All Classes
AboutBox
AbstractAdditiveSite
AbstractAvailableListModel
AbstractByte2D
AbstractDisplayPlugin
AbstractFixedEffectLM
AbstractForwardRegression
AbstractGenotypeTableMask
AbstractMaskMatrix
AbstractPETags
AbstractPETagsOnPhysicalMap
AbstractPlugin
AbstractPluginAction
AbstractTableReport
AbstractTag
AbstractTags
AbstractTagsByTaxa
AbstractTagsHDF5
AbstractTagsOnPhysicalMap
AddDistanceMatrixPlugin
AddDomPermutationTestSpliterator
AdditiveModelForwardRegression
AdditiveResidualForwardRegression
AdditiveSite
AdditiveSite.CRITERION
AdditiveSiteStorePlugin
AddPlusDomModelEffect
AddReferenceAlleleToHDF5Plugin
AddReferenceToGenotypePlugin
AdjustPhasingPlugin
AGPMap
AlignmentBlock
AlignmentInfo
AlignmentTableCellRenderer
AlignmentTableCellRenderer.RENDERING_TYPE
AlignmentTableModel
Allele
AlleleDepth
AlleleDepthBuilder
AlleleDepthUtil
AlleleFreqCache
AlleleProbability
AlleleProbabilityBuilder
AlleleProbabilityFELM
AMatrixPlugin
AnnotateTOPM
AnnotateTOPM.EvidenceType
AnnotateTOPMwSAMPlugin
ApproxFastChiSquareDistribution
ArchaeopteryxPlugin
ArgsEngine
AssociationConstants
AssociationUtils
AttributeNode
AvgPhenotype
AvgPhenotypeByTaxaPlugin
AvroConstants
AvroConstants.CHROMOSOME_INDICES
AvroConstants.GENOTYPE_TABLE_COMPONENTS
AvroConstants.POSITION_INDICES
AvroConstants.TAXON_INDICES
B4RPhenotypeUtils
BackwardForwardAlgorithm
BackwardForwardVariableStateNumber
BarChartPanel
Barcode
BarcodeTrie
BaseEncoder
BasicChartPanel
BasicFileFilter
BasicGenotypeMergeRule
BasicGraphFrame
BasicLevel
BasicScoringScheme
BasicShuffler
BinaryToTextPlugin
BinaryToTextPlugin.FILE_TYPES
BiparentalHaplotypeFinder
BitSet
BitSet.BitSetListCollector
BitStorage
BitUtil
BlasDoubleMatrix
BlasEigenvalueDecomposition
BlasSingularValueDecomposition
BMSConnection
BoxCoxTransformation
BoxCoxTransformationPlugin
BranchLimits
BuilderFromGenotypeHDF5
BuilderFromGVCF
BuilderFromHapMap
BuilderFromHapMapLIX
BuilderFromPLINK
BuilderFromVCF
BuilderFromVCFUsingHTSJDK
BuilderFromVCFUtil
BuildUnfinishedHDF5GenotypesPlugin
Byte2D
Byte2DBuilder
CallParentAllelesPlugin
CategoricalAttribute
ChangeLog
CharSequence
ChartDisplayPlugin
CheckSum
ChiSquareDistribution
ChiSquareTest
Chromosome
CladeSystem
ClassicMds
ClusterGenotypesPlugin
Clusters
ColtDoubleMatrix
ColtEigenvalueDecomposition
ColtSingularValueDecomposition
ColumnMatrix
ColumnMatrix.Builder
ColumnsToBinaryFullGenomeTablePlugin
ColumnsToBinarySNPOnlyTablePlugin
ColumnsToBinaryUtils
CombineDataSetsPlugin
CombineGenotypeCallTable
CombineGenotypeTable
CompareGenosBetweenHapMapFilesPlugin
CompareGenosBetweenHapMapFilesPlugin.SiteCompareType
CompressedDoubleMatrix
CompressedMLMusingDoubleMatrix
ContigencyTable
ContigPETagCountPlugin
ConvertAlignmentCoordinatesPlugin
ConvertOldFastqToModernFormatPlugin
ConvertTreeNamesPlugin
ConvertTreeNamesPluginKt
CoreGenotypeTable
CorePhenotype
