on a substitution matrix. It is useful to represent PAM and BLOSUM family of amino acids scoring matrices. Its constructor loads such matrices from a file (or any other character stream). The following is an extract of a BLOSUM62 scoring matrix file:
A R N D C Q E G H I L K M F P S T W Y V B Z X *
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
...
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
- ScoringMatrix(input) - Constructor for class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Creates a new instance of a substitution matrix loaded from the character stream. The case of characters is significant when subsequently computing their score.
- ScoringMatrix(input, case_sensitive) - Constructor for class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Creates a new instance of a substitution matrix loaded from the character stream. If case_sensitive is true, the case of characters is significant when subsequently computing their score; otherwise the case is ignored.
- ScoringScheme - Class in net.maizegenetics.analysis.gbs.neobio
-
This abstract class is the superclass of all scoring schemes. It defines basic operations that must be provided by all subclasses. Scoring schemes are used by sequence alignment algorithms to compute the score of an alignment.
- ScoringScheme() - Constructor for class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Creates a new instance of an scoring scheme. The case of characters is significant when subsequently computing their score.
- ScoringScheme(case_sensitive) - Constructor for class net.maizegenetics.analysis.gbs.neobio.ScoringScheme
-
Creates a new instance of an scoring scheme. If case_sensitive is true, the case of characters is significant when subsequently computing their score; otherwise the case is ignored.
- screenPrint(rc) - Method in class net.maizegenetics.analysis.gbs.UNetworkFilter
-
- screenPrintTps() - Method in class net.maizegenetics.analysis.gbs.UNetworkFilter
-
- searchBiDirectional(searchBiDirectional) - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Builder
-
- searchReverseComplement() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Search of the reverse complements of the reference sequences
- searchReverseComplement(value) - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
Set Search reverse complement. Search of the reverse complements of the reference sequences
- seedLen() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Length of seed kmers
- seedLen(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Seed kmer length. Length of seeds to use in aligning.
- seedLen() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Length of seed kmers
- seedLen(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Seed kmer length. Length of seeds to use in aligning.
- seedWindow() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Length of window between positions when creating seed from DB tags
- seedWindow(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
-
Set Seed window length. Length of window between positions when creating seed from DB tags
- seedWindow() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Length of window between positions when creating seed from DB tags
- seedWindow(value) - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
-
Set Seed window length. Length of window between positions when creating seed from DB tags
- select(connection, sql, processor, params) - Static method in class net.maizegenetics.util.db.SQL
-
- selectedFilesList() - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
The name and path of a file containing the names of the breakpoint files to be merged.
- selectedFilesList(value) - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
Set List of files to merge. The name and path of a file containing the names of the breakpoint files to be merged.
- SelectedListModel() - Constructor for class net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
-
- selectFiles() - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
Select the files to merge. Alternatively, merge all files in a directory. (Default = false)
- selectFiles(value) - Method in class net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
-
Set Select Files to Merge. Select the files to merge. Alternatively, merge all files in a directory. (Default = false)
- SelectFromAvailableDialog - Class in net.maizegenetics.gui
-
- SelectFromAvailableDialog(frame, title, availableModel) - Constructor for class net.maizegenetics.gui.SelectFromAvailableDialog
-
- SelectFromAvailableDialog.SelectedListModel - Class in net.maizegenetics.gui
-
- SelectFromAvailableSitesDialog - Class in net.maizegenetics.gui
-
- SelectFromAvailableSitesDialog(frame, title, availableModel) - Constructor for class net.maizegenetics.gui.SelectFromAvailableSitesDialog
-
- selectionCriterion - Variable in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- selectionCriterion() - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- selectionCriterion() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- SelfedHaplotypeFinder - Class in net.maizegenetics.analysis.imputation
-
- SelfedHaplotypeFinder(window, minProportionNotMissing) - Constructor for class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- sendErrorMessage(text) - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- sendLogToConsole() - Method in class net.maizegenetics.tassel.PreferencesDialog
-
Flag whether to send logging to the console.
- sendLogToConsole(value) - Method in class net.maizegenetics.tassel.PreferencesDialog
-
Set Send Log To Console. Flag whether to send logging to the console.
- sendMessage(text) - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- sendMessage(subject, msg) - Method in class net.maizegenetics.util.SMTPClient
-
- sendMessageWithAttachment(subject, msg, fileAttachment) - Method in class net.maizegenetics.util.SMTPClient
-
- separateAlignmentIntoLoci(alignment, dataSetName) - Static method in class net.maizegenetics.analysis.data.SeparatePlugin
-
- separateAlignmentIntoLoci(alignment, dataSetName, chromosomesToSeparate) - Static method in class net.maizegenetics.analysis.data.SeparatePlugin
-
- separateOn(factors) - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- SeparatePlugin - Class in net.maizegenetics.analysis.data
-
- SeparatePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SeparatePlugin
-
Creates a new instance of SeparatePlugin
- seq - Variable in class net.maizegenetics.analysis.clustering.Haplotype
-
The haplotype (or genotype) sequence
- seq1 - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
The first factorised sequence being aligned.
- seq1 - Variable in class net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
-
The first sequence of an alignment.
- seq1 - Variable in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
The first sequence of an alignment.
- seq1 - Variable in class net.maizegenetics.analysis.gbs.SmithWaterman
-
The first sequence of an alignment.
- seq2 - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
The second factorised sequence being aligned.
- seq2 - Variable in class net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
-
The second sequence of an alignment.
- seq2 - Variable in class net.maizegenetics.analysis.gbs.neobio.SmithWaterman
-
The second sequence of an alignment.
- seq2 - Variable in class net.maizegenetics.analysis.gbs.SmithWaterman
-
The second sequence of an alignment.
- seq2Bit() - Method in interface net.maizegenetics.dna.tag.Tag
-
- seq2BitAsBytes() - Method in class net.maizegenetics.dna.tag.AbstractTag
-
- seq2BitAsBytes() - Method in interface net.maizegenetics.dna.tag.Tag
-
- seqDifferences(seq1, seq2, maxDivergence) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the number of bp differences between two 2-bit encoded longs. Maximum divergence is used to save time when only interested in very similar sequences.
- seqDifferences(seq1, seq2) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the number of bp differences between two 2-bit encoded longs.
- seqDifferencesForSubset(seq1, seq2, lengthOfComp, maxDivergence) - Static method in class net.maizegenetics.dna.BaseEncoder
-
Returns the number of sequencing differences between two 2-bit encoded longs. Maximum divergence is used to save time when only interested in very similar sequences.
- seqlen - Variable in class net.maizegenetics.analysis.clustering.Haplotype
-
The length of the sequence
- seqLength() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
Length of sequence represented by this line
- seqLength() - Method in class net.maizegenetics.dna.tag.AbstractTag
-
- seqLength() - Method in interface net.maizegenetics.dna.tag.Tag
-
- SeqToTBTHDF5Plugin - Class in net.maizegenetics.analysis.gbs
-
This pipeline converts a series of fastq or qseq files to a single TagsByTaxa HDF5 file. It requires a list of existing tags (Tags object), which may come from a TagCounts file or TOPM file.
- SeqToTBTHDF5Plugin() - Constructor for class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- SeqToTBTHDF5Plugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
- sequence - Variable in class net.maizegenetics.analysis.gbs.neobio.CharSequence
-
Stores the sequence as an array of characters.
- sequence() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- sequence() - Method in class net.maizegenetics.dna.tag.AbstractTag
-
- sequence() - Method in interface net.maizegenetics.dna.tag.Tag
-
- SequenceDiversityPlugin - Class in net.maizegenetics.analysis.popgen
-
- SequenceDiversityPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
- sequences_loaded - Variable in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Flags whether sequences have been loaded. It is set to true after subclasses successfully load two sequences.
- SeqViewerPanel - Class in net.maizegenetics.tassel
-
- SeqViewerPanel.MyTableUI - Class in net.maizegenetics.tassel
-
- serial_number - Variable in class net.maizegenetics.analysis.gbs.neobio.Factor
-
This factor's serial number, which indicates the order of this factor inside the linked list of factors of a text.
- serializeAdditiveSites(geno, outFile) - Static method in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- serializePhasedHaplotypes(phasedHaps, filename) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- serializePhasedHaplotypes(phasedHaps, savePath) - Static method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- set(index, element) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- set(index, element) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- set(index, element) - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
Replaces the element at the specified position in this list with the specified element.
- set(index, element) - Method in class net.maizegenetics.dna.snp.FilterList
-
- set(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskedGenotypes
-
- set(taxon, site) - Method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- set(row, col, value) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- set(row, col, value) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- set(row, col, value) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Sets the matrix value at row, col. The coordinates are not checked to make sure they fall in the matrix.
- set(row, col, value) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- set(x, y, value) - Method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- set(x, y, value) - Method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- set(index) - Method in interface net.maizegenetics.util.BitSet
-
Sets a bit, expanding the set size if necessary
- set(startIndex, endIndex) - Method in interface net.maizegenetics.util.BitSet
-
Sets a range of bits, expanding the set size if necessary
- set(row, column, value) - Method in class net.maizegenetics.util.ColumnMatrix.Builder
-
- set(columns) - Method in interface net.maizegenetics.util.db.DBTuple
-
- set(index) - Method in class net.maizegenetics.util.OpenBitSet
-
sets a bit, expanding the set size if necessary
- set(startIndex, endIndex) - Method in class net.maizegenetics.util.OpenBitSet
-
Sets a range of bits, expanding the set size if necessary
- set(row, column, value) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Sets value at given row and column.
- set(row, column, value) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- set(row, column, value) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- set(row, column, value) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- set(row, column, value) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- set(index) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- set(startIndex, endIndex) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- setAlgorithmName(algorithm) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setAlignment(pChr, pPos, ifMap, ifRef, ifUnique) - Method in class net.maizegenetics.dna.map.TagGWASMapInfo
-
- setAlignmentFileType(type) - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- setAlignmentFileType(type) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Deprecated.
- setAlignmentFileTypes(types) - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- setAll(value) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Sets value for all elements.
- setAll(value) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- setAll(value) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- setAll(value) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- setAll(value) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- setAllVariantInfo(tagIndex, defAndOffset) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Preferred method for setting variant information
- setAllVariantInfo(tagIndex, defAndOffset) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
Preferred method for setting variant information
- setAlpha(alpha) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setAlternateMinorAllelesToMajor(myGenotype) - Static method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- setAlternateMinorAllelesToMinor(myGenotype) - Static method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- setAlternateMinorAllelesToMissing(myGenotype) - Static method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- setAlternateTagMappingInfo(index, mapIndex, theTMI) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setAnalyzeByColumn(analyzeByColumn) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setAnalyzeByColumn(analyzeByColumn) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setAnnotations(annotationsIn) - Method in class net.maizegenetics.dna.pd.SiteAnnotation
-
- setAttribute(name, value) - Method in interface net.maizegenetics.taxa.tree.AttributeNode
-
Sets a named attribute to the given value.
- setAttribute(name, value) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Sets a named attribute to the given value.
- setAttribute(node, name, value) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Sets an named attribute for a given node.
- setAttribute(node, name, value) - Method in interface net.maizegenetics.taxa.tree.Tree
-
Sets an named attribute for a given node.
- setAverageSegmentLength(length) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- setBar(bar) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setBase(taxon, site, value) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- setBaseFile(baseFile) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setBaseRangeForTaxon(taxon, startSite, value) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- setBases(data) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- setBases(data) - Method in class net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
-
- setBins(bins) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setBits(bits) - Method in interface net.maizegenetics.util.BitSet
-
Expert: sets a new long[] to use as the bit storage
- setBits(bits) - Method in class net.maizegenetics.util.OpenBitSet
-
Expert: sets a new long[] to use as the bit storage
- setBits(bits) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- setBlockSchematic(blockSchematic) - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- setBoxWhisker(boxWhisker) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setBranchLength(value) - Method in interface net.maizegenetics.taxa.tree.Node
-
Set the length of the branch attaching this node to its parent.
- setBranchLength(value) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Set the length of the branch attaching this node to its parent.
- setBranchLengthSE(value) - Method in interface net.maizegenetics.taxa.tree.Node
-
Set the length SE of the branch attaching this node to its parent.
- setBranchLengthSE(value) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Set the length SE of the branch attaching this node to its parent.
- setBreakpointBaseName(bkptBase) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setByFactor(byFactor) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setCalculatePEV(calculatePEV) - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- setChartMode(chartMode) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setChecked(row, col, value) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- setChecked(row, col, value) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- setChecked(row, col, value) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
Sets the matrix value at row, col. The coordinates are checked to make sure they fall in the matrix.
- setChecked(row, col, value) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- setCheckSubPops(checkSubPops) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setChild(n, node) - Method in interface net.maizegenetics.taxa.tree.Node
-
set child node
- setChild(n, node) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
set child node
- setChromoPosition(index, chromosome, strand, positionMin, positionMax) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setChromoPosition(index, chromosome, strand, positionMin, positionMax) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setChromoPosition(index, chromosome, strand, positionMin, positionMax) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setChromoPosition(index, chromosome, strand, positionMin, positionMax) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Sets chromosome, strand, start position, and end position for given tag.
- setChromosomalView(chromosomalView) - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- setChromosomesToSeparate(chrs) - Method in class net.maizegenetics.analysis.data.SeparatePlugin
-
- setCitation(citation) - Method in class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- setColor(color) - Method in class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- setColor(color) - Method in interface net.maizegenetics.gui.GenotypeTableMask
-
- setColumnNameType(type) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- setColumnTypes(types) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setColumnTypes(types) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setCompressionType(type) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setCompressionType(type) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setConfigParameters() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setCount(x, y, value) - Method in class net.maizegenetics.taxa.distance.DistanceMatrixBuilder
-
- setcssDmin(css) - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- setCustomCompression(value) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setCustomCompression(value) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setData(dist, input_border, dim, lc) - Method in class net.maizegenetics.analysis.gbs.neobio.OutMatrix
-
Sets this interface's data to represent an OUT matrix for a block. This method is typically executed once for each block being aligned.
- setDcoP(index, dcoP) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setDefault(type) - Static method in class net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
-
- setDeleteHetsInBreakpoints(hetsToMissing) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setDelimiter(theDelimiter) - Method in class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
- setDepthRangeForTaxon(taxon, siteOffset, values) - Method in class net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
-
Set values for range of sites and alleles for a taxon simultaneously.
- setDepthRangeForTaxon(taxon, siteOffset, depths) - Method in class net.maizegenetics.dna.snp.score.AlleleDepthBuilder
-
Set depth for range of sites and alleles for a taxon simultaneously. First dimension of depths is number of alleles (6 for Nucleotide) and second dimension is sites.
- setDivergence(index, divergence) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setDivergence(index, divergence) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setDivergence(index, divergence) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setDivergence(index, divergence) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Set Divergence for given tag
- setDminFromA() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- setDoSlidingHaps(doSlidingHaps) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setEmissionProbability(probabilityMatrix) - Method in class net.maizegenetics.analysis.imputation.EmissionProbability
-
- setEnd(end) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setEndPos(end) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setEnterlimit(enterlimit) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setEnterLimit(enterLimit) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- setEnterlimits(enterlimits) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setErrBar(errBar) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setExitlimit(exitlimit) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setExitLimit(exitLimit) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- setExitlimits(exitlimits) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setExtractIndels(extractIndels) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setFactors(namelist) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setFamilyList(familyList) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setFastPointReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- setFastReadCountForAdjacentTagTaxonSet(tagIndex, firstTaxaIndex, values) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- setFillGapsInAlignment(fillGapsInAlignment) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- setFilterBitSet(newFilterBitSet) - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- setFilterMinorSNPs(filterMinorSNPs) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setFilterOutput(filterOutput) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setFilterOutput(filterOutput) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setFinalIterMarker(myFinalIterMarker) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setFinalIterMarker(myFinalIterMarker) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setGenotype(genotype) - Method in class net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
-
- setGenotypeTable(genotype) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- setGlobalMax(max) - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- setGraphSize(graphX, graphY) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- setGwasResults(gwasResultsIn) - Method in class net.maizegenetics.dna.pd.SiteAnnotation
-
- setHaplotypeMap(parentHaplotypeFilename) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setHetsTo(value) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Changes all heterozygous values to give value.
- setHetsTo(value) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- setHetsTo(value) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- setHetsTo(value) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- setHetsTo(value) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- setHetTreatment(treatment) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setHorizontalPageSize(horizontalSize) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- setID(id) - Method in class net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect
-
- setID(id) - Method in class net.maizegenetics.stats.linearmodels.CovariateModelEffect
-
- setID(id) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- setID(id) - Method in interface net.maizegenetics.stats.linearmodels.ModelEffect
-
- setID(id) - Method in class net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect
-
- setIdentifier(id) - Method in interface net.maizegenetics.taxa.tree.Node
-
Set identifier for this node.