CovariateModelEffect
CovariatePermutationTestSpliterator
CreateHybridGenotypesPlugin
CreateTreePlugin
CreateTreePlugin.CLUSTERING_METHOD
CrochemoreLandauZivUkelson
CrochemoreLandauZivUkelsonGlobalAlignment
CrochemoreLandauZivUkelsonLocalAlignment
CrossProgenyEmissionMatrix
DataAccessException
DataSet
DataTreePanel
Datum
DBTuple
DefaultDBTuple
DefaultPluginListener
DialogUtils
DifferenceGenotypeCallTable
DirectedGraph
DirectoryCrawler
DiscoverySNPCallerPlugin
DiscoverySNPCallerPluginV2
DiscreteSitesFELM
DistanceMatrix
DistanceMatrixBuilder
DistanceMatrixPlugin
DistanceMatrixRangesPlugin
DistanceMatrixUtils
DistanceMatrixWithCounts
DiversityAnalyses
DominanceNormalizedIBSMatrix
DominanceRelationshipMatrix
DonorHaplotypes
DonorHypoth
Dosage
DosageBuilder
DoubleFormat
DoubleMatrix
DoubleMatrixFactory
DynamicBitStorage
EigenvalueDecomposition
EJMLDoubleMatrix
EJMLEigenvalueDecomposition
EJMLSingularValueDecomposition
EmissionProbability
EMMAforDoubleMatrix
EndelmanDistanceMatrix
EqtlAssociationPlugin
ErrorFunction
ExceptionUtils
ExponentialDistribution
ExportAvro
ExportMultiplePlugin
ExportPlugin
ExportUtils
ExtractHapmapSubsetPlugin
Factor
FactorModelEffect
FactorSequence
FastMultithreadedAssociationPlugin
FastqChunk
FastqReader
FastqToPETagCountPlugin
FastqToTagCountPlugin
FastqToTBTPlugin
FeatureListToPositionsPlugin
FileBrowserUtils
FileLoadPlugin
FILLINDonorGenotypeUtils
FILLINFindHaplotypesPlugin
FILLINImputationAccuracy
FILLINImputationPlugin
FILLINImputationUtils
Filter
FilterAlignmentPlugin
FilterAlleleDepth
FilterAlleleProbability
FilterAndMaskGVCFGenomeSequence
FilterBySites
FilterByTaxa
FilterDataSetPlugin
FilterDosage
FilterGenotypeTable
FilterHDF5AlleleDepth
FilterJSONUtils
FilterList
FilterPhenotype
FilterReferenceProbability
FilterSite
FilterSiteBuilderPlugin
FilterSiteNamePlugin
FilterSubsetPlugin
FilterTableReport
FilterTaxa
FilterTaxa.FILTER_TAXA_ATTRIBUTES
FilterTaxaBuilderPlugin
FilterTaxaPropertiesPlugin
FilterTraitsDialog
FilterTraitsPlugin
FindInversionsPlugin
FindInversionsPlugin.WINDOW_UNIT
FindMatchByWordHash
FindMatchByWordHash.Builder
FindMergeHaplotypesPlugin
FisherExact
FixedEffectLM
FixedEffectLMPlugin
FlapjackUtils
FolderParser
FormattedInput
FormattedOutput
ForwardRegression
ForwardStepAddDomSpliterator
ForwardStepAdditiveSpliterator
ForwardStepNestedAdditiveSpliterator
ForwardStepSubsettingAdditiveSpliterator
ForwardStepSubsettingNestedAdditiveSpliterator
FSFHapImputationPlugin
GammaDistribution
GammaFunction
GBSEnzyme
GBSHDF5Constants
GBSSeqToTagDBPlugin
GBSUtils
GCTADistanceMatrix
GeneralAnnotation
GeneralAnnotationStorage
GeneralAnnotationStorage.Builder
GeneralPosition
GeneralPosition.Builder
GeneratePluginCode
GenerateRCode
GenerateRCode.PositionVectors
GenerateRCode.TableReportVectors
GenericArrayPositions
GenericArrayTaxa
GenericMapAnnotations
GenericRecordChromosome
GenericRecordGenotype
GenericRecordGenotypeTable
GenericRecordPosition
GenericRecordTaxon
GenomeAnnosDBQueryToPositionListPlugin
GenomeFeature
GenomeFeatureBuilder
GenomeFeatureMap
GenomeFeatureMapBuilder
GenomeSequence
GenomeSequenceBuilder
GenomicSelectionPlugin
GenosToABHPlugin
GenosToABHPlugin.OUTPUT_CHECK
GenotypeAdditiveSite
GenotypeCallTable
GenotypeCallTableBuilder
GenotypeMergeRule
GenotypePhenotype
GenotypePhenotypeBuilder
GenotypeSummaryPlugin
GenotypeTable
GenotypeTable.ALLELE_SORT_TYPE
GenotypeTable.GENOTYPE_TABLE_COMPONENT
GenotypeTableBuilder
GenotypeTableMask
GenotypeTableMaskBoolean
GenotypeTableMaskGeneticDistance
GenotypeTableMaskReference
GenotypeTableUtils
GenotypeToAdditiveValuesPlugin
GetPhenotypeFromB4RPlugin
GetPositionListPlugin
GetTagSequenceFromDBPlugin
GetTagTaxaDistFromDBPlugin
GetTaxaListPlugin
GOBII_IFLUtils
GOBIIAvroGenotypeCallTable
GOBIIDbUtils
GOBIIGenotypeCallTable
GOBIIPlugin
GOBIIPostgresConnection
Graph
Graph.GraphType
GraphBuilder
GraphUtils
GVCFGenomeSequence
GVCFGenomeSequenceBuilder
GWAS_IFLPlugin
HapBreakpoints_IFLFilePlugin
Haplotype
HaplotypeCluster
HaplotypeClusterer
HaplotypeClusterer.TYPE
HapMapHDF5Constants
HDF5AlleleDepth
HDF5AlleleDepthBuilder
HDF5Byte2D
HDF5SummaryPlugin
HDF5TableReport
HDF5Utils
HelpDialog
HetsToUnknownPlugin
HighestDepthGenotypeMergeRule
HistogramPanel
HMatrixPlugin
HybridGenotypeCallTable
IBSDistanceMatrix
IBSDistanceMatrix2Alleles
IBSDistanceMatrix3Alleles
IBSDistanceMatrixOneByAll
IdentifierSynonymizer
IdentityRecognitionPlugin
ImportAvro
ImportUtils
ImputationAccuracyPlugin
ImputationByMean
ImputationPlugin
ImputationUtils
ImputeCrossProgeny
ImputeProgenyStatesPlugin
IncompatibleScoringSchemeException
IndelsToUnknownPlugin
InputSource
IntersectionAlignmentPlugin
InvalidScoringMatrixException
InvalidSequenceException
JSONUtils
KeepSpecifiedReadsinFastqPlugin
KeepSpecifiedSitesInTOPMPlugin
Kinship
Kinship.KINSHIP_TYPE
KinshipPlugin
KinshipPlugin.ALGORITHM_VARIATION
KinshipPlugin.KINSHIP_METHOD
KmerCountingPlugin
KmerCountingPluginKt
KmerToTagCountPlugin
KmerToTBTPlugin
kNearestNeighbors
LabelMapping
LambdaTuplesContext
LDKNNiImputationHetV2Plugin
LDKNNiImputationHetV3Plugin
LDKNNiImputationPlugin
LDResult
LDResult.Builder
Level
LikelihoodRatioTest
LinearModelForStepwiseRegression
LinearModelUtils
LineIndex
LineIndexBuilder
LineIndexHapmapGenotypeCallTable
LinkageDiseqDisplayPlugin
LinkageDisequilibrium
LinkageDisequilibrium.HetTreatment
LinkageDisequilibrium.testDesign
LinkageDisequilibriumComponent
LinkageDisequilibriumMinimapComponent
LinkageDisequilibriumPlugin
ListPluginParameters
ListPluginParameters.Companion
ListPluginParametersKt
ListPlugins
ListStats
ListStatsFilterSite
ListStatsFilterTaxa
ListStatsSite
ListStatsTaxa
LittleEndianDataOutputStream
LIXPlugin