- setIdentifier(id) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Set identifier for this node.
- setIfPAV(index, value) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Set PAV value of tag
- setImageSize(width, height) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- setImputedGenotypeOutFilename(imputedGenotypeOutFilename) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setIncludeAnnotations(include) - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- setIncludeDepth(include) - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- setIncludeList(includeList) - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- setIndex(index) - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- setInitialTransitionCounts(chr) - Method in class net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
-
- setInput(filename) - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- setInputFiles(files) - Method in class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
-
- setIsAccumulateResults(accumulate) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setIsRandom(isRandom) - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- setKeyFileStringToInt(inputKeyFile) - Static method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
- setLDType(type) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setLocus(locus) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- setLocus(locus) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setLocusStr(name) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setLogFile(logname) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setLogTransform(logTransform) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setLong(wordNum, bits) - Method in interface net.maizegenetics.util.BitSet
-
Expert: sets specified word with given bits.
- setLong(wordNum, bits) - Method in class net.maizegenetics.util.OpenBitSet
-
Expert: sets specified word with given bits.
- setLong(wordNum, bits) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- SetLowDepthGenosToMissingPlugin - Class in net.maizegenetics.analysis.data
-
Set genotypes below a minimum depth to missing. Set each genotype in the input genotypes to missing if the underlying allelic depth is below a user- specified minimum. Input: GenotypeTable stored as a Datum within a DataSet Output: GenotypeTable stored as a Datum within a DataSet
- SetLowDepthGenosToMissingPlugin() - Constructor for class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- SetLowDepthGenosToMissingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
-
- setLowerCorner(lowerCorner) - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- setLowerCorner(ldMeasure) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This determines what is displayed in the lower left corner. Options are: P_VALUE, DPRIME, and RSQUARE
- setMainText(text) - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- setMapP(index, mapP) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setMapP(index, mapP) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setMapP(index, mapP) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setMapP(index, mapP) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setMapP(index, mapP) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setMapP(index, mapP) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setMapP(index, mapP) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Set MapP for given tag
- setMapP(index, mapP) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
- setMappingNum(mappingNum) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Set mappingNum attribute in HDF5
- setMappingRank(mappingRank) - Method in class net.maizegenetics.dna.map.TagMappingInfoV3
-
- setMappingSource(mappingSource) - Method in class net.maizegenetics.dna.map.TagMappingInfoV3
-
- setMaskBitSet(newMaskBitSet) - Method in interface net.maizegenetics.dna.map.GVCFGenomeSequence
-
- setMasks(masks) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- setMasks(masks) - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- setMatrix(tcontig) - Method in class net.maizegenetics.stats.statistics.ContigencyTable
-
sets the data for the contigency table, must be set before other methods are called. If tcontig has a greater count than maxSize, then the contig is set to null
- setMaxDifference(maxDifference) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setMaxFreq(maxFreq) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setMaxHetDev(maxHetDev) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setMaximumNumOfIteration(max) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setMaximumNumOfIteration(max) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setMaxMafForMono(maxMafForMono) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setMaxMissing(maxMissing) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setMaxNumberOfMarkers(maxNumberOfMarkers) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setMaxP(maxp) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- setMaxp(maxp) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setMaxp(maxp) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setMergeAlignments(mergeAlignments) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setMethodByRows(rowSetMethod) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
- setMethodByRows(rowSetMethod) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- setMethodByRows(rowSetMethod) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- setMethodByRows(rowSetMethod) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- setMethodByRows(rowSetMethod) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- setMethodByRows(rowSetMethod) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- setMethodByRows(rowSetMethod) - Method in class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- setMinCount(minCount) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setMinDepth(mindepth) - Method in class net.maizegenetics.analysis.imputation.RephaseParents
-
- setMinFreq(minFreq) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setMinMinorAlleleFrequency(minMinorAlleleFrequency) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setMinRforSnps(minRforSnps) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setMinSnpCoverage(minSnpCoverage) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setMinStartPosition(newMinStartPosition) - Method in class net.maizegenetics.dna.map.TagLocus
-
- setMinUsedClusterSize(minUsedClusterSize) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setModelSS(modelss) - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- setModelType(modelType) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setMultimaps(index, multimaps) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setMultimaps(index, multimaps) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setMultimaps(index, multimaps) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setMyBase(myBase) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setMyGenotype(myGenotype) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setName() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Name to be given to this set of breakpoints. This name will be stored in the breakpointSet table.
- setName(value) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Set Breakpoint Set Name. Name to be given to this set of breakpoints. This name will be stored in the breakpointSet table.
- setName(s) - Method in class net.maizegenetics.plugindef.Datum
-
- setNested(isNested) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setNestingEffectIndex(nestingFactorIndex) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setNext(next) - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
Sets this factor's next pointer to point to the specified factor. Although the next factor has typically a serial number equal to this factor's serial number plus 1, no attempt is made to guarantee this rule. This allows special constructs or a different order in the factorisation.
- setNext(value) - Method in class net.maizegenetics.dna.snp.MaskMatrixBuilder
-
- setNode(node) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- setNode(node) - Method in class net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
-
- setNodeHeight(value) - Method in interface net.maizegenetics.taxa.tree.Node
-
Set the height of this node relative to the most recent node.
- setNodeHeight(value, adjustChildBranchLengths) - Method in interface net.maizegenetics.taxa.tree.Node
-
Set the height of this node relative to the most recent node.
- setNodeHeight(value) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Set the height of this node relative to the most recent node.
- setNodeHeight(value, adjustChildBranchLengths) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Set the height of this node relative to the most recent node.
- setNodeToGroup(aNode, group, groups) - Method in class net.maizegenetics.taxa.tree.TreeClusters
-
- setNoteText(text) - Method in class net.maizegenetics.tassel.TASSELMainFrame
-
- setNumAccumulateIntervals(numIntervals) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setNumber(number) - Method in interface net.maizegenetics.taxa.tree.Node
-
set the index of this node
- setNumber(n) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- setNumberOfGroups(numberOfGroups) - Method in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
This sets the number of groups and calculates the output matrices. It must be run to set the number of groups before retrieving the compressed and adjustment matrices.
- setNumberOfPermutations(nperm) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- setNumberOfPermutations(numberOfPermutations) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- setNumWords(nWords) - Method in interface net.maizegenetics.util.BitSet
-
Expert: sets the number of longs in the array that are in use
- setNumWords(nWords) - Method in class net.maizegenetics.util.OpenBitSet
-
Expert: sets the number of longs in the array that are in use
- setNumWords(nWords) - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- setOpenFiles(openFiles) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- setOpenFiles(openFile) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- setOpenFiles(openFiles) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- setOutformat(theOutformat) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- setOuthapsAllProgeny(filename) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- setOutput(filename) - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- setOutputDiploid(outputDiploid) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setOutputFile(name) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- setOutputFile(filename) - Method in class net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
-
- setOutputName(outputName) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setOutputName(outputName) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setOverallDescription(description) - Method in class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- setOverlap(overlap) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setParameter(param, value) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setParameter(key, value) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setParameter(key, value) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setParameter(param, value) - Method in interface net.maizegenetics.plugindef.Plugin
-
Sets parameter value for a given plugin
- setParameter(key, value) - Method in interface net.maizegenetics.plugindef.Plugin
-
Sets parameter value for given parameter key.
- setParameter(key, value) - Method in interface net.maizegenetics.plugindef.Plugin
-
Sets parameter value for given parameter key.
- setParameter(param, n) - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- setParameter(param, n) - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- setParameter(param, n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- setParameter(param, n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- setParameter(param, n) - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
set model parameter
- setParameterizedBase(base) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
Set's the base parameterized object...
- setParameters(args) - Method in class net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.distance.KinshipPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.FastqToTBTPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.KmerToTBTPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.MergePETagCountPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.QseqToTBTPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setParameters(args) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setParameters(args) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setParameters(args) - Method in interface net.maizegenetics.plugindef.Plugin
-
Allows self-describing Plugins to use args to set parameters specific to itself.
- setParameterSE(paramSE, n) - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- setParameterSE(paramSE, n) - Method in class net.maizegenetics.taxa.tree.Parameterized.Null
-
- setParameterSE(paramSE, n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
- setParameterSE(paramSE, n) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
-
- setParameterSE(paramSE, n) - Method in interface net.maizegenetics.taxa.tree.Parameterized
-
set standard errors for model parameter
- setParametersToDefault() - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setParametersToDefault() - Method in interface net.maizegenetics.plugindef.Plugin
-
Sets all parameter values to default.
- setParent(node) - Method in interface net.maizegenetics.taxa.tree.Node
-
Set the parent node of this node.
- setParent(node) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Set the parent node of this node.
- setParentage(parentageFilename) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setParentage(filename) - Method in class net.maizegenetics.analysis.imputation.PhaseHighCoverage
-
- setParentCallInputFilename(parentCallFilename) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setParentcallOutFilename(parentcallOutFilename) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setPedfileName(pedfileName) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setPermutationNumber(permutationNumber) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setPermute(permute) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
- setPersistPreferences(persist) - Static method in class net.maizegenetics.prefs.TasselPrefs
-
Whether to Persist Preferences. Preference changes should be persisted when executing GUI and set only temporarily from Command Line Flags. Also getting preferences should use stored values when executing GUI. And should use default values (if not temporarily set) when executing from Command Line.
- setPhasedParentOutFilename(phasedParentOutFilename) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setPhysicalPositions(positions) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- setPhysicalPositions(positions) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- setPlotList(plotList) - Method in class net.maizegenetics.analysis.imputation.ImputeCrossProgeny
-
- setPositions(positions) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- setPower(power) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setPowerTransform(powerTransform) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setPredictedDistance(predictedDistance) - Method in class net.maizegenetics.dna.map.TagGWASMapInfo
-
- setProbHeterozygous(probHeterozygous) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- setRandom(random) - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- setRandomSeed(seed) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
This method is used mainly for testing in order to generate reproducible permutation results. If the seed is not set, the current time is used to initialize the random number generator.
- setRandomSeed(seed) - Method in class net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
-
Initializes the random number generator with a seed. Primarily used for testing to generate reproducible results.
- setRapidAnalysis(rapidAnalysis) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Set the read depth for a specific tag and taxon. Overwrite the depth that was previously there.
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- setReadCountForTagTaxon(tagIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- setReadCountForTaxa(readIndex, taxaIndex, value) - Method in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- setRegression(regression) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setRenderingType(type) - Method in class net.maizegenetics.gui.AlignmentTableCellRenderer
-
- setRenderingType(type) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- setRestricted(restricted) - Method in class net.maizegenetics.stats.linearmodels.FactorModelEffect
-
- setRoot(r) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Set a new node as root node.
- setRoot(root) - Method in interface net.maizegenetics.taxa.tree.Tree
-
This method constructs a tree from the given root node.
- setSaveFile(theSaveFile) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- setSaveFile(theSaveFile) - Method in class net.maizegenetics.analysis.chart.AbstractDisplayPlugin
-
- setSaveFile(saveFile) - Method in class net.maizegenetics.analysis.data.ExportPlugin
-
Deprecated.
- setSaveFiles(saveFiles) - Method in class net.maizegenetics.analysis.data.ExportMultiplePlugin
-
- setScaleOfView(chromosomalScale) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets the scale of the LD view, either sites are organized by chromosomes if chromosomalScale is true, otherwise they are organized by genes
- setScore(newScore) - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
Sets the score of this haplotype to the new score.
- setScoringScheme(scoring) - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
-
Sets the scoring scheme to be used for the next alignments. Any alignment or score already computed is lost. If the scoring scheme supports partial matches, this PairwiseAlignmentAlgorithm is set not to use the MATCH_TAG tag because in this case the score tag line be confusing. If the scoring scheme does not support partial matches, then the use of the MATCH_TAG tag is enabled.
- setSeed(seed) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- setSeed(seed) - Method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Initalize the pseudo random number generator. The Mersenne Twister only uses an integer for its seed; It's best that you don't pass in a long that's bigger than an int.
- setSelectionPath(theDatum) - Method in class net.maizegenetics.tassel.DataTreePanel
-
- setSequence(array) - Method in interface net.maizegenetics.taxa.tree.Node
-
Sets the sequence using an array of bytes.
- setSequence(s) - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
Sets the sequence at this node, in the form of an array of bytes.
- setSeries1(series1) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setSeries2(series2) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setSeries3(series3) - Method in class net.maizegenetics.analysis.chart.ChartDisplayPlugin
-
- setShowLabels(includeLabels) - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- setShowLabels(includeLabels) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
- setShown(search) - Method in class net.maizegenetics.gui.AbstractAvailableListModel
-
- setShowSchematic(includeBlockSchematic) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets whether a schematic is displayed. If true a schematic of genes or chromosomes is displayed, otherwise no schematic is displayed
- setSiteNamesToCovariates(mySitesToCovariates) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSiteNamesToFactors(mySitesToFactors) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSiteNamesToKeep(sitesToKeep) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSiteNamesToRemove(sitesToRemove) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSitesToCovariatesIndex(index) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSitesToFactorsIndex(index) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSitesToKeep(sitesToKeep) - Method in class net.maizegenetics.analysis.filter.FilterSiteNamePlugin
-
Deprecated.
- setSiteSubset(subset_val) - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- setSource(parameters, lowerLimits, upperLimits, defaultValues) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
Set's the base arrays...
- setSource(parameters, lowerLimits, upperLimits, defaultValues, parametersSE) - Method in class net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
-
Set's the base arrays...
- setStandardize(standardize) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setStart(start) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setStartPos(start) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setStateProbability(probTrueState) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithm
-
- setStateProbability(probTrueState) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
-
- setStepSize(stepSize) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setTableReport(theTable, seriesCategory, seriesY) - Method in class net.maizegenetics.analysis.chart.TableReportBoxWhiskerCatDataset
-
- setTableReport(theTable) - Method in class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- setTableReport(theTable, seriesCategory) - Method in class net.maizegenetics.analysis.chart.TableReportPieDataset
-
- setTableReport(theTable) - Method in class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- setTableReport(theTable, seriesCategory, seriesY) - Method in class net.maizegenetics.analysis.chart.TableReportStatCategoryDataset
-
- setTableReport(theTable, seriesX, seriesY1, seriesY2) - Method in class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- setTag(sequence, length, count, index) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- setTagAlignmentBest(tag, position, isBest) - Method in interface net.maizegenetics.dna.tag.RepGenDataWriter
-
- setTagAlignmentBest(tag, position, isBest) - Method in class net.maizegenetics.dna.tag.RepGenSQLite
-
- setTagAlignmentBest(tag, position, isBest) - Method in class net.maizegenetics.dna.tag.TagDataSQLite
-
- setTagAlignmentBest(tag, position, isBest) - Method in interface net.maizegenetics.dna.tag.TagDataWriter
-
- setTagLenException() - Method in class net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
-
- setTagLenException() - Method in class net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
-
- setTagLenException() - Method in class net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
-
- setTagLenException() - Method in class net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
-
- setTagLenException() - Method in class net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
-
- setTagLenException() - Static method in class net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
-
- setTaxaSubset(subset_val) - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- setTaxon(taxon) - Method in class net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
-
- setTestMarkers(testMarkers) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- setTestSite(site) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setTestSiteName(siteName) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setTheFileType(theFileType) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
- setThreaded(threaded) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- setThreaded(threaded) - Method in interface net.maizegenetics.plugindef.Plugin
-
Set whether this plugin is threaded.
- setTolerance(tolerance) - Method in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- SetToNGenotypeMergeRule - Class in net.maizegenetics.dna.snp.genotypecall
-
- setTraits(namelist) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setTraitsToTransform(traitsToTransform) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- setTransitionCounts(transitionCounts, chromosomeLength, numberOfTaxa) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
- setTransitionCounts(transitionCounts, chromosomeLength, numberOfTaxa) - Method in class net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
-
- setTransitionProbability(probabilityMatrix) - Method in class net.maizegenetics.analysis.imputation.TransitionProbability
-
Use this function to set the transition probability matrix when it is to be used without specifying nodes for getTransitionProbability
- setType(type) - Method in class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- setTypeChangeList(typeChangeList) - Method in class net.maizegenetics.analysis.filter.FilterTraitsPlugin
-
- setUnits(units) - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
Sets the units that this tree is expressed in.
- setup(ps, baseLookup, baseParameter) - Static method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- setupDebugLogfile(logFileName) - Static method in class net.maizegenetics.util.LoggingUtils
-
Sends all logging messages (including log4j) to specified file. The logging level will be DEBUG.
- setupDebugLogging() - Static method in class net.maizegenetics.util.LoggingUtils
-
Sends all logging messages (including log4j) to standard out. The logging level will be DEBUG.
- setupDebugLogging(stream) - Static method in class net.maizegenetics.util.LoggingUtils
-
Sends all logging messages (including log4j) to specified PrintStream. The logging level will be DEBUG. This is used to direct logging messages to the GUI.
- setupLogfile(logFileName) - Static method in class net.maizegenetics.util.LoggingUtils
-
Sends all logging messages (including log4j) to specified file. The logging level will be INFO, unless executed by the GUI and the user preference has been set level to DEBUG.
- setupLogging() - Static method in class net.maizegenetics.util.LoggingUtils
-
Sends all logging messages (including log4j) to standard out. The logging level will be INFO, unless executed by the GUI and the user preference has been set level to DEBUG.
- setupLogging(stream) - Static method in class net.maizegenetics.util.LoggingUtils
-
Sends all logging messages (including log4j) to specified PrintStream. The logging level will be INFO, unless executed by the GUI and the user preference has been set level to DEBUG. This is used to direct logging messages to the GUI.
- setupLoggingOff() - Static method in class net.maizegenetics.util.LoggingUtils
-
Turns off logging
- setUpperCorner(upperCorner) - Method in class net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
-
- setUpperCorner(ldMeasure) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This determines what is displayed in the upper right corner. Options are: P_VALUE, DPRIME, and RSQUARE
- setupStdOutLogging() - Static method in class net.maizegenetics.util.LoggingUtils
-
- setUseAllSiteTypes(useAllSiteTypes) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setUseBCFilter(useBCFilter) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setUseClusterAlgorithm(useClusterAlgorithm) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setUseGenotype(useGenotype) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setUseGenotype(useGenotype) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setUseHets(useHets) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setUseMultipleBCFilter(useMultipleBCFilter) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setUseP3D(useP3D) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setUseP3D(useP3D) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setUseRefProb(useRefProb) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setUseRefProb(useRefProb) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setUseVariableTransition(useVariableTransition) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- setUseWindowLD(useWindowLD) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setUTA(A) - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- setValueAt(aValue, rowIndex, columnIndex) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
No operation.
- setValueAt(aValue, rowIndex, columnIndex) - Method in class net.maizegenetics.gui.TableReportNoPagingTableModel
-
No operation.
- setVarCompEst(value) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setVarCompEst(value) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setVariableRecombFilename(variableRecombFilename) - Method in class net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
-
- setVariantDef(tagIndex, variantIndex, def) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setVariantDef(tagIndex, variantIndex, def) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setVariantDef(tagIndex, variantIndex, def) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setVariantDef(tagIndex, variantIndex, def) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Set variant definition at given tag and variant index.
- setVariantPosOff(tagIndex, variantIndex, offset) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- setVariantPosOff(tagIndex, variantIndex, offset) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- setVariantPosOff(tagIndex, variantIndex, offset) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- setVariantPosOff(tagIndex, variantIndex, offset) - Method in interface net.maizegenetics.dna.map.TOPMInterface
-
Set variant position offset at given tag and variant index.
- setWindowSize(windowSize) - Method in class net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
-
- setWindowSize(newSize, newX, newY, ldMeasureLower, ldMeasureUpper) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets a new viewable size
- setWindowSize(windowSize, windowX, windowY) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
-
resets myWindowSize
- setWindowX(newX, ldMeasureLower, ldMeasureUpper) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets a new X position
- setWindowX(windowX) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
-
resets myWindowX
- setWindowY(newY, ldMeasureLower, ldMeasureUpper) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets a new Y position
- setWindowY(windowY) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
-
resets myWindowY
- setWinSize(winSize) - Method in class net.maizegenetics.analysis.filter.FilterAlignmentPlugin
-
- setWinSize(winSize) - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
-
- setWriteNucleotides(writeNucleotides) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setWriteOutputToFile(writeOutputToFile) - Method in class net.maizegenetics.analysis.association.MLMPlugin
-
- setWriteOutputToFile(writeOutputToFile) - Method in class net.maizegenetics.analysis.association.WeightedMLMPlugin
-
- setWriteParentCalls(writeParentCalls) - Method in class net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
-
- setXStart() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets the X start and end positions
- setYStart() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
-
This sets the Y start and end positions
- sex(val) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Set sex: 0=both, 1=female, 2=male (default=0 Both)
- SexKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for the sex of the taxon
- SHORT_UNIT_NAMES - Variable in interface net.maizegenetics.taxa.tree.Units
-
- shortenStrLineLen(str, preferredLen) - Static method in class net.maizegenetics.util.Utils
-
- shortenStrLineLen(str, preferredLen, preferredLines) - Static method in class net.maizegenetics.util.Utils
-
- ShortReadBarcodeResult - Class in net.maizegenetics.analysis.gbs
-
Container class for returning the results of parsed barcoded sequencing read. The length of read is in short. Max length is 32767 bp.
- ShortReadBarcodeResult(read, length, taxon) - Constructor for class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
- ShortReadBarcodeResult(sequence) - Constructor for class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
Construct object with genomic sequence
- showDialog() - Method in class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- showError(str, parent) - Static method in class net.maizegenetics.gui.DialogUtils
-
- showError(e, parent) - Static method in class net.maizegenetics.gui.DialogUtils
-
- showErrorCause(e, parent) - Static method in class net.maizegenetics.gui.DialogUtils
-
- ShowParameterCachePlugin - Class in net.maizegenetics.tassel
-
- ShowParameterCachePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.tassel.ShowParameterCachePlugin
-
- showWarning(str, parent) - Static method in class net.maizegenetics.gui.DialogUtils
-
- shrinkToCurrentRows() - Method in class net.maizegenetics.dna.tag.TagCountMutable
-
- shuffle(anArray) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffle(anArray) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffle(anArray) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffle(anArray) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffle(anArray) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffle(anArray) - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffle(source, randomizer) - Static method in class net.maizegenetics.stats.linearmodels.LinearModelUtils
-
- shuffle(columnMatrix, randomizer) - Static method in class net.maizegenetics.stats.linearmodels.LinearModelUtils
-
- shuffle(array) - Method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Shuffles an array.
- shuffle(array) - Method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Shuffles an array of objects.
- shuffle(array, numberOfShuffles) - Method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Shuffles an array by repeatedly choosing two random members and swapping them.
- shuffled(l) - Method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Generates an array of ints that are shuffled
- shuffleDouble() - Static method in class net.maizegenetics.stats.linearmodels.BasicShuffler
-
- shuffleSubset(startIndex, length, array) - Method in class net.maizegenetics.stats.math.MersenneTwisterFast
-
Shuffles an array of objects.
- sibling - Variable in class net.maizegenetics.analysis.gbs.neobio.Trie
-
A pointer to this node's next sibling.
- sigSiteEnd - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Ending significant site on the best chromosome, inclusive, unknown = Integer.MIN_VALUE
- sigSiteNum - Variable in class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
Number of sites passing P-value threshold
- sigSiteRange - Variable in class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
Range of sites passing P-value threshold, for the first significant site to the last
- sigSiteStart - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Starting significant site on the best chromosome, unknown = Integer.MIN_VALUE
- SimpleAllele - Class in net.maizegenetics.dna.snp
-
Basic implementation of allele. TODO: Consider whether this should be kept. TODO: Should there be a builder? TODO: Should there simple nucleotide one versus other states. Memory could be an important consideration.
- SimpleAllele(myAllele, myPosition) - Constructor for class net.maizegenetics.dna.snp.SimpleAllele
-
- SimpleGenotypeSBit - Class in net.maizegenetics.analysis.gbs
-
Store sBit for tag genetic mapping and LD detection, optimized for really fast calculation
- SimpleGenotypeSBit(genotypeH5FileS, sBitFileS) - Constructor for class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
Convert HDF5 Alignment/Genotype file to SimpleGenotypeSBit
- SimpleGenotypeSBit(inputfileS) - Constructor for class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
Read in HDF5 SimpleGenotypeSBit
- SimpleNode - Class in net.maizegenetics.taxa.tree
-
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree
- SimpleNode() - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
constructor default node
- SimpleNode(name, branchLength) - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
- SimpleNode(children, branchLength) - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
Constructor
- SimpleNode(children) - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
- SimpleNode(n) - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
constructor used to clone a node and all children
- SimpleNode(n, keepIds) - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
- SimpleNode(n, lm) - Constructor for class net.maizegenetics.taxa.tree.SimpleNode
-
- SimpleTableReport - Class in net.maizegenetics.util
-
Created by IntelliJ IDEA. User: ed Date: Sep 28, 2006 Time: 9:37:46 PM
- SimpleTableReport(theName, columnNames, theData) - Constructor for class net.maizegenetics.util.SimpleTableReport
-
- SimpleTableReport(tr) - Constructor for class net.maizegenetics.util.SimpleTableReport
-
- SimpleTree - Class in net.maizegenetics.taxa.tree
-
data structure for a binary/non-binary rooted/unrooted trees
- SimpleTree() - Constructor for class net.maizegenetics.taxa.tree.SimpleTree
-
constructor tree consisting solely of root node
- SimpleTree(r) - Constructor for class net.maizegenetics.taxa.tree.SimpleTree
-
constructor taking a root node
- SimpleTree(tree) - Constructor for class net.maizegenetics.taxa.tree.SimpleTree
-
clone constructor
- SimpleTree(tree, keepIdentifiers) - Constructor for class net.maizegenetics.taxa.tree.SimpleTree
-
clone constructor
- SimpleTree(tree, lm) - Constructor for class net.maizegenetics.taxa.tree.SimpleTree
-
clone constructor
- SingularValueDecomposition - Interface in net.maizegenetics.matrixalgebra.decomposition
-
- singularValueDecompositionDgesdd(jobz, m, n, A, lda, S, U, ldu, VT, ldvt) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- singularValueDecompositionDgesvd(jobu, jobvt, m, n, A, lda, S, U, ldu, VT, ldvt) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- site(site) - Method in class net.maizegenetics.dna.snp.Translate
-
- site1() - Method in class net.maizegenetics.analysis.popgen.LDResult
-
- site2() - Method in class net.maizegenetics.analysis.popgen.LDResult
-
- SITE_BLOCK_MASK - Static variable in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- SITE_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- SiteAnnotation - Class in net.maizegenetics.dna.pd
-
User: dkroon Date: 6/26/13 Time: 2:07 PM
- SiteAnnotation(aSite, aChromosome, aPosition) - Constructor for class net.maizegenetics.dna.pd.SiteAnnotation
-
- siteCount(value) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- siteCount() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- SITECOV - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- SITECOV - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- siteCoverage(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set site coverage annotation (default=Float.NaN)
- siteData - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteFilter() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
True if filtering by site numbers. False if filtering by chromosome and position
- siteFilter(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Site Filter. True if filtering by site numbers. False if filtering by chromosome and position
- siteFilterType() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- SITEHET - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- siteIndex - Variable in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- siteList - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- siteMask(site) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- siteMask(site) - Method in class net.maizegenetics.dna.snp.MaskGenotypeMatrix
-
- siteMask(site) - Method in class net.maizegenetics.dna.snp.MaskGenotypeStatsMatrix
-
- siteMaxAlleleFreq() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Site Maximum Minor Allele Frequency
- siteMaxAlleleFreq(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Site Max Allele Freq. Site Maximum Minor Allele Frequency
- siteMaxAlleleFreq() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- siteMinAlleleFreq() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Site Minimum Minor Allele Frequency
- siteMinAlleleFreq(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Site Min Allele Freq. Site Minimum Minor Allele Frequency
- siteMinAlleleFreq() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- siteMinCount() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Site Minimum Count of Alleles not Unknown
- siteMinCount(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Site Min Count. Site Minimum Count of Alleles not Unknown
- siteMinCount() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- siteName() - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- siteName() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- siteName(site) - Method in interface net.maizegenetics.dna.map.PositionList
-
Get SNP ID for specified site.
- siteName(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- siteName(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- siteName(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Get SNP ID for specified site.
- siteName(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- siteName(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- siteNameList() - Method in class net.maizegenetics.plugindef.PluginParameter.Builder
-
- siteNames(value) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- siteNames() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- siteNames() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- SiteNamesAvailableListModel - Class in net.maizegenetics.gui
-
- SiteNamesAvailableListModel(positions) - Constructor for class net.maizegenetics.gui.SiteNamesAvailableListModel
-
- siteNamesList() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Site Names List
- siteNamesList(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Site Names List. Site Names List
- siteNum - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- siteNumber() - Method in class net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
-
- siteNumber() - Method in interface net.maizegenetics.analysis.modelfitter.AdditiveSite
-
- siteOfPhysicalPosition(physicalPosition, chromosome) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return site of given physical position in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown.
- siteOfPhysicalPosition(physicalPosition, chromosome, snpName) - Method in interface net.maizegenetics.dna.map.PositionList
-
Return site of given physical position / SNP ID in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown. This is to support multiple sites with the same physical position but different SNP IDs.
- siteOfPhysicalPosition(physicalPosition, locus) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, locus, snpName) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, chromosome) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, chromosome, snpName) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, chromosome) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return site of given physical position in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown.
- siteOfPhysicalPosition(physicalPosition, chromosome, snpName) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return site of given physical position / SNP ID in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown. This is to support multiple sites with the same physical position but different SNP IDs.
- siteOfPhysicalPosition(physicalPosition, chromosome) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, chromosome, snpName) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, chromosome) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- siteOfPhysicalPosition(physicalPosition, chromosome, snpName) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- siteReport() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteReport() - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- siteReportBuilder - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteReportColumnNames() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteReportColumnNames() - Method in class net.maizegenetics.analysis.association.ReferenceProbabilityFELM
-
- siteReportFilename - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteReportFilename() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
The name of the file to which these results will be saved.
- siteReportFilename(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Statistics File. The name of the file to which these results will be saved.
- siteReportFilepath(savefile) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteReportFilepath(savefile) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- SiteScore - Interface in net.maizegenetics.dna.snp.score
-
- SiteScore.SITE_SCORE_TYPE - Enum in net.maizegenetics.dna.snp.score
-
- SiteScoresIO - Class in net.maizegenetics.dna.snp.io
-
- siteScoreType() - Method in class net.maizegenetics.dna.snp.byte2d.AbstractByte2D
-
- siteScoreType() - Method in interface net.maizegenetics.dna.snp.byte2d.Byte2D
-
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- siteScoreTypes() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return the site scores types that have value for this genotype table.
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.score.AlleleDepth
-
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.score.AlleleProbability
-
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.score.Dosage
-
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.score.ReferenceProbability
-
- siteScoreTypes() - Method in interface net.maizegenetics.dna.snp.score.SiteScore
-
Return the site scores types.
- siteScoreTypes() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- SiteScoreUtil - Class in net.maizegenetics.dna.snp.score
-
- siteStatFilename() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Site Stat File
- siteStatFilename(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Site Stat File. Site Stat File
- siteStats(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
- siteStatsFile - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteStatsFile(filename) - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteStatsFile(filename) - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
- siteStatsOutput() - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Generate an output dataset with only p-val, F statistic, and number of obs per site for all sites.
- siteStatsOutput(value) - Method in class net.maizegenetics.analysis.association.FixedEffectLMPlugin
-
Set Output Site Stats. Generate an output dataset with only p-val, F statistic, and number of obs per site for all sites.
- sitesToKeep() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- siteSubset() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- siteSummary() - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
Get Site Summary
- siteSummary(value) - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
Set Site Summary. Get Site Summary
- siteTableReportRows - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- siteTranslations() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- siteTranslations() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- siteTranslations() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
- siteTranslations() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- siteTranslations() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- siteTranslations() - Method in class net.maizegenetics.dna.snp.Translate
-
- size() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- size() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- size() - Method in class net.maizegenetics.analysis.avro.GenericMapAnnotations
-
- size() - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
Returns the size (number of positions) in the current list
- size() - Method in class net.maizegenetics.dna.snp.FilterList
-
- size() - Method in class net.maizegenetics.dna.snp.genotypecall.ListStats
-
- size - Variable in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- size() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- size() - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- size() - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- size() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- size() - Method in interface net.maizegenetics.util.BitSet
-
- size() - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- size() - Method in class net.maizegenetics.util.DirectedGraph
-
- size(weighted) - Method in class net.maizegenetics.util.DirectedGraph
-
- size() - Method in interface net.maizegenetics.util.Graph
-
Gets the number of edges in the graph
- size(weighted) - Method in interface net.maizegenetics.util.Graph
-
Gets the sum of edges in the graph
- size() - Method in class net.maizegenetics.util.OpenBitSet
-
- size() - Method in class net.maizegenetics.util.UndirectedGraph
-
- size(weighted) - Method in class net.maizegenetics.util.UndirectedGraph
-
- size() - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- size() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- Sizeof - Class in net.maizegenetics.util
-
- skipWhiteSpace(in) - Method in class net.maizegenetics.util.FormattedInput
-
go to first non-whitespace character
- slice(inputFileName, sequences) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
- smawk - Variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
An instance of the Smawk class that implements the SMAWK algorithm to compute the column maxima of a totally monotone matrix. It is used to speed up the computation of the output border of a block.