LoadRNAContigsToGBSDBPlugin
LocalAlignmentBlock
LoggingUtils
LowLevelCopyOfHDF5
ManhattanDisplayPlugin
ManhattanNumberFormat
MarkerDNARun_IFLFilePlugin
MarkerDNARun_IFLFilePlugin.HmpTaxaData
MaskAlleleDepth
MaskAlleleProbability
MaskDosage
MaskedGenotypes
MaskGenotypeCallTable
MaskGenotypeMatrix
MaskGenotypePlugin
MaskGenotypeStatsMatrix
MaskMatrix
MaskMatrixBuilder
MaskReferenceProbability
MaskSiteMatrix
MaskTaxaMatrix
Matrix
MemoryByte2D
MemoryUsagePlugin
MergeAlignmentsSameSitesPlugin
MergeBreakpointFilesPlugin
MergedGenotypeCallTable
MergedGenotypeTable
MergeDuplicateSNPsPlugin
MergeGenotypeTablesPlugin
MergeGenotypeTablesPluginV2
MergeGenotypeTablesPluginV2.CALL_MERGE
MergeGenotypeTablesPluginV2.DEPTH_MERGE
MergeGenotypeTablesPluginV2.MERGE_TYPES
MergeHDF5GenotypesSameSitesPlugin
MergeMultipleTagCountPlugin
MergeMultipleTOPMPlugin
MergePETagCountPlugin
MergeRenameDeleteTaxaPlugin
MergeTagsByTaxaFilesByRowPlugin
MergeTagsByTaxaFilesPlugin
MergeTreesPlugin
MergeTreesPluginKt
MersenneTwisterFast
MigrateHDF5FromT4T5
MLMPlugin
ModelEffect
ModelEffectUtils
ModifyTBTHDF5Plugin
MonetDB_IFLFilePlugin
MultiDimensionalScalingPlugin
MultiMemberGZIPInputStream
MultiParameterized
MultiParameterized.ParameterAccessWatcher
NeedlemanWunsch
NeighborJoiningTree
NestedCovariateModelEffect
NestedCovariatePermutationTestSpliterator
NewickUtils
Node
NodeFactory
NodeUtils
NormalDistribution
NucleotideAlignmentConstants
NucleotideImputationUtils
NumericalGenotypePlugin
NumericalGenotypePlugin.TRANSFORM_TYPE
NumericAttribute
OpenBitSet
OrderEnumerator
OrderEnumerator.OEFactory
OrderEnumerator.Utils
OrthogonalHints
OrthogonalHints.Utils
OutMatrix
Pair
PairwiseAlignment
PairwiseAlignmentAlgorithm
PanAAddPosToTagMapPlugin
PanABuildPivotTBTPlugin
PanABuildTagBlockPosPlugin
PanABuildTagGWASMapPlugin
PanABuildTrainingSetPlugin
PanAFilteringTagMapPlugin
PanAH5ToAnchorPlugin
PanAMergeMappingResultPlugin
PanAModelTrainingPlugin
PanAPredictionPlugin
PanAReadDigestPlugin
PanAReadToKmerPlugin
PanASamToMultiPositionTOPMPlugin
PanASplitTagBlockPosPlugin
PanASplitTBTPlugin
PanATagGWASMappingPlugin
PanATagMapToFastaPlugin
PanAUsageExample
ParameterCache
Parameterized
Parameterized.Null
Parameterized.ParameterizedBase
Parameterized.ParameterizedUser
Parameterized.Utils
ParentPhasingPlugin
ParetoDistribution
ParseBarcodeRead
ParseGVCF
ParseGVCF.GVCFLine
ParseGVCF.ProcessLines
PartitionedLinearModel
PassThroughPlugin
PDAnnotation
PDReport
PEFastqChunk
PenalizedLikelihood
PEParseBarcodeRead
PERead
PEReadBarcodeResult
PETagCounts
PETags
PETagsOnPhysicalMap
PETagsOnPhysicalMapV3
PhaseHighCoverage
Phenotype
PhenotypeAttribute
PhenotypeBuilder
PhenotypeLM
PhenotypeUtils
PieChartPanel
PlinkLoadPlugin
Plugin
PluginAction
PluginEvent
PluginListener
PluginParameter
PluginParameter.Builder
PluginProgressUnit
PolymorphismDistribution