- Smawk - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described.
- SmithWaterman - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implement the classic local alignment algorithm (with linear gap penalty function) due to T.F.Smith and M.S.Waterman (1981).
- SmithWaterman - Class in net.maizegenetics.analysis.gbs
-
This class implement the classic local alignment algorithm (with linear gap penalty function) due to T.F.Smith and M.S.Waterman (1981).
- SmithWaterman() - Constructor for class net.maizegenetics.analysis.gbs.SmithWaterman
-
- SmithWaterman(rows, cols) - Constructor for class net.maizegenetics.analysis.gbs.SmithWaterman
-
- SmithWaterman(b1, b2) - Constructor for class net.maizegenetics.analysis.gbs.SmithWaterman
-
- SMTPClient - Class in net.maizegenetics.util
-
This class can be used to send email. When the host is "appsmtp.mail.cornell.edu", any machine within the Cornell network can be used to send an email. Reference: https://confluence.cornell.edu/login.action?os_destination=https%3A%2F%2Fconfluence.cornell.edu%2Fdisplay%2Fcitapps%2FHow%2Bto%2Bconfigure%2Bapplications%2Bto%2Bsend%2Bmail%2Bthrough%2Bthe%2BCornell%2Bmail%2Bservers.
- SMTPClient(host, toAddresses) - Constructor for class net.maizegenetics.util.SMTPClient
-
- SNP - Class in net.maizegenetics.analysis.modelfitter
-
- SNP(name, locus, positionInLocus, index) - Constructor for class net.maizegenetics.analysis.modelfitter.SNP
-
- SNP() - Constructor for class net.maizegenetics.analysis.modelfitter.SNP
-
- SNP_IDS - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- SNP_IDS - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- SNPCutPosTagVerificationPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
This class allows a user to specify a Cut or SNP position for which they would like data printed. For a Cut Position, the tags associated with that position are printed along with the number of times it appears in each taxa. For a SNP Position, each allele and the tags associated with that allele are printed along with the number of times the tag appears in each taxa. The tag is shown both as it is stored in the db, and as a forward strand. The SNP alignments are based on forward strand.
- SNPCutPosTagVerificationPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- SNPCutPosTagVerificationPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- SNPCutPosTagVerificationPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
- snpIndex - Variable in class net.maizegenetics.analysis.imputation.PopulationData
-
- SNPLogging - Class in net.maizegenetics.analysis.gbs
-
- SNPLogging(filename, creator) - Constructor for class net.maizegenetics.analysis.gbs.SNPLogging
-
- snpName(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set SNP name (default="S"+Chromosome+"_"+position)
- snpPosToIDMap - Variable in class net.maizegenetics.dna.tag.RepGenSQLite
-
- snpPosToIDMap - Variable in class net.maizegenetics.dna.tag.TagDataSQLite
-
- SNPQualityProfilerPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
Scores all discovered SNPs for various coverage, depth, and genotypic statistics for a given set of taxa (samples). For each subset of taxa, there are expectations for segregation that can be used to determine whether the SNP is behaving appropriately.
- SNPQualityProfilerPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
- SNPQualityProfilerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
- snpsAsFloatVector(alleles, nsnps) - Static method in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- solve() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- solve() - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- solve() - Method in interface net.maizegenetics.analysis.association.FixedEffectLM
-
Solves the linear model
- solve() - Method in class net.maizegenetics.analysis.association.PhenotypeLM
-
- solve() - Method in class net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
-
Solve the mixed model for line GEBVs and marker estimates
- solve(Y) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- solve(Y) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- solve(Y) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- solve(Y) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- solve() - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- SolveByOrthogonalizing - Class in net.maizegenetics.stats.linearmodels
-
- SolveByOrthogonalizing.Marker - Class in net.maizegenetics.stats.linearmodels
-
- solveForR(marker) - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- solveForR(pos, values) - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- solveForR(pos, add, dom) - Method in class net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
-
- solveLSdgelsd(A, Arows, Acols, B, Bcols, rcond, rank) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- solveLSdgelsy(A, Arows, Acols, B, Bcols, rcond, rank) - Static method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- solveWithNewData(y) - Method in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- son - Variable in class net.maizegenetics.analysis.gbs.neobio.Trie
-
A pointer to the first of this node's children.
- sort() - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Sort the class based on 64 bp tags
- sort() - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
- sort() - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
sort PE tags by Long primitive data type value
- sort() - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- sort() - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- sort() - Method in class net.maizegenetics.dna.tag.TagCounts
-
- sortAlphabetically() - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- sortByOrder() - Method in class net.maizegenetics.dna.tag.UTagPairs
-
- sortByPosition() - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Sort TOGM by genetic position
- sortBySeq() - Method in class net.maizegenetics.dna.tag.UTagPairs
-
- sortClusters() - Method in class net.maizegenetics.analysis.clustering.HaplotypeClusterer
-
Sorts clusters according to HaplotypeCluster sort order.
- SortGenotypeFilePlugin - Class in net.maizegenetics.analysis.data
-
Created by jgw87 on 6/5/14. This plugin takes a Hapmap or VCF genotype file and sorts it according to TASSEL's conventions which rely on the position, locus (chromosome), strand, and SNP name (to facilitate searching).
- SortGenotypeFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SortGenotypeFilePlugin
-
- SortGenotypeFilePlugin.SupportedFileTypes - Enum in net.maizegenetics.analysis.data
-
- sortPositions() - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
Whether to sort genotype positions if that's possible.
- sortPositions(value) - Method in class net.maizegenetics.analysis.data.FileLoadPlugin
-
Set Sort Positions. Whether to sort genotype positions if that's possible.
- sortPositions() - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Whether to sort genotype positions.
- sortPositions(value) - Method in class net.maizegenetics.analysis.data.PlinkLoadPlugin
-
Set Sort Positions. Whether to sort genotype positions.
- sortPositions(genotypes) - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
- sortPositions() - Method in class net.maizegenetics.dna.map.PositionListBuilder
-
- sortPositions() - Method in class net.maizegenetics.dna.snp.io.BuilderFromHapMap
-
Set the builder so that when built it will sort positions.
- sortPositions() - Method in class net.maizegenetics.dna.snp.io.BuilderFromPLINK
-
Set the builder so that when built it will sort the positions.
- sortTable(byHaplotype) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- sortTable(byHaplotype) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
- sortTaxa() - Method in class net.maizegenetics.dna.snp.GenotypeTableBuilder
-
Set the builder so that when built it will sort the taxa
- sortTaxa() - Method in class net.maizegenetics.dna.snp.io.BuilderFromHapMap
-
Set the builder so that when built it will sort the taxa alphabetically.
- sortTaxa() - Method in class net.maizegenetics.dna.snp.io.BuilderFromPLINK
-
Set the builder so that when built it will sort the taxa
- sortTaxaAlphabetically(genotypes) - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- sortTaxaAlphabetically() - Method in class net.maizegenetics.taxa.TaxaListBuilder
-
- SortTaxaAlphabeticallyPlugin - Class in net.maizegenetics.analysis.data
-
- SortTaxaAlphabeticallyPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
-
- soundex2(s1, ignoreCase, ignoreWhite, ignorePunc) - Static method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- source_path - Variable in class net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
-
An array of indexes to the source of the highest scoring path for each entry in the output border.
- space(size, c) - Static method in class net.maizegenetics.util.FormattedOutput
-
returns of string of a given length of a single character.
- sparsity(inputFileName, format) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Write out only the taxa that match a list of names
- SpeciesKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for a species of the taxon
- spellDown(c) - Method in class net.maizegenetics.analysis.gbs.neobio.Trie
-
Follows a path from this node to one of its children by spelling the character supplied as an argument. If there is no such a path, null is returned. Otherwise, the reached child node is returned.
- spellRight(c) - Method in class net.maizegenetics.analysis.gbs.neobio.Trie
-
Follows a path from this node to one of its sibling by spelling the character supplied as an argument. If there is no such a path, null is returned. Otherwise, the reached sibling node is returned.
- spliterator() - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- spliterator() - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- spliterator() - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- SplitFile_IFLFilePlugin - Class in net.maizegenetics.analysis.gobii
-
- SplitFile_IFLFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
- SplitFile_IFLFilePlugin() - Constructor for class net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
-
- SplitHDF5ByChromosomePlugin - Class in net.maizegenetics.analysis.data
-
- SplitHDF5ByChromosomePlugin() - Constructor for class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
- SplitHDF5ByChromosomePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
-
- splitIFLFile(infile, outdir, maxSize) - Static method in class net.maizegenetics.analysis.gobii.GOBII_IFLUtils
-
This method is created to break up very large files that GOBII can't handle. For example: one dataset has 83M+ lines. Takes GOBII overnight just to load the marker_linkage_group or dataset_marker data. Yaw suggests we break it into files of size 10M. So pass in the file, give an output directory, and split the file into smaller files. Each smaller file must retain the header, and it must end with the same table name (e.g. DS_4.marker_linkage_gropu must still
- SplitSystem - Class in net.maizegenetics.taxa.tree
-
data structure for a set of splits
- SplitSystem(idGroup, size) - Constructor for class net.maizegenetics.taxa.tree.SplitSystem
-
- splitTable(table) - Method in class net.maizegenetics.analysis.chart.XYScatterAndLinePanel
-
- splitTagBlockPositionPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- splitTBTPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- SplitUtils - Class in net.maizegenetics.taxa.tree
-
utilities for split systems
- SQL - Class in net.maizegenetics.util.db
-
Set of utilities for working with JDBC User: julian3 Date: 2013/11/10 Time: 7:14 PM PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- SQLAction<T> - Interface in net.maizegenetics.util.db
-
Created with IntelliJ IDEA. User: julian3 Date: 2013/12/05 Time: 3:28 PM To change this template use File | Settings | File Templates. Description: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- squaredDistance(mat, weighted) - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
compute squared distance to second distance matrix
- squaredDistance(mat1, mat2, weighted) - Static method in class net.maizegenetics.taxa.distance.DistanceMatrixUtils
-
compute squared distance to second distance matrix. If both matrices have the same size it is assumed that the order of the taxa is identical.
- src_dataset() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Name of the dataset from which these breakpoints were created. Must match an existing name in the dataset table.
- src_dataset(value) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Set src_dataset. Name of the dataset from which these breakpoints were created. Must match an existing name in the dataset table,
- ssError - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- ssModel - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- SST - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- standardize() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataDialog
-
- standardize(original) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- standardize(original, byFactors) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- start() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- start(start) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- start(start) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- start() - Method in class net.maizegenetics.dna.snp.io.ReadBedfile.BedFileRange
-
Returns start position (inclusive)
- startAndEndOfChromosome(chromosome) - Method in interface net.maizegenetics.dna.map.PositionList
-
Get the first (inclusive) and last (inclusive) site of the specified chromosome in this alignment.
- startAsString() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- startBlock - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- startChr() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Start Chr
- startChr(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Start Chr. Start Chr
- startChr() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- startChromosome() - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Start Chromosome
- startChromosome(value) - Method in class net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
-
Set Start Chromosome. Start Chromosome
- startChromosome() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Chromosome to start numbering at
- startChromosome(value) - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Set Start chromosome. Chromosome to start numbering at
- startChromosome() - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Start Chromosome
- startChromosome(value) - Method in class net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
-
Set Start Chromosome. Start Chromosome
- startLambda() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Start Lambda
- startLambda(value) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Set Start Lambda. Start Lambda
- startLine() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
-
- startPos() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Start Pos
- startPos(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Start Pos. Start Pos
- startPos() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- startPos - Variable in class net.maizegenetics.plugindef.GenerateRCode.PositionVectors
-
- startPosition() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
Start physical position (inclusive)
- startPosition - Variable in class net.maizegenetics.dna.map.TagMappingInfo
-
Chromosomal position of the barcoded end of the tag
- startPosition - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Chromosomal position of the barcoded end of the tag, unknown = Integer.MIN_VALUE
- startSite() - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Start Site
- startSite(value) - Method in class net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
-
Set Start Site. Start Site
- startSite - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- startSite() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
Start Site
- startSite(value) - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
Set Start Site. Start Site
- startSite() - Method in class net.maizegenetics.dna.snp.FilterSite
-
- state - Variable in exception net.maizegenetics.util.db.DataAccessException
-
- stateChanged(e) - Method in class net.maizegenetics.gui.AlignmentTableModel
-
- statesFile() - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
The output file containing the new progeny states (parentcalls) in hapmap format
- statesFile(value) - Method in class net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
-
Set Progeny States Output File. The output file containing the new progeny states (parentcalls) in hapmap format
- statFile() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Name of output file (e.g. GBSv2.db)
- statFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Set GBS DB File. Name of output file (e.g. GBSv2.db)
- statNames() - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
Comma separated list of column names from which to pull data. These names must match values in the statistics field of the gwas_method table for the specified method name.
- statNames(value) - Method in class net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
-
Set Statistic Names. Comma separated list of column names from which to pull data. These names must match values in the statistics field of the gwas_method table for the specified method name.
- Stats - Class in net.maizegenetics.dna.snp.genotypecall
-
- STATS_HEADER_CHR - Static variable in class net.maizegenetics.analysis.association.AssociationConstants
-
- STATS_HEADER_MARKER - Static variable in class net.maizegenetics.analysis.association.AssociationConstants
-
- STATS_HEADER_P_VALUE - Static variable in class net.maizegenetics.analysis.association.AssociationConstants
-
- STATS_HEADER_POSITION - Static variable in class net.maizegenetics.analysis.association.AssociationConstants
-
- STATS_HEADER_TRAIT - Static variable in class net.maizegenetics.analysis.association.AssociationConstants
-
- stepLambda() - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Step Lambda
- stepLambda(value) - Method in class net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
-
Set Step Lambda. Step Lambda
- stepSize() - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
Step Size
- stepSize(value) - Method in class net.maizegenetics.analysis.data.FindInversionsPlugin
-
Set Step Size. Step Size
- stepSize() - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
Step Size
- stepSize(value) - Method in class net.maizegenetics.analysis.distance.VCAPScanPlugin
-
Set Step Size. Step Size
- stepSize() - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
Step Size
- stepSize(value) - Method in class net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
-
Set Step Size. Step Size
- StepwiseAddDomModelFitter - Class in net.maizegenetics.analysis.modelfitter
-
Fits an additive plus dominance model in a stepwise fashion. See StepwiseAdditiveModelFitter for a desription of outputs available.
- StepwiseAddDomModelFitter(genopheno, datasetName) - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
-
- StepwiseAdditiveModelFitter - Class in net.maizegenetics.analysis.modelfitter
-
A multi-threaded stepwise model fitter for additive only models. To use it first construct an object then call runAnalysis(). After the analysis has run, any of several reports will be available using getters. If a permutation test is requested it is run first. The analysis then fits SNPs consecutively, then rescans the full model to determine if any of the SNPs has a better choice given all the other SNPs in the model. As part of the rescan it calculates a support interval for each of the SNPs. Reports available include the steps taken to fit the model with sequential p-values, an anova with marginal p-values, a report of marker effects, a post-scan anova, post-scan marker effects, and a permutation report. It will also output a list of model residuals by chromosome. For each chromosome, it reports the residuals from a model that includes all effects, except the markers on that chromosome.
- StepwiseAdditiveModelFitter(genopheno, datasetName) - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- StepwiseAdditiveModelFitterPlugin - Class in net.maizegenetics.analysis.modelfitter
-
- StepwiseAdditiveModelFitterPlugin() - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- StepwiseAdditiveModelFitterPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
-
- StepwiseOLSModelFitter - Class in net.maizegenetics.analysis.modelfitter
-
- StepwiseOLSModelFitter(genoPheno, datasetName) - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
-
- StepwiseOLSModelFitter.MODEL_TYPE - Enum in net.maizegenetics.analysis.modelfitter
-
- StepwiseOLSModelFitter.VIF_TYPE - Enum in net.maizegenetics.analysis.modelfitter
-
- StepwiseOLSModelFitterPlugin - Class in net.maizegenetics.analysis.modelfitter
-
Stepwise Ordinary Least Squares model fitter
- StepwiseOLSModelFitterPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- StepwiseOLSModelFitterPlugin() - Constructor for class net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
-
- stop() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- stop(stop) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- stop(stop) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- STOP_DIRECTION - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
A constant that indicates that the source of an optimal path has been reached in a block and that the trace back procedure to retrieve a high scoring alignment can stop.
- stopAsString() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- strand() - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Strand direction
- strand(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
-
Set strand direction.
- strand(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
Set strand (default=1)
- strand(val) - Method in class net.maizegenetics.dna.map.GeneralPosition.Builder
-
- strand - Variable in class net.maizegenetics.dna.map.TagMappingInfo
-
Strand relative to reference genome. 1 = same sense as reference FASTA file. -1 = opposite sense. unknown = Byte.MIN_VALUE
- strand - Variable in class net.maizegenetics.dna.map.TagMappingInfoV3
-
Strand relative to reference genome. 1 = same sense as reference FASTA file. -1 = opposite sense. unknown = Byte.MIN_VALUE
- strand - Variable in class net.maizegenetics.plugindef.GenerateRCode.PositionVectors
-
- STRAND_MINUS - Static variable in interface net.maizegenetics.dna.map.Position
-
- STRAND_MINUS_STR - Static variable in interface net.maizegenetics.dna.map.Position
-
- STRAND_PLUS - Static variable in interface net.maizegenetics.dna.map.Position
-
- STRAND_PLUS_STR - Static variable in interface net.maizegenetics.dna.map.Position
-
- STRAND_UNKNOWN - Static variable in interface net.maizegenetics.dna.map.Position
-
- STRAND_UNKNOWN_STR - Static variable in interface net.maizegenetics.dna.map.Position
-
- strandB - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- strandContig - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- strandF - Variable in class net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
-
- stream(filename) - Static method in class net.maizegenetics.analysis.phg.ParseGVCF
-
The returns a list of the GVCF header lines and a stream of the processed data lines. If you want the stream to return the data lines in order found in the file, do not call parallel().
- stream() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns a Stream over the genotype calls.
- stream(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
- stream(connection, sql, parms) - Static method in class net.maizegenetics.util.db.SQL
-
- stream() - Method in interface net.maizegenetics.util.SuperByteMatrix
-
Returns a Stream over the bytes of this matrix.
- stream(row) - Method in interface net.maizegenetics.util.SuperByteMatrix
-
- stream() - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- stream(row) - Method in class net.maizegenetics.util.SuperByteMatrixMultiple
-
- stream() - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- stream(row) - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- stream() - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- stream(row) - Method in class net.maizegenetics.util.SuperByteMatrixSingleValue
-
- stream() - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- stream(row) - Method in class net.maizegenetics.util.SuperByteMatrixTranspose
-
- streamBinaryToText(inputFileName, maxRecords) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Converts a binary .tbt file to text, using only the memory required for the file buffer.
- streamGenotype() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- streamGenotype(taxon) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- streamGenotype() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- streamGenotype(taxon) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- streamGenotype() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
- streamGenotype(taxon) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
- streamGenotype() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- streamGenotype(taxon) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- streamGenotype() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- streamGenotype(taxon) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- streamTextToBinary(inputFileName, outputFileName) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Converts a text .tbt file to binary, using only the memory required for the file buffer.
- StringNumberComparator - Class in net.maizegenetics.util
-
Title: TASSEL Description: A java program to deal with diversity Copyright: Copyright (c) 2000 Company: USDA-ARS/NCSU
- StringNumberComparator() - Constructor for class net.maizegenetics.util.StringNumberComparator
-
- studyName() - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
Name of the study
- studyName(value) - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
Set Study Name. Name of the study
- subHaplotype(size, fromStart) - Method in class net.maizegenetics.analysis.clustering.Haplotype
-
- subintervalCount - Variable in class net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
-
- subList(fromIndex, toIndex) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- subList(fromIndex, toIndex) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- subList(fromIndex, toIndex) - Method in class net.maizegenetics.dna.snp.FilterList
-
- SubpopulationFinder - Class in net.maizegenetics.analysis.imputation
-
- subset(obs, newName) - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- subset(obs, newName) - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- subset(obs, newName) - Method in interface net.maizegenetics.phenotype.PhenotypeAttribute
-
- subset(obs, newName) - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- subsetGenotypesToNewFile(t5File, subT5File, subsetTaxa) - Static method in class net.maizegenetics.analysis.data.LowLevelCopyOfHDF5
-
- subsets(byFactors) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- subsetTaxaListByAnnotation(baseTaxaList, annotation, annoValue) - Static method in class net.maizegenetics.taxa.TaxaListIOUtils
-
Returns a subsetted taxa list based on annotation value. For example, return all taxa where GermType=Inbred.
- subsetTree(tree, taxaList) - Static method in class net.maizegenetics.taxa.tree.NewickUtils
-
Returns a tree that is a subset of the
original containing only the taxa specified.
- subsetTree(tree, namesToKeep) - Static method in class net.maizegenetics.taxa.tree.NewickUtils
-
Returns a tree that is a subset of the
original containing only the names specified.
- SubsetTreePlugin - Class in net.maizegenetics.analysis.tree
-
- SubsetTreePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- SubsetTreePlugin() - Constructor for class net.maizegenetics.analysis.tree.SubsetTreePlugin
-
- SubsetTreePluginKt - Class in net.maizegenetics.analysis.tree
-
- SubtractDistanceMatrixPlugin - Class in net.maizegenetics.analysis.distance
-
- SubtractDistanceMatrixPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
-
- subtractEndelmanDistance(matrices, superMatrix, listener) - Static method in class net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
-
- subtractGCTADistance(matrices, superMatrix, listener) - Static method in class net.maizegenetics.analysis.distance.GCTADistanceMatrix
-
- SubtractGenotypesPlugin - Class in net.maizegenetics.analysis.data
-
- SubtractGenotypesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SubtractGenotypesPlugin
-
- SubtractPhenotype - Class in net.maizegenetics.analysis.numericaltransform
-
- subtractPhenotype(pheno1, pheno2, useAbsDiff) - Method in class net.maizegenetics.analysis.numericaltransform.SubtractPhenotype
-
- SubtractPhenotypeByTaxaPlugin - Class in net.maizegenetics.analysis.numericaltransform
-
- SubtractPhenotypeByTaxaPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
-
- SUBTREE_PROBABILITY - Variable in interface net.maizegenetics.taxa.tree.AttributeNode
-
attribute name for the probability of the subtree defined by an internal node.
- subtreeCount(subtree, trees) - Static method in class net.maizegenetics.taxa.tree.RootedTreeUtils
-
- subTuple(subset) - Method in interface net.maizegenetics.util.db.DBTuple
-
- successful - Variable in class net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition
-
- successors(n) - Method in class net.maizegenetics.util.DirectedGraph
-
Gets the successors of the node n
- sumCounts(inputFileName, format, progressIndication) - Static method in class net.maizegenetics.dna.tag.TagsByTaxaUtils
-
Returns a list of taxa in the specified TagsByTaxa file, along with the total count of all tags found in that taxon.
- sumOf(integers) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
- sumOf(integers) - Static method in class net.maizegenetics.analysis.imputation.FILLINImputationUtils
-
- SuperByteMatrix - Interface in net.maizegenetics.util
-
- SuperByteMatrixBuilder - Class in net.maizegenetics.util
-
- SuperByteMatrixMultiple - Class in net.maizegenetics.util
-
- SuperByteMatrixSingle - Class in net.maizegenetics.util
-
- SuperByteMatrixSingleValue - Class in net.maizegenetics.util
-
- SuperByteMatrixTranspose - Class in net.maizegenetics.util
-
- supplier() - Method in class net.maizegenetics.dna.map.PositionList.PositionListCollector
-
- supplier() - Method in class net.maizegenetics.taxa.TaxaList.TaxaListCollector
-
- supplier() - Method in class net.maizegenetics.util.BitSet.BitSetListCollector
-
- supressSystemOut() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Supress system out
- supressSystemOut(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Supress system out. Express system out
- supressSystemOut() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Supress system out
- supressSystemOut(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Supress system out. Supress system out
- swap(index1, index2) - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- swap(index1, index2) - Method in class net.maizegenetics.dna.map.TagsOnGeneticMap
-
- swap(index1, index2) - Method in class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- swap(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractPETags
-
Swap two PE tags
- swap(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractTags
-
- swap(index1, index2) - Method in class net.maizegenetics.dna.tag.AbstractTagsHDF5
-
- swap(index1, index2) - Method in class net.maizegenetics.dna.tag.PETagCounts
-
- swap(index1, index2) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- swapSynonyms() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- swapTagMappingInfo(index, mapIndex, mapIndex2) - Method in class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- SweepFast - Class in net.maizegenetics.stats.linearmodels
-
- SweepFast(X, y) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFast
-
- SweepFast(XTX, XTy, yty) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFast
-
- SweepFast(xtxMatrices, xtyMatrices, yty) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFast
-
- SweepFast() - Constructor for class net.maizegenetics.stats.linearmodels.SweepFast
-
- SweepFastLinearModel - Class in net.maizegenetics.stats.linearmodels
-
- SweepFastLinearModel(effects, data) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- SweepFastLinearModel(effects, data) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- SweepFastLinearModel(effects, xtx, xty, data) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFastLinearModel
-
- SweepFastNestedModel - Class in net.maizegenetics.stats.linearmodels
-
- SweepFastNestedModel(modelEffects, data) - Constructor for class net.maizegenetics.stats.linearmodels.SweepFastNestedModel
-
The constructor for this class. It will calculate the SS and df for marker after all other effects in the model except taxa nested in marker. Taxa in marker will then be added to the model and its SS and df calculated. Error SS and df will be the final residual.
- sweepSingularColumns() - Method in class net.maizegenetics.stats.linearmodels.SweepFast
-
- SymmetricEigenvalueDecomposition - Class in net.maizegenetics.matrixalgebra.decomposition
-
- SymmetricEigenvalueDecomposition(matrix) - Constructor for class net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition
-
- SymmetricMatrixInverterDM - Class in net.maizegenetics.stats.linearmodels
-
- SymmetricMatrixInverterDM(symmetricMatrix) - Constructor for class net.maizegenetics.stats.linearmodels.SymmetricMatrixInverterDM
-
- synonym(val) - Method in class net.maizegenetics.taxa.Taxon.Builder
-
Set text definition of pedigree (default=null)
- synonymizeKeys(key) - Static method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
Method that takes common synonyms of annotation types and standardizes them according to the following rules: (1) Make lowercase (2) Standardize according to following rules. (Any not on this list are returned as just lowercased) name, id -> id chr, chrom, chromosome -> chromosome stop, end -> stop parentid, parent_id, parent -> parent_id pos, position -> position
- SynonymizerPlugin - Class in net.maizegenetics.analysis.data
-
- SynonymizerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.SynonymizerPlugin
-
Creates a new instance of SynonymizerPlugin
- SynonymKey - Static variable in class net.maizegenetics.taxa.Taxon
-
Standard key for a synonym of the taxon
- t1t2_pearson() - Method in class net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
-
- t1t2_spearman() - Method in class net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
-
- T_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- T_DIPLOID_ALLELE - Static variable in class net.maizegenetics.dna.snp.NucleotideAlignmentConstants
-
- tab - Static variable in class net.maizegenetics.analysis.imputation.ImputationUtils
-
- tab - Static variable in class net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
-
- tableChanged(e) - Method in class net.maizegenetics.analysis.filter.FilterTraitsDialog
-
- tableChanged(e) - Method in class net.maizegenetics.tassel.SeqViewerPanel
-
- TableDisplayPlugin - Class in net.maizegenetics.analysis.chart
-
- TableDisplayPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.chart.TableDisplayPlugin
-
Creates a new instance of TableDisplayPlugin
- TableReport - Interface in net.maizegenetics.util
-
Interface for classes with data that can be presented in tables
- TableReportBoxWhiskerCatDataset - Class in net.maizegenetics.analysis.chart
-
Title:
- TableReportBoxWhiskerCatDataset(theTable, seriesCategory, seriesY) - Constructor for class net.maizegenetics.analysis.chart.TableReportBoxWhiskerCatDataset
-
- TableReportBuilder - Class in net.maizegenetics.util
-
- TableReportManhattanDataset - Class in net.maizegenetics.analysis.chart
-
- TableReportManhattanDataset(theTable, start, end) - Constructor for class net.maizegenetics.analysis.chart.TableReportManhattanDataset
-
- TableReportNoPagingTableModel - Class in net.maizegenetics.gui
-
- TableReportNoPagingTableModel(table) - Constructor for class net.maizegenetics.gui.TableReportNoPagingTableModel
-
- TableReportPanel - Class in net.maizegenetics.tassel
-
- TableReportPieDataset - Class in net.maizegenetics.analysis.chart
-
Title:
- TableReportPieDataset(theTable, seriesCategory) - Constructor for class net.maizegenetics.analysis.chart.TableReportPieDataset
-
- TableReportQQDataset - Class in net.maizegenetics.analysis.chart
-
- TableReportQQDataset(table) - Constructor for class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- TableReportQQDataset(table, startIndex, endIndex, countToDisplay) - Constructor for class net.maizegenetics.analysis.chart.TableReportQQDataset
-
- TableReportStatCategoryDataset - Class in net.maizegenetics.analysis.chart
-
Title:
- TableReportStatCategoryDataset(theTable, seriesCategory, seriesY) - Constructor for class net.maizegenetics.analysis.chart.TableReportStatCategoryDataset
-
- TableReportStatCategoryDataset(theTable, seriesCategory, seriesY, stderr) - Constructor for class net.maizegenetics.analysis.chart.TableReportStatCategoryDataset
-
- tableReportToVectors(tableReport) - Static method in class net.maizegenetics.plugindef.GenerateRCode
-
Temporary place for this experimental method.
- TableReportUtils - Class in net.maizegenetics.util
-
- TableReportVectors(columnNames, columnType, annotation, dataVector) - Constructor for class net.maizegenetics.plugindef.GenerateRCode.TableReportVectors
-
- TableReportXYDataset - Class in net.maizegenetics.analysis.chart
-
Title:
- TableReportXYDataset(theTable, seriesX, seriesY) - Constructor for class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- TableReportXYDataset(theTable, seriesX, seriesY1, seriesY2) - Constructor for class net.maizegenetics.analysis.chart.TableReportXYDataset
-
- TableRowHeaderListModel - Class in net.maizegenetics.gui
-
- TableRowHeaderListModel(list) - Constructor for class net.maizegenetics.gui.TableRowHeaderListModel
-
TableRowHeaderListModel Constructor.
- tag() - Method in class net.maizegenetics.analysis.gbs.repgen.RefTagData
-
- tag() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- Tag - Interface in net.maizegenetics.dna.tag
-
Interface for tags (sequences without N) that captures these bit encoded sequence and there length.
- tag2() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- tag2() - Method in class net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
-
- tag2chrom() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- tag2pos() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- TAG_ATTRIBUTES_PATH - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_COUNT - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_DIST - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_DIST_OFFSETS - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_LENGTH_LONG - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_LENGTHS - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_LOCKED - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_MODULE - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAG_SEQ - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TagAgainstAnchor - Class in net.maizegenetics.analysis.gbs
-
- TagAgainstAnchor(hapMapHDF5, tbtHDF5, blockFileS, outfileS, pThresh, minCount, coreNum, chunkSize) - Constructor for class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
Constructor to run genetic mapping on one node
- TagAgainstAnchor(hapMapHDF5, tbtHDF5, blockFileS, outfileS, pThresh, minCount, coreNum, chunkSize, chunkStartIndex, chunkEndIndex) - Constructor for class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
Constructor to run genetic mapping on specific chunk of TBT. This is for "qsub" in clusters.
- TagAgainstAnchorHypothesis - Class in net.maizegenetics.analysis.gbs
-
- TagAgainstAnchorHypothesis(hapMapHDF5, tbtHDF5, topmFileS, software, testSiteNum, pThresh, minCount, coreNum) - Constructor for class net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
-
Constructor to run genetic mapping
- TagAgainstAnchorPlugin - Class in net.maizegenetics.analysis.gbs
-
Genetic mapping of GBS tags. Steps: 1. Using -pc and -t option to calculate the number of TBT chunks. 2. When -pc is 0, run the program on cluster. Submit jobs to nodes by specifying chunkStartIndex and chunkEndIndex
- TagAgainstAnchorPlugin() - Constructor for class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- TagAgainstAnchorPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
-
- tagBLength - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Length of backward tags
- TagBlockPosition - Class in net.maizegenetics.analysis.gbs
-
Stores physical position of tags. The physical position of tag is used to block the corresponding marker in genetic mapping if the tag is mapping to the marker coming from itself Positions come from TOPM alignment hypothesis or the best position from machine learning prediction
- TagBlockPosition(tbtH5FileS, topmFileS, TOPMVersionValue) - Constructor for class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- TagBlockPosition(tbtH5FileS, topmH5FileS, software) - Constructor for class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- TagBlockPosition(blockFileS) - Constructor for class net.maizegenetics.analysis.gbs.TagBlockPosition
-
- TagBuilder - Class in net.maizegenetics.dna.tag
-
Builder for tags that optimizes the memory footprint. Tags are encoded in long with 2 bits per bp. In GBS, we generally use only record the 64 or 96bp. Custom classes are generated with 32, 64 or 96bp tags (1, 2 or 3 longs) otherwise an array is used.