PolymorphismFinder
PopulationData
Position
PositionList
PositionList.PositionListCollector
PositionListBuilder
PositionListIOUtils
PositionListTableReport
PreferencesDialog
PreProcessGOBIIMappingFilePlugin
PrincipalComponentsPlugin
PrincipalComponentsPlugin.PCA_LIMIT
PrinComp
PrintHeapAction
PrintTextArea
ProductionPipeline
ProductionPipelineMain
ProductionSNPCallerPlugin
ProductionSNPCallerPluginV2
ProgressListener
ProgressPanel
ProjectionBuilder
ProjectionGenotypeCallTable
ProjectionGenotypeIO
ProjectionLoadPlugin
ProjectPcsAndRunModelSelectionPlugin
QQDisplayPlugin
QRDecomposition
QseqToPETagCountPlugin
QseqToTagCountPlugin
QseqToTBTPlugin
RampSeqAlignFromBlastTags
RandomGenotypeImputationPlugin
Read
ReadBarcodeResult
ReadBedfile
ReadBedfile.BedFileRange
ReadDistanceMatrix
ReadNumericMarkerUtils
Reads
ReadsByTaxa
ReadSequenceAlignmentUtils
ReadUtils
ReadUtils.ReadFormat
ReferenceProbability
ReferenceProbabilityBuilder
ReferenceProbabilityFELM
RefProbAdditiveSite
RefTagData
RegRidgeEmmaDoubleMatrix
ReImputeUpdatedTaxaByFILLINPlugin
RemoveBranchLengthsPlugin
RemoveBranchLengthsPluginKt
RemoveIndelsForBeaglePlugin
RemoveNaNFromDistanceMatrixPlugin
RepGenAlignerPlugin
RepGenData
RepGenDataWriter
RepGenLDAnalysisPlugin
RepGenLoadSeqToDBPlugin
RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap
RepGenPhase2AlignerPlugin
RepGenSQLite
RephaseParents
ReportDestinationDialog
ResamplingGWASPlugin
ResultSetIterator
ResultSetProcessor
RGBSProductionSNPCallerPlugin
RidgeRegressionEmmaPlugin
RNADeMultiplexProductionPlugin
RNADeMultiPlexSeqToDBPlugin
RootedTreeUtils
RowHeaderRenderer
SAMConverterPlugin
SAMToGBSdbPlugin
SAMUtils
SAMWGMapConverterPlugin
ScoringMatrix
ScoringScheme
SelectFromAvailableDialog
SelectFromAvailableSitesDialog
SelfedHaplotypeFinder
SeparatePlugin
SeqToTBTHDF5Plugin
SequenceDiversityPlugin
SeqViewerPanel
SetLowDepthGenosToMissingPlugin
SetToNGenotypeMergeRule
ShortReadBarcodeResult
ShowParameterCachePlugin
SimpleAllele
SimpleGenotypeSBit
SimpleNode
SimpleTableReport
SimpleTree
SingularValueDecomposition
SiteAnnotation
SiteNamesAvailableListModel
SiteScore
SiteScore.SITE_SCORE_TYPE
SiteScoresIO
SiteScoreUtil
Sizeof
Smawk
SmithWaterman
SmithWaterman
SMTPClient
SNP
SNPCutPosTagVerificationPlugin
SNPLogging
SNPQualityProfilerPlugin
SolveByOrthogonalizing
SolveByOrthogonalizing.Marker
SortGenotypeFilePlugin
SortGenotypeFilePlugin.SupportedFileTypes
SortTaxaAlphabeticallyPlugin
SplitFile_IFLFilePlugin
SplitHDF5ByChromosomePlugin
SplitSystem
SplitUtils
SQL
SQLAction
Stats
StepwiseAddDomModelFitter
StepwiseAdditiveModelFitter
StepwiseAdditiveModelFitterPlugin
StepwiseOLSModelFitter
StepwiseOLSModelFitterPlugin
StringNumberComparator
SubpopulationFinder
SubsetTreePlugin
SubsetTreePluginKt
SubtractDistanceMatrixPlugin
SubtractGenotypesPlugin
SubtractPhenotype
SubtractPhenotypeByTaxaPlugin