- TagCorrelationInfo - Class in net.maizegenetics.analysis.gbs.repgen
-
- TagCorrelationInfo(tag2, t1t2_pearson, t1t2_spearman, pres_abs_pearson, r2) - Constructor for class net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
-
- tagCount() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- TAGCOUNT - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- tagCountFile() - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Tag count file. (Only -t or -m allowed)
- tagCountFile(value) - Method in class net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
-
Set Tag Count File. Tag count file. (Only -t or -m allowed)
- TagCountMutable - Class in net.maizegenetics.dna.tag
-
Resizeable tags count container. Tags sequences are compressed in long, tags lengths are tracked, and read counts are stored. Has basic filtering methods. Read counts can be modified.
- TagCountMutable(tagLengthInLong, maxSize) - Constructor for class net.maizegenetics.dna.tag.TagCountMutable
-
- TagCountMutable(origTagCount, maxSize) - Constructor for class net.maizegenetics.dna.tag.TagCountMutable
-
- TagCounts - Class in net.maizegenetics.dna.tag
-
Holds tags counts. Tags sequences are compressed in long, tags lengths are tracked, and read counts are stored. Has basic filtering methods. Read counts can be modified. This class is not resizable in terms of new tags - for growing tag count lists use TagCountMutable.java User: ed
- TagCounts() - Constructor for class net.maizegenetics.dna.tag.TagCounts
-
- TagCounts(tagLengthInLong, maxSize) - Constructor for class net.maizegenetics.dna.tag.TagCounts
-
- TagCounts(inFile, binary) - Constructor for class net.maizegenetics.dna.tag.TagCounts
-
- TagCountToFastqPlugin - Class in net.maizegenetics.analysis.gbs
-
- TagCountToFastqPlugin() - Constructor for class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- TagCountToFastqPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- TagCountToFastqPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
-
- TagData - Interface in net.maizegenetics.dna.tag
-
Interface to GBS Tag Data. Replaces TagsCounts, TBT, and TOPM TODO: TAS-476
- TagDataSQLite - Class in net.maizegenetics.dna.tag
-
Defines xxxx TAS-480
- TagDataSQLite(filename) - Constructor for class net.maizegenetics.dna.tag.TagDataSQLite
-
- TagDataWriter - Interface in net.maizegenetics.dna.tag
-
Defines writer to modify the GBS tag data store
- TagExportToFastqPlugin - Class in net.maizegenetics.analysis.gbs.v2
-
Converts a TagCounts binary (*.cnt) file (presumably a master tag list) to a fastq file that can be used as input for BWA or bowtie2 (and possibly additional aligners). The same function can be performed with MergeMultipleTagCountPlugin using the -t option and a single Master Tag List file in the input directory, but having a separate plugin to do this reduces confusion and eliminates the risk of merging the master tag list back on itself.
- TagExportToFastqPlugin() - Constructor for class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- TagExportToFastqPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- TagExportToFastqPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
-
- tagFile() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
Input file with list of tags to process. Any number of tab-delimited columns, but must have 1 called Tags.
- tagFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
-
Set Tag File. Input file with list of tags to process. Any number of tab-delimited columns, but must have 1 called Tags.
- tagFLength - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Length of forward tags
- TagGeneticMappingInfo - Class in net.maizegenetics.dna.map
-
Class used to to store genetic mapping for hypothesis and output to H5 format
- TagGeneticMappingInfo() - Constructor for class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
- TagGeneticMappingInfo(p, chromosome, position, sigSiteNum, sigSiteRange) - Constructor for class net.maizegenetics.dna.map.TagGeneticMappingInfo
-
- TagGWASMap - Class in net.maizegenetics.dna.map
-
Holding tag genetic mapping result from GWAS. It includes attributes and methods for machine learning prediction of mapping accuracy
- TagGWASMap(tagGWASMapFileS) - Constructor for class net.maizegenetics.dna.map.TagGWASMap
-
- TagGWASMap(gwasMappingResultFileS, tagCountFileS, tagGWASMapFileS) - Constructor for class net.maizegenetics.dna.map.TagGWASMap
-
- TagGWASMap(gwasMappingFileS, topmFileS, tagCountFileS, tagGWASMapFileS) - Constructor for class net.maizegenetics.dna.map.TagGWASMap
-
- TagGWASMapInfo - Class in net.maizegenetics.dna.map
-
Stores variables from tag genetic mapping from GWAS. This class is used for I/O of HDF5.
- TagGWASMapInfo() - Constructor for class net.maizegenetics.dna.map.TagGWASMapInfo
-
- TagGWASMapInfo(readCount, gChr, gPos, gwasPValue, numSigSite, tagTaxaCount, numSigChr, lRatioSB, lRatioMB, numSiteOnBestChrThanSecondBest, sigSiteStart, sigSiteEnd) - Constructor for class net.maizegenetics.dna.map.TagGWASMapInfo
-
- TagGWASMapInfo(readCount, pChr, pPos, ifMap, ifRef, ifUnique, gChr, gPos, gwasPValue, numSigSite, tagTaxaCount, numSigChr, lRatioSB, lRatioMB, numSiteOnBestChrThanSecondBest, sigSiteStart, sigSiteEnd) - Constructor for class net.maizegenetics.dna.map.TagGWASMapInfo
-
- tagIndex() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
-
- tagLength() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- tagLength(value) - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- tagLength - Variable in class net.maizegenetics.dna.tag.AbstractTags
-
- TAGLENGTH - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- tagLength - Variable in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- tagLengthInLong - Variable in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
- tagLengthInLong - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Tag length in Long primitive data type
- tagLengthInLong - Variable in class net.maizegenetics.dna.tag.AbstractTags
-
- TAGLENGTHINLONG - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- tagLengthInLong - Variable in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- TagLocus - Class in net.maizegenetics.dna.map
-
Aligns and calls SNPs for all tags at a given locus.
- TagLocus(chromosome, strand, startPosition, tagLength, includeRefGenome, fuzzyStartPositions, errorRate) - Constructor for class net.maizegenetics.dna.map.TagLocus
-
- TagMappingInfo - Class in net.maizegenetics.dna.map
-
Container class for information on mapping position.
- TagMappingInfo() - Constructor for class net.maizegenetics.dna.map.TagMappingInfo
-
- TagMappingInfo(chromosome, strand, startPosition, endPosition, divergence) - Constructor for class net.maizegenetics.dna.map.TagMappingInfo
-
- TagMappingInfo(chromosome, strand, startPosition, endPosition, divergence, variantPosOff, variantDef, dcoP, mapP) - Constructor for class net.maizegenetics.dna.map.TagMappingInfo
-
- TagMappingInfoV3 - Class in net.maizegenetics.dna.map
-
Container class for information on mapping position.
- TagMappingInfoV3() - Constructor for class net.maizegenetics.dna.map.TagMappingInfoV3
-
- TagMappingInfoV3(chromosome, strand, startPosition, endPosition, divergence, perfectMatch, mappingSource, mappingScore) - Constructor for class net.maizegenetics.dna.map.TagMappingInfoV3
-
- TagMappingInfoV3(chromosome, strand, startPosition, endPosition, divergence, perfectMatch, mappingSource, mappingScore, variantPosOff, variantDef, dcoP, mapP) - Constructor for class net.maizegenetics.dna.map.TagMappingInfoV3
-
- TagMappingInfoV3.Aligner - Enum in net.maizegenetics.dna.map
-
MappingSource definition
- tagMapToFastaPlugin() - Method in class net.maizegenetics.analysis.gbs.pana.PanAUsageExample
-
- TagMatchFinder - Class in net.maizegenetics.analysis.gbs
-
Very simple but fast homology finder. Very similar to BLAT, with long word searches. A in memory index is created from any set of Tags, and this list many then be quickly queried for high homology hits.
- TagMatchFinder(theTags) - Constructor for class net.maizegenetics.analysis.gbs.TagMatchFinder
-
- tags - Variable in class net.maizegenetics.dna.tag.AbstractTags
-
- TAGS - Static variable in class net.maizegenetics.dna.tag.GBSHDF5Constants
-
- Tags - Interface in net.maizegenetics.dna.tag
-
Basic interface for holding sets of sequence tag (these are compressed into 2-bit codings of tags). The length of tag in good sequence is also tracked.
- TAGS - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAGS_BIN_NUM - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- tagsB - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Backward tags in Long array Columns are sequence, rows are index of sequence. This is faster than the other way
- TagsByTaxa - Interface in net.maizegenetics.dna.tag
-
Tags by Taxa is the interface for tracking the distribution of tags across taxa. It can be thought of as a matrix of nTaxa by nTags. Taxa names are also maintained by this interface.
- TagsByTaxa.FilePacking - Enum in net.maizegenetics.dna.tag
-
Types of file packing used by GBS data structures. Bit compresses all information to presence/absence, while Byte/Short/Int tradeoff memory size with depth of coverage. Text is only used for file storage.
- TagsByTaxaByte - Class in net.maizegenetics.dna.tag
-
A bit implementation of TagByTaxa, so only counts as high as 127 can be maintained.
- TagsByTaxaByte() - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- TagsByTaxaByte(infile, binary) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- TagsByTaxaByte(taxaNames, theDistinctReads) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- TagsByTaxaByte(tags, tagLength, tagDist, namesForTaxa) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- TagsByTaxaByte(reads, readDist, namesForTaxa) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByte
-
- TagsByTaxaByteFileMap - Class in net.maizegenetics.dna.tag
-
A byte implementation of TagByTaxa, maximum depth of tags is 127. This version works directly from a RandomAccessFile, which is slow but can work with very large files. It will need to be transitioned nio2, when Java 7 comes out. If possible, it holds the current row cached in memory, so try to work with the files sequentially.
- TagsByTaxaByteFileMap(infile) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
- TagsByTaxaByteFileMap(outFile, taxaNames, theTags) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
-
Creates an empty Byte File Map
- TagsByTaxaByteFileMapSeq - Class in net.maizegenetics.dna.tag
-
A bit implementation of TagByTaxa, so only presence or absence of a tags is known. This version works directly from a RandomAccessFile, which is slow but can work with very large files. It will need to be transitioned nio2, when Java 7 comes out. If possible, it holds the current row cached in memory, so try to work with the files sequentially.
- TagsByTaxaByteFileMapSeq(infile) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
-
- TagsByTaxaByteHDF5TagGroups - Class in net.maizegenetics.dna.tag
-
Tags by Taxa file based on the HDF5 data structure. This version is optimized for rapid access of taxa within Tag (ie it buffers the taxa counts within one tag).
- TagsByTaxaByteHDF5TagGroups(inTags, newHDF5file) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- TagsByTaxaByteHDF5TagGroups(infile) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
-
- TagsByTaxaByteHDF5TaxaGroups - Class in net.maizegenetics.dna.tag
-
Tags by Taxa file based on the HDF5 data structure. This version is optimized for rapid access of tags within taxa (ie it buffers the tag counts within one taxon). It is good for adding, removing, and combining taxa
- TagsByTaxaByteHDF5TaxaGroups(inTags, newHDF5file) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- TagsByTaxaByteHDF5TaxaGroups(infile) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
-
- TagsByTaxaShort - Class in net.maizegenetics.dna.tag
-
Tags by taxa that supports depths captured by a short (max 32767)
- TagsByTaxaShort() - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- TagsByTaxaShort(infile, binary) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- TagsByTaxaShort(taxaNames, theDistinctReads) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- TagsByTaxaShort(reads, readDist, namesForTaxa) - Constructor for class net.maizegenetics.dna.tag.TagsByTaxaShort
-
- TagsByTaxaUtils - Class in net.maizegenetics.dna.tag
-
This class contains methods which process TagsByTaxa files one line at a time, as opposed to the methods in
class AbstractTagsByTaxa, which hold an entire file in memory.
- tagSeqs() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- tagSequence() - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
Tag sequence user would like to verify exists in DB.
- tagSequence(value) - Method in class net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
-
Set User tag sequence. This is tag user wants to verify exists in DB.
- tagsF - Variable in class net.maizegenetics.dna.tag.AbstractPETags
-
Forward tags in Long array Columns are sequence, rows are index of sequence. This is faster than the other way
- TagsOnGeneticMap - Class in net.maizegenetics.dna.map
-
Class that hold genetic position of tags, genetic positions are the position of markers associated with tags
- TagsOnGeneticMap(infileS, format) - Constructor for class net.maizegenetics.dna.map.TagsOnGeneticMap
-
Construct TOGM from a file
- TagsOnPhysicalMap - Class in net.maizegenetics.dna.map
-
Holds tag data compressed in long and a physical position. This can have two variations either include redundant positions or only unique positions. If redundant than tags that map to multiple regions should be placed adjacently Default 40 bytes per position. If we have 10,000,000 million positions then this will be at 400M byte data structure. User: ed
- TagsOnPhysicalMap() - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- TagsOnPhysicalMap(inFile, binary) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- TagsOnPhysicalMap(rows) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- TagsOnPhysicalMap(rows, tagLengthInLong, maxVariants) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- TagsOnPhysicalMap(readList) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- TagsOnPhysicalMap(oldTOPM, filterDuplicates) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMap
-
- TagsOnPhysicalMap.SAMFormat - Enum in net.maizegenetics.dna.map
-
- TagsOnPhysicalMapV3 - Class in net.maizegenetics.dna.map
-
HDF5 version of TagsOnPhysical Map. This is the preferred version of physical map as it uses less memory, loads faster, and is more flexible with mapping positions.
- TagsOnPhysicalMapV3(theHDF5file) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysicalMapV3
-
Constructor from a HDF5 TOPM file
- TagsOnPhysMapHDF5 - Class in net.maizegenetics.dna.map
-
HDF5 version of TagsOnPhysical Map. This is the preferred version of physical map as it uses less memory, loads faster, and is more flexible with mapping positions.
- TagsOnPhysMapHDF5(filename) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- TagsOnPhysMapHDF5(theHDF5file, cacheAllMappingBlocks) - Constructor for class net.maizegenetics.dna.map.TagsOnPhysMapHDF5
-
- tagsWCountsGreaterThanMin(minCount) - Method in class net.maizegenetics.dna.tag.TagCounts
-
- tagTaxaCount - Variable in class net.maizegenetics.dna.map.TagGWASMapInfo
-
Number of taxa where tag exist, unknown = Integer.MIN_VALUE
- targetFile() - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Input HapMap file of target genotypes to impute or all genotypes available for target taxon. Accepts all file types supported by TASSEL5.
- targetFile(value) - Method in class net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
-
Set Target file. Input HapMap file of target genotypes to impute or all genotypes available for target taxon. Accepts all file types supported by TASSEL5.
- targetFile() - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Input HapMap file of target genotypes to impute. Accepts all file types supported by TASSEL5
- targetFile(value) - Method in class net.maizegenetics.analysis.imputation.FILLINImputationPlugin
-
Set Target file. Input HapMap file of target genotypes to impute. Accepts all file types supported by TASSEL5
- targetTaxon - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- targetTBTHDF5File() - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- targetTBTHDF5File(value) - Method in class net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
-
- Tassel5HDF5Constants - Class in net.maizegenetics.util
-
Definition of attributes and paths for Tassel HDF5 file format.