SuperByteMatrix
SuperByteMatrixBuilder
SuperByteMatrixMultiple
SuperByteMatrixSingle
SuperByteMatrixSingleValue
SuperByteMatrixTranspose
SweepFast
SweepFastLinearModel
SweepFastNestedModel
SymmetricEigenvalueDecomposition
SymmetricMatrixInverterDM
SynonymizerPlugin
TableDisplayPlugin
TableReport
TableReportBoxWhiskerCatDataset
TableReportBuilder
TableReportManhattanDataset
TableReportNoPagingTableModel
TableReportPanel
TableReportPieDataset
TableReportQQDataset
TableReportStatCategoryDataset
TableReportUtils
TableReportXYDataset
TableRowHeaderListModel
Tag
TagAgainstAnchor
TagAgainstAnchorHypothesis
TagAgainstAnchorPlugin
TagBlockPosition
TagBuilder
TagCorrelationInfo
TagCountMutable
TagCounts
TagCountToFastqPlugin
TagData
TagDataSQLite
TagDataWriter
TagExportToFastqPlugin
TagGeneticMappingInfo
TagGWASMap
TagGWASMapInfo
TagLocus
TagMappingInfo
TagMappingInfoV3
TagMappingInfoV3.Aligner
TagMatchFinder
Tags
TagsByTaxa
TagsByTaxa.FilePacking
TagsByTaxaByte
TagsByTaxaByteFileMap
TagsByTaxaByteFileMapSeq
TagsByTaxaByteHDF5TagGroups
TagsByTaxaByteHDF5TaxaGroups
TagsByTaxaShort
TagsByTaxaUtils
TagsOnGeneticMap
TagsOnPhysicalMap
TagsOnPhysicalMap.SAMFormat
TagsOnPhysicalMapV3
TagsOnPhysMapHDF5
Tassel5HDF5Constants
TasselLogging
TASSELMainApp
TASSELMainFrame
TasselPipeline
TasselPipeline.FLAGS
TasselPipelineStepsDialog
TasselPipelineXMLUtil
TasselPrefs
TaxaAttribute
TaxaAvailableListModel
TaxaDistBuilder
TaxaDistribution
TaxaList
TaxaList.TaxaListCollector
TaxaListBuilder
TaxaListIOUtils
TaxaListTableReport
TaxaListUtils
TaxaTissueDist
Taxon
Taxon.Builder
TerryPipelines
TextToBinaryPlugin
ThinSitesByPositionPlugin
ThreadedPluginListener
TOPMGenotypeTable
TOPMGenotypeTableCellRenderer
TOPMInterface
TOPMSummaryPlugin
TOPMTableReport
TOPMUtils
Transformations
TransformDataDialog
TransformDataPlugin
TransformerService
TransitionProbability
TransitionProbabilityWithVariableRecombination
Translate
TranslateBuilder
TranslateIndex
TranslateIndexBuilder
TranslateIndexRange
TranslateIndexRedirect
TranslateIndexRedirectUnordered
TranslateNegative
Tree
TreeClusters
TreeParseException
TreeUtils
Trie
Tuple
TypeTransformer
UndirectedGraph
UNetworkFilter
UnionAlignmentPlugin
Units
UnitsProvider
UnmodifiableBitSet
UpdateMarkerAndDNA_idxes
UpdateSNPPositionQualityPlugin
UpdateTOPMWithGeneticMapping
UPGMATree
UseParentHaplotypes
UTagCountMutable
UTagCountToTagPairPlugin
UTagPairFinder
UTagPairs
UTagPairToTOPMPlugin
Utils
VCAPScanPlugin
VCAPScanPlugin.SCAN_METHOD
VCFUtil
VerticalLabelUI
ViterbiAlgorithm
ViterbiAlgorithmPlugin
ViterbiAlgorithmVariableStateNumber
WeightedMLMPlugin
WHICH_ALLELE
WithinPopulationPermuter
WorkflowPlugin
WriteDistanceMatrix
WritePopulationAlignmentPlugin
XYAndLineToolTipGenerator
XYMultipleYToolTipGenerator
XYScatterAndLinePanel
XYScatterMultipleYPanel
XYScatterPanel