- TASSEL_CONFIG_FILE - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_CONFIG_FILE_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOCALE - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_DEBUG - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_DEBUG_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_SEND_TO_CONSOLE - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_SEND_TO_CONSOLE_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_X_DIM - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_X_DIM_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_Y_DIM - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_LOG_Y_DIM_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_MAX_THREADS - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_MAX_THREADS_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_OPEN_DIR - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_OPEN_DIR_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_SAVE_DIR - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_SAVE_DIR_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_TOP - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_X_DIM - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_X_DIM_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_Y_DIM - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TASSEL_Y_DIM_DEFAULT - Static variable in class net.maizegenetics.prefs.TasselPrefs
-
- TasselLogging - Class in net.maizegenetics.tassel
-
- TASSELMainApp - Class in net.maizegenetics.tassel
-
- TASSELMainFrame - Class in net.maizegenetics.tassel
-
TASSELMainFrame
- TASSELMainFrame() - Constructor for class net.maizegenetics.tassel.TASSELMainFrame
-
- TasselPipeline - Class in net.maizegenetics.pipeline
-
- TasselPipeline(args, frame) - Constructor for class net.maizegenetics.pipeline.TasselPipeline
-
Creates a new instance of TasselPipeline
- TasselPipeline(args, frame, interactive, name) - Constructor for class net.maizegenetics.pipeline.TasselPipeline
-
Creates a new instance of TasselPipeline
- TasselPipeline.FLAGS - Enum in net.maizegenetics.pipeline
-
- TasselPipelineStepsDialog - Class in net.maizegenetics.pipeline
-
- TasselPipelineStepsDialog(mainFrame, name) - Constructor for class net.maizegenetics.pipeline.TasselPipelineStepsDialog
-
- TasselPipelineXMLUtil - Class in net.maizegenetics.pipeline
-
- TasselPrefs - Class in net.maizegenetics.prefs
-
- taxa() - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- taxa() - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- taxa() - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return taxa list of this genotype table.
- TAXA - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- taxa() - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- taxa() - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- taxa() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- taxa() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- taxa() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- TAXA_ATTRIBUTES_PATH - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAXA_DESC - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- TAXA_LIST_NONE - Static variable in class net.maizegenetics.plugindef.AbstractPlugin
-
- TAXA_LOCKED - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAXA_MODULE - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAXA_NUM_TAXA - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAXA_ORDER - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- TAXA_SCHEMA - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- taxaAttribute() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- taxaAttribute() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- taxaAttribute() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- TaxaAttribute - Class in net.maizegenetics.phenotype
-
- TaxaAttribute(taxa, name) - Constructor for class net.maizegenetics.phenotype.TaxaAttribute
-
- TaxaAttribute(taxa) - Constructor for class net.maizegenetics.phenotype.TaxaAttribute
-
- TaxaAvailableListModel - Class in net.maizegenetics.gui
-
- TaxaAvailableListModel(taxa) - Constructor for class net.maizegenetics.gui.TaxaAvailableListModel
-
- taxaCount(value) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- taxaCount() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- TAXACOV - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- TAXACOV - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- taxaDepthMap() - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Multiset version of the taxa depth. This is a convenient data structure, but it is slow to create compared to depths or taxaWithDepths. Do not use this if performance is key.
- TaxaDistBuilder - Class in net.maizegenetics.dna.tag
-
Builder for TaxaDistribution. Deals with the
- TaxaDistribution - Interface in net.maizegenetics.dna.tag
-
This is a specialized multiset for recording the distribution of a single across taxa. HashMap or Multiset or large arrays could be reasonable approaches by they do not scale well with hundreds of taxa scored out of the thousands. Instead this the general implementations use primitive arrays.
- taxaEffect() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- taxaEffectNumber - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- taxaFile() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Name of taxa list input file in taxa list format
- taxaFile(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Set Taxa List File. Name of taxa list input file in taxa list format
- TAXAHET - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- TAXAHET - Static variable in class net.maizegenetics.util.Tassel5HDF5Constants
-
- taxaIndex - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- taxaIndex - Variable in class net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
-
- taxaInModel - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- taxaInModelMap - Variable in class net.maizegenetics.analysis.association.PhenotypeLM
-
- taxaList() - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Taxa List
- taxaList(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
Set Taxa List.
- taxaList(value) - Method in class net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
-
- taxaList(connection, gids) - Static method in class net.maizegenetics.analysis.gobii.BMSConnection
-
- taxaList(postgres, datasetName, bms) - Static method in class net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
-
- taxaList() - Method in class net.maizegenetics.dna.snp.FilterTaxa
-
- taxaList - Variable in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- TaxaList - Interface in net.maizegenetics.taxa
-
- TaxaList.TaxaListCollector - Class in net.maizegenetics.taxa
-
- TaxaListBuilder - Class in net.maizegenetics.taxa
-
A builder for creating immutable
interface TaxaList instances. Example:
TaxaListBuilder tlb=new TaxaListBuilder();
for (int i = 0; i < 10; i++) {
Taxon at= new Taxon.Builder("Z"+i+":Line:mays:Zea")
.inbreedF(0.99f)
.parents("B73","B97")
.pedigree("(B73xB97)S6I1")
.build();
tlb.add(at);
}
TaxaList tl=tlb.build();
- TaxaListBuilder() - Constructor for class net.maizegenetics.taxa.TaxaListBuilder
-
- TaxaListIOUtils - Class in net.maizegenetics.taxa
-
Utilities for reading and writing IdGroup and PedigreeIdGroups.
- taxaListName() - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Name of taxa set for database
- taxaListName(value) - Method in class net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
-
Set Name for taxa set in DB. Name of taxa set for database
- TaxaListTableReport - Class in net.maizegenetics.taxa
-
- TaxaListTableReport(taxaList) - Constructor for class net.maizegenetics.taxa.TaxaListTableReport
-
- TaxaListUtils - Class in net.maizegenetics.taxa
-
- taxaMapFile() - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
tab-delimited File containing a TaxaColumn name to be used to map breakFile taxa with a GID. This may be a different file than was used for adding germplasm and marker data.
- taxaMapFile(value) - Method in class net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
-
Set mappingFile. tab-delimited File containing a TaxaColumn name to be used to map breakFile taxa with a GID. This may be a different file than was used for adding germplasm and marker data.
- taxaMergeSelection() - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Selection for Taxa Merge Rule
- taxaMergeSelection(value) - Method in class net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
-
Set Taxa Merge Rule. Selection for Taxa Merge Rule
- taxaName() - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
Name of the taxa
- taxaName(value) - Method in class net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
-
Set Taxa Name. Name of the taxa
- taxaName(index) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- taxaName(index) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- taxaName(index) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Return taxa name at given index.
- taxaName(index) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- taxaName(index) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- taxaName(index) - Method in interface net.maizegenetics.taxa.TaxaList
-
Return taxa name at given index.
- taxaNames(value) - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- taxaNames() - Method in class net.maizegenetics.analysis.data.HDF5SummaryPlugin
-
- taxaNames - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- taxaNames - Variable in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
Deprecated.
- taxaNames - Variable in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- taxaNum - Variable in class net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
-
- taxaNum - Variable in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
- taxaNum - Variable in class net.maizegenetics.dna.tag.ReadsByTaxa
-
- taxaRedirect(fromNames, toNames) - Static method in class net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
-
- taxaRenameKey() - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Tab-delimited file with original and new taxa names. Taxa with the same new name will be merged. Taxa with the new name "delete" will be removed. Any other columns (and the header line) are ignored.
- taxaRenameKey(value) - Method in class net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
-
Set Taxa Rename Key. Tab-delimited file with original and new taxa names. Taxa with the same new name will be merged. Taxa with the new name "delete" will be removed. Any other columns (and the header line) are ignored.
- taxaSubset() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- taxaSummary() - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
Get Taxa Summary
- taxaSummary(value) - Method in class net.maizegenetics.analysis.data.GenotypeSummaryPlugin
-
Set Taxa Summary. Get Taxa Summary
- TaxaTissueDist - Class in net.maizegenetics.taxa
-
- TaxaTissueDist(mtissue, mtaxa) - Constructor for class net.maizegenetics.taxa.TaxaTissueDist
-
- taxaToKeep() - Method in class net.maizegenetics.analysis.filter.FilterSubsetPlugin
-
- taxaTranslations() - Method in class net.maizegenetics.dna.snp.Translate
-
- taxaWithDepths() - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Two arrays with the list of taxa with the tag (i.e. depth>0) int[0], and the depth of the taxa in the second array int[1]
- taxon(taxon) - Method in class net.maizegenetics.dna.snp.Translate
-
- taxon(obs) - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- Taxon - Class in net.maizegenetics.taxa
-
An identifier for some sampled data. This will most often be for example, the accession number of a DNA sequence, or the taxonomic name that the sequence represents, et cetera. The generally used class for defining a taxon. Contains its name, plus a series of optional annotations. Use the builder to create immutable instances.
- Taxon(name) - Constructor for class net.maizegenetics.taxa.Taxon
-
- Taxon(name, anno) - Constructor for class net.maizegenetics.taxa.Taxon
-
- Taxon.Builder - Class in net.maizegenetics.taxa
-
A builder for creating immutable Taxon instances.
- TAXON_SCHEMA - Static variable in class net.maizegenetics.analysis.avro.AvroConstants
-
- taxonDonors(taxon, site) - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- taxonIndex - Variable in class net.maizegenetics.analysis.clustering.Haplotype
-
The index of the taxon from the originating alignment from which this sequence was taken
- taxonMask(taxon) - Method in class net.maizegenetics.dna.snp.AbstractMaskMatrix
-
- taxonMask(taxon) - Method in class net.maizegenetics.dna.snp.MaskGenotypeMatrix
-
- taxonMask(taxon) - Method in class net.maizegenetics.dna.snp.MaskGenotypeStatsMatrix
-
- taxonSite(taxon, site) - Method in class net.maizegenetics.dna.snp.Translate
-
- taxonSite(taxon, site) - Method in class net.maizegenetics.dna.snp.TranslateNegative
-
- taxonStats(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
- TBIT - Static variable in class net.maizegenetics.dna.snp.HapMapHDF5Constants
-
- tCons(name, value) - Static method in class net.maizegenetics.util.db.DefaultDBTuple
-
- tcrossproduct() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- tcrossproduct(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- tcrossproduct() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- tcrossproduct(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- tcrossproduct() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- tcrossproduct(dm) - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- tcrossproduct() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- tcrossproduct(dm) - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- TerryPipelines - Class in net.maizegenetics.analysis.gbs
-
- testAddedTerm(testedTerm, addedTerm, theModel) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
-
- testAddedTerm(testedTerm, addedTerm, theModel) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- testMarkerUsingEMMA(result, y, X, K, Z, nAlleles, markerIds) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- testMarkerUsingP3D(result, y, X, invV, markerdf, markerIds) - Method in class net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
-
- testNewEffect(me) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- testNewEffect(covariate) - Method in class net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
-
- testNewModelEffect(me) - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- testNewModelEffect(covariate) - Method in class net.maizegenetics.stats.linearmodels.PartitionedLinearModel
-
- testPhenotypeForMissingData(pheno) - Method in class net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
-
- testSites(obsTdist, obsMajor, obsMinor, maf, binomFunc) - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
Test association using binomial test, collecting P-value
- testSites(obsTdist, obsMajor, obsMinor, binomFunc) - Static method in class net.maizegenetics.analysis.gbs.TagAgainstAnchor
-
Test association using binomial test, collecting P-value
- testSites(obsTdist, obsMajor, obsMinor, maf, binomFunc) - Method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
-
Test association using binomial test, collecting P-value
- testSites(obsTdist, obsMajor, obsMinor, binomFunc) - Static method in class net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
-
Test association using binomial test, collecting P-value
- testTaxaReplication() - Method in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- testTaxaReplication() - Method in class net.maizegenetics.analysis.association.PhenotypeLM
-
- TEXT - Static variable in class net.maizegenetics.gui.PrintHeapAction
-
- textOutput() - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- textOutput(value) - Method in class net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
-
- textOutputFormat() - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- textOutputFormat(value) - Method in class net.maizegenetics.analysis.gbs.SAMConverterPlugin
-
- TextToBinaryPlugin - Class in net.maizegenetics.analysis.gbs
-
- TextToBinaryPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.TextToBinaryPlugin
-
- theClusters - Variable in class net.maizegenetics.analysis.association.CompressedDoubleMatrix
-
- theEnzyme - Static variable in class net.maizegenetics.analysis.gbs.ParseBarcodeRead
-
- ThinSitesByPositionPlugin - Class in net.maizegenetics.analysis.data
-
Plugin to thin out sites based on their physical position on the chromosome. Expects the user to enter a minimum distance between sites in base pair. Accepts and writes .hmp.txt, .hmp.txt.gz, .vcf, .vcf.gz and .h5 files.
- ThinSitesByPositionPlugin() - Constructor for class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- ThinSitesByPositionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
-
- thirdAllele(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Return the second minor allele at given site (Third allele state). Gap is included as state. Heterozygous count one for each allele value. Homozygous counts two for the allele value.
- thirdAlleleForAllSites() - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns third (second minor) allele for all sites.
- ThreadedPluginListener - Class in net.maizegenetics.plugindef
-
- ThreadedPluginListener(pluginListener, event) - Constructor for class net.maizegenetics.plugindef.ThreadedPluginListener
-
- tissueNameField - Static variable in class net.maizegenetics.analysis.gbs.v2.GBSUtils
-
- tissueNameField - Static variable in class net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
-
- to1DArray() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- to1DArray() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- to1DArray() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- to1DArray() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- to_sibling - Variable in class net.maizegenetics.analysis.gbs.neobio.Trie
-
The character that labels the edge from this node to the sibling pointer by sibling.
- to_son - Variable in class net.maizegenetics.analysis.gbs.neobio.Trie
-
The character that labels the edge from this node to the child node pointer by son.
- toArray() - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- toArray(a) - Method in class net.maizegenetics.analysis.avro.GenericArrayPositions
-
- toArray() - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- toArray(a) - Method in class net.maizegenetics.analysis.avro.GenericArrayTaxa
-
- toArray() - Method in class net.maizegenetics.dna.snp.FilterList
-
- toArray(a) - Method in class net.maizegenetics.dna.snp.FilterList
-
- toArray() - Method in class net.maizegenetics.dna.tag.UTagCountMutable
-
- toArray() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- toArray() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- toArray() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- toArray() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- toArray() - Method in class net.maizegenetics.util.UndirectedGraph.UndirectedSet
-
- toBigDecimal(number) - Static method in class net.maizegenetics.util.db.Transformations
-
- toBinary() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
File to output TOPM in binary format
- toBinary(value) - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Set To Binary. File to output TOPM in binary format
- toBoolean(o) - Static method in class net.maizegenetics.util.db.Transformations
-
- toBoolean(o) - Static method in class net.maizegenetics.util.db.Transformations
-
- toBoolean(o) - Static method in class net.maizegenetics.util.db.Transformations
-
- toCSVString() - Method in interface net.maizegenetics.dna.tag.Tag
-
- toFASTA(outfile) - Method in class net.maizegenetics.dna.tag.TagCounts
-
Convert TagCounts to FASTA file for alignment using Blast
- toFASTQ(infile, outfile) - Method in class net.maizegenetics.dna.tag.TagCounts
-
Reads in a binary tag count file line-by-line and constructs a FASTQ file for alignment.
- TOL - Static variable in class net.maizegenetics.stats.linearmodels.SweepFast
-
- toNumber(number, target) - Static method in class net.maizegenetics.util.db.Transformations
-
- TOP_DIRECTION - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
A constant that indicates that the top direction must be followed to reach the source of an optimal path in a block during the trace back procedure to retrieve a high scoring alignment.
- toPadString(A) - Static method in class net.maizegenetics.util.BitUtil
-
- toPadStringLowSiteToHighSite(A) - Static method in class net.maizegenetics.util.BitUtil
-
Returns the bits in the same order that we store them for TASSEL
- TOPMGenotypeTable - Class in net.maizegenetics.dna.snp
-
- TOPMGenotypeTable(topm) - Constructor for class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- TOPMGenotypeTableCellRenderer - Class in net.maizegenetics.gui
-
- TOPMGenotypeTableCellRenderer(model, genotypeTable) - Constructor for class net.maizegenetics.gui.TOPMGenotypeTableCellRenderer
-
- TOPMInterface - Interface in net.maizegenetics.dna.map
-
Tags on Physical Map (TOPM) Interface. Define methods for the TOPM classes. The TOPM class holds information relating tags to the physical map, variants (SNPs) called by the tag, and quality of mapping information.
- TOPMSummaryPlugin - Class in net.maizegenetics.analysis.gbs
-
- TOPMSummaryPlugin(parentFrame) - Constructor for class net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
-
- TOPMTableReport - Class in net.maizegenetics.dna.map
-
- TOPMTableReport(topm) - Constructor for class net.maizegenetics.dna.map.TOPMTableReport
-
- TOPMUtils - Class in net.maizegenetics.dna.map
-
Utility method for reading and writing TOPM files based on their file name suffixes.
- toReadableString(bitSet) - Static method in class net.maizegenetics.util.BitUtil
-
- toReverseComplement() - Method in interface net.maizegenetics.dna.tag.Tag
-
- toString() - Method in class net.maizegenetics.analysis.clustering.Haplotype
-
- toString() - Method in class net.maizegenetics.analysis.clustering.HaplotypeCluster
-
- toString() - Method in class net.maizegenetics.analysis.data.CombineDataSetsPlugin
-
- toString() - Method in enum net.maizegenetics.analysis.data.FileLoadPlugin.TasselFileType
-
- toString() - Method in class net.maizegenetics.analysis.gbs.Barcode
-
- toString() - Method in class net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
-
Returns a String representation of this scoring scheme.
- toString() - Method in class net.maizegenetics.analysis.gbs.neobio.CharSequence
-
Returns a string representation of the sequence.
- toString() - Method in class net.maizegenetics.analysis.gbs.neobio.Factor
-
Returns a string representation of the text represented by this factor. It inspects its chain of ancestors up until as far as the root factor, spelling their new characters out.
- toString() - Method in class net.maizegenetics.analysis.gbs.neobio.FactorSequence
-
Reconstructs the sequence from the list of factors induced by the LZ78 parsing of the text.
- toString() - Method in class net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
-
Returns a four-line String representation of this alignment in the following order: first gapped sequence, score tag line, second gapped sequence and the score value.
- toString() - Method in class net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
-
Returns a String representation of this scoring matrix.
- toString() - Method in class net.maizegenetics.analysis.gbs.ReadBarcodeResult
-
- toString() - Method in class net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
-
- toString() - Method in class net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
-
- toString() - Method in class net.maizegenetics.analysis.modelfitter.SNP
-
- toString() - Method in class net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
-
- toString() - Method in class net.maizegenetics.analysis.popgen.DiversityAnalyses
-
- toString() - Method in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- toString() - Method in class net.maizegenetics.analysis.popgen.LDResult
-
- toString() - Method in class net.maizegenetics.analysis.popgen.LinkageDisequilibrium
-
Returns representation of the LD results as a string
- toString() - Method in class net.maizegenetics.analysis.popgen.PolymorphismDistribution
-
- toString() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash
-
- toString() - Method in class net.maizegenetics.dna.map.Chromosome
-
- toString() - Method in class net.maizegenetics.dna.map.DonorHaplotypes
-
- toString() - Method in class net.maizegenetics.dna.map.GeneralPosition
-
- toString() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- toString() - Method in class net.maizegenetics.dna.tag.AbstractTag
-
- toString() - Method in class net.maizegenetics.gui.AbstractGenotypeTableMask
-
- toString() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- toString() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- toString() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- toString() - Method in class net.maizegenetics.phenotype.CategoricalAttribute
-
- toString() - Method in class net.maizegenetics.phenotype.NumericAttribute
-
- toString() - Method in class net.maizegenetics.phenotype.TaxaAttribute
-
- toString() - Method in enum net.maizegenetics.pipeline.TasselPipeline.FLAGS
-
- toString() - Method in class net.maizegenetics.plugindef.DataSet
-
- toString() - Method in class net.maizegenetics.plugindef.Datum
-
- toString() - Method in class net.maizegenetics.stats.linearmodels.BasicLevel
-
- toString() - Method in class net.maizegenetics.taxa.distance.DistanceMatrix
-
returns representation of this alignment as a string
- toString() - Method in class net.maizegenetics.taxa.IdentifierSynonymizer
-
- toString() - Method in class net.maizegenetics.taxa.Taxon
-
- toString() - Method in class net.maizegenetics.taxa.tree.CladeSystem
-
print clade system
- toString() - Method in class net.maizegenetics.taxa.tree.MultiParameterized
-
- toString() - Method in class net.maizegenetics.taxa.tree.SimpleNode
-
- toString() - Method in class net.maizegenetics.taxa.tree.SimpleTree
-
- toString() - Method in class net.maizegenetics.taxa.tree.SplitSystem
-
print split system
- toString() - Method in exception net.maizegenetics.util.db.DataAccessException
-
- toString() - Method in class net.maizegenetics.util.db.DefaultDBTuple
-
- toString() - Method in class net.maizegenetics.util.db.Pair
-
- toString() - Method in class net.maizegenetics.util.Tuple
-
- toStringTabDelim() - Method in interface net.maizegenetics.util.TableReport
-
- toStringWithVCFAnnotation() - Method in class net.maizegenetics.taxa.Taxon
-
- totalcfmSSdf - Variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- totalDepth() - Method in interface net.maizegenetics.dna.tag.TaxaDistribution
-
Total depth across all taxa of the tag
- totalGametesNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- totalGametesNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- totalGametesNonMissingForSite(alleles) - Static method in class net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
-
- totalGametesNonMissingForSite(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns total number of non-missing allele values for given site. This can be twice the number of taxa, as diploid values are supported.
- totalGametesNonMissingForSite() - Method in class net.maizegenetics.dna.snp.genotypecall.Stats
-
- totalGametesNonMissingForSite(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns total number of non-missing allele values for given site. This can be twice the number of taxa, as diploid values are supported.
- totalGametesNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- totalGametesNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- totalGametesNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- totalGametesNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- totalGametesNonMissingForTaxon(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns total number of non-missing allele values for given taxon. This can be twice the number of sites, as diploid values are supported.
- totalGametesNonMissingForTaxon(taxon) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns total number of non-missing allele values for given taxon. This can be twice the number of sites, as diploid values are supported.
- totalGametesNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- totalGametesNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- totalNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- totalNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- totalNonMissingForSite(site) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns total number of non-missing taxa for given site. Taxa are considered missing only if both allele values are Unknown (N).
- totalNonMissingForSite(site) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns total number of non-missing taxa for given site. Taxa are considered missing only if both allele values are Unknown (N).
- totalNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- totalNonMissingForSite(site) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- totalNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
- totalNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.CoreGenotypeTable
-
- totalNonMissingForTaxon(taxon) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Returns total number of non-missing sites for given taxon. Sites are considered missing only if both allele values are Unknown (N).
- totalNonMissingForTaxon(taxon) - Method in interface net.maizegenetics.dna.snp.GenotypeTable
-
Returns total number of non-missing sites for given taxon. Sites are considered missing only if both allele values are Unknown (N).
- totalNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.MergedGenotypeTable
-
- totalNonMissingForTaxon(taxon) - Method in class net.maizegenetics.dna.snp.TOPMGenotypeTable
-
- totalNumberOfTags() - Method in class net.maizegenetics.analysis.rna.FindMatchByWordHash
-
Total number of tags (reference sequences)
- totalSites - Variable in class net.maizegenetics.analysis.popgen.DonorHypoth
-
- totalVariance() - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
The first principal components that together explain this proportion of the total variance will be returned.
- totalVariance(value) - Method in class net.maizegenetics.analysis.data.PrincipalComponentsPlugin
-
Set total variance. The first principal components that together explain this proportion of the total variance will be returned.
- toText() - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
File to output TOPM in text format
- toText(value) - Method in class net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
-
Set To Text. File to output TOPM in text format
- trace(indent) - Method in class net.maizegenetics.plugindef.AbstractPlugin
-
- traitname - Variable in class net.maizegenetics.analysis.modelfitter.AbstractForwardRegression
-
- traitsToTransform() - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataDialog
-
- trancateTag() - Method in class net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
-
Full length PE tags are truncated to certain size (2 longs in GBS Build V3.0)
- transform(instance) - Method in interface net.maizegenetics.util.db.TypeTransformer
-
- Transformations - Class in net.maizegenetics.util.db
-
A Utility class for various type transformations User: julian3 Date: 2013/11/13 Time: 7:20 AM PROJECT: lambda tuples DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- transformAttribute(myAttribute) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- TransformDataDialog - Class in net.maizegenetics.analysis.numericaltransform
-
- TransformDataDialog(parentFrame, dataAttributes, factorAttributes) - Constructor for class net.maizegenetics.analysis.numericaltransform.TransformDataDialog
-
- TransformDataPlugin - Class in net.maizegenetics.analysis.numericaltransform
-
- TransformDataPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- TransformDataPlugin.BASE - Enum in net.maizegenetics.analysis.numericaltransform
-
- TransformerService - Class in net.maizegenetics.util.db
-
Service for type transformation User: julian3 Date: 2013/11/13 Time: 9:41 AM PROJECT: ${PROJECT} DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples
- transformToAlleleProbability(myGenotype) - Static method in class net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
-
- transformTraits(myPhenotype, myData) - Method in class net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
-
- transition(transition) - Method in class net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
-
- transition(transition) - Method in class net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
-
- TransitionProbability - Class in net.maizegenetics.analysis.imputation
-
- TransitionProbabilityWithVariableRecombination - Class in net.maizegenetics.analysis.imputation
-
- TransitionProbabilityWithVariableRecombination(chromosome) - Constructor for class net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
-
- Translate - Class in net.maizegenetics.dna.snp
-
This translates filtered taxa and sites. Also indicates masking, but this implementation has no mask.
- translate(index) - Method in class net.maizegenetics.dna.snp.TranslateIndex
-
Translates index to base index. This class has no translation.
- translate(index) - Method in class net.maizegenetics.dna.snp.TranslateIndexRange
-
- translate(index) - Method in class net.maizegenetics.dna.snp.TranslateIndexRedirect
-
Translates index to base index.
- TranslateBuilder - Class in net.maizegenetics.dna.snp
-
- TranslateIndex - Class in net.maizegenetics.dna.snp
-
No translation to index.
- TranslateIndexBuilder - Class in net.maizegenetics.dna.snp
-
- TranslateIndexRange - Class in net.maizegenetics.dna.snp
-
- TranslateIndexRedirect - Class in net.maizegenetics.dna.snp
-
Translation redirects index to corresponding index in base genotype table.
- TranslateIndexRedirectUnordered - Class in net.maizegenetics.dna.snp
-
- TranslateNegative - Class in net.maizegenetics.dna.snp
-
- translateSite(site) - Method in class net.maizegenetics.dna.snp.CombineGenotypeTable
-
Returns which genotypeTable to use.
- translateSitesBackToOriginal(sites, translation) - Static method in class net.maizegenetics.analysis.imputation.NucleotideImputationUtils
-
- translateToRealIndices(shownIndices) - Method in class net.maizegenetics.gui.AbstractAvailableListModel
-
- transpose() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- transpose() - Method in class net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix
-
- transpose() - Method in interface net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
-
- transpose() - Method in class net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix
-
- transpose(matrix, numDataRows, numRows, numColumns, listener) - Static method in class net.maizegenetics.util.BitUtil
-
This converts taxa optimized Bit Sets to site optimized Bit Sets and vice versa.
- transpose(orig) - Static method in class net.maizegenetics.util.BitUtil
-
Transposes 64 x 64 bit matrix. The below before and after locations. 1 2 4 2 3 4 3 1
- transpose() - Method in class net.maizegenetics.util.SuperByteMatrixSingle
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in interface net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
-
Tells this Genotype to transpose it's data to optimize performance for given iteration nesting. If siteInnerLoop is true, performance better when looping through sites inside taxa loop. If false, performance better when looping through taxa inside site loop.
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
-
- transposeData(siteInnerLoop) - Method in class net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
-
- transposeInPlace() - Method in class net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix
-
- traverseBlock(block, source, gapped_seq1, tag_line, gapped_seq2) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
-
Traverses a block to retrieve a part of an optimal alignment from the specified source in the output border to an entry in the input border.
- traverseBlockCrossingPath(block, gapped_seq1, tag_line, gapped_seq2) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Traverses a series of block crossing paths to retrieve an optimal alignment. A block-crossing path consists of a (possibly empty) S-path (a path that starts inside a block and ends in its output border), followed by any number of paths that cross a block from its input border to its output border, and ending in an E-path (a path that starts in the input border of a block and ends inside the block).
- traverseS_Path(block, gapped_seq1, tag_line, gapped_seq2) - Method in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
Traverses an S-path of a block to retrieve a part of an optimal alignment from the new vertex of a block to entry in its input border. This method is essentially similar to the traverseBlock. The only difference is that it uses the information of the S_direction field of the LocalAlignmentBlock class.
- Tree - Interface in net.maizegenetics.taxa.tree
-
Interface for a phylogenetic or genealogical tree.
- TreeClusters - Class in net.maizegenetics.taxa.tree
-
- TreeClusters(theTree) - Constructor for class net.maizegenetics.taxa.tree.TreeClusters
-
- TreeParseException - Exception in net.maizegenetics.taxa.tree
-
exception thrown by ReadTree
- TreeParseException() - Constructor for exception net.maizegenetics.taxa.tree.TreeParseException
-
- TreeParseException(msg) - Constructor for exception net.maizegenetics.taxa.tree.TreeParseException
-
- TreeUtils - Class in net.maizegenetics.taxa.tree
-
various utility functions on trees.
- Trie - Class in net.maizegenetics.analysis.gbs.neobio
-
This class implements a trie, or a digital search tree. A trie is a multiway tree (each node can have multiple children) that represents a set of strings.
- Trie(data) - Constructor for class net.maizegenetics.analysis.gbs.neobio.Trie
-
Creates a new trie node with the specified data. This constructor is typically used by the client only once to instantiate the root node. After that, all new nodes are implicitly instantiated by the add method.
- trimTrailingZeros() - Method in interface net.maizegenetics.util.BitSet
-
Lowers numWords, the number of words in use, by checking for trailing zero words.
- trimTrailingZeros() - Method in class net.maizegenetics.util.OpenBitSet
-
Lowers numWords, the number of words in use, by checking for trailing zero words.
- trimTrailingZeros() - Method in class net.maizegenetics.util.UnmodifiableBitSet
-
- truncateTaxonNames() - Method in class net.maizegenetics.dna.tag.AbstractTagsByTaxa
-
Truncates each taxon name to everything up to the first colon, and converts all letters to lower case. This causes tag counts from taxa with identical names to be merged.
- truncateTaxonNames() - Method in interface net.maizegenetics.dna.tag.TagsByTaxa
-
Deprecated.
- truSeqIAdaptor1 - Static variable in class net.maizegenetics.dna.read.ReadUtils
-
Illumina TruSeq index adaptor part 1, before barcode
- truSeqIAdaptor2 - Static variable in class net.maizegenetics.dna.read.ReadUtils
-
Illumina TruSeq index adaptor part 2, after barcode
- truSeqUAdaptor - Static variable in class net.maizegenetics.dna.read.ReadUtils
-
Illumina TruSeq universal adaptor
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.AddDomPermutationTestSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepAddDomSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepNestedAdditiveSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingAdditiveSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingNestedAdditiveSpliterator
-
- tryAdvance(action) - Method in class net.maizegenetics.analysis.modelfitter.NestedCovariatePermutationTestSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepAddDomSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepNestedAdditiveSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingAdditiveSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingNestedAdditiveSpliterator
-
- trySplit() - Method in class net.maizegenetics.analysis.modelfitter.NestedCovariatePermutationTestSpliterator
-
- tuple(list) - Static method in class net.maizegenetics.util.db.DefaultDBTuple
-
- Tuple<X,Y> - Class in net.maizegenetics.util
-
Based on response in http://stackoverflow.com/questions/2670982/using-pairs-or-2-tuples-in-java
- Tuple(x, y) - Constructor for class net.maizegenetics.util.Tuple
-
Instantiates a tuple object, which just holds 2 values
- type() - Method in class net.maizegenetics.dna.map.GenomeFeature
-
- type(type) - Method in class net.maizegenetics.dna.map.GenomeFeatureBuilder
-
- TYPE_C_PATH - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
A constant that indicates that the high scoring path ending in a given block is a C-path, i.e. one that starts inside the block.
- TYPE_CROSSING_PATH - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
A constant that indicates that the best path ending at a given entry of the output border is a block-crossing path (one that starts outside the block).
- TYPE_E_PATH - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
A constant that indicates that the high scoring path ending in a given block is an E-path, i.e. one that starts at its input border.
- TYPE_S_PATH - Static variable in class net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
-
A constant that indicates that the best path ending at a given entry of the output border is a S-path (one that starts inside the block).
- typeListCopy() - Method in class net.maizegenetics.phenotype.CorePhenotype
-
- typeListCopy() - Method in class net.maizegenetics.phenotype.FilterPhenotype
-
- typeListCopy() - Method in interface net.maizegenetics.phenotype.Phenotype
-
- typeNameMap - Static variable in class net.maizegenetics.analysis.association.AbstractFixedEffectLM
-
- typesOfRetainedAttributes(attributeTypes) - Method in class net.maizegenetics.phenotype.PhenotypeBuilder
-
- TypeTransformer<T,K> - Interface in net.maizegenetics.util.db
-
Functional interface for transforming instance of one type to another User: julian3 Date: 2013/11/13 Time: 9:42 AM PROJECT: lambda-tuples DESCRIPTION: Code Borrowed from http://java.dzone.com/articles/adding-java-8-lambda-goodness Original package can be downloaded from https://github.com/jexenberger/lambda-tuples