Hierarchy For All Packages

Package Hierarchies:

• net.maizegenetics.analysis,
• net.maizegenetics.analysis.association,
• net.maizegenetics.analysis.avro,
• net.maizegenetics.analysis.b4r,
• net.maizegenetics.analysis.chart,
• net.maizegenetics.analysis.clustering,
• net.maizegenetics.analysis.data,
• net.maizegenetics.analysis.distance,
• net.maizegenetics.analysis.filter,
• net.maizegenetics.analysis.gbs,
• net.maizegenetics.analysis.gbs.neobio,
• net.maizegenetics.analysis.gbs.pana,
• net.maizegenetics.analysis.gbs.repgen,
• net.maizegenetics.analysis.gbs.v2,
• net.maizegenetics.analysis.gobii,
• net.maizegenetics.analysis.imputation,
• net.maizegenetics.analysis.modelfitter,
• net.maizegenetics.analysis.monetdb,
• net.maizegenetics.analysis.numericaltransform,
• net.maizegenetics.analysis.phg,
• net.maizegenetics.analysis.popgen,
• net.maizegenetics.analysis.rna,
• net.maizegenetics.analysis.tree,
• net.maizegenetics.analysis.workflow,
• net.maizegenetics.dna,
• net.maizegenetics.dna.map,
• net.maizegenetics.dna.pd,
• net.maizegenetics.dna.read,
• net.maizegenetics.dna.snp,
• net.maizegenetics.dna.snp.bit,
• net.maizegenetics.dna.snp.byte2d,
• net.maizegenetics.dna.snp.genotypecall,
• net.maizegenetics.dna.snp.io,
• net.maizegenetics.dna.snp.score,
• net.maizegenetics.dna.tag,
• net.maizegenetics.gui,
• net.maizegenetics.matrixalgebra.Matrix,
• net.maizegenetics.matrixalgebra.decomposition,
• net.maizegenetics.phenotype,
• net.maizegenetics.pipeline,
• net.maizegenetics.plugindef,
• net.maizegenetics.prefs,
• net.maizegenetics.progress,
• net.maizegenetics.stats.EMMA,
• net.maizegenetics.stats.PCA,
• net.maizegenetics.stats.linearmodels,
• net.maizegenetics.stats.math,
• net.maizegenetics.stats.statistics,
• net.maizegenetics.tassel,
• net.maizegenetics.taxa,
• net.maizegenetics.taxa.distance,
• net.maizegenetics.taxa.tree,
• net.maizegenetics.util,
• net.maizegenetics.util.db

Class Hierarchy

• net.maizegenetics.analysis.numericaltransform.AvgPhenotype
• net.maizegenetics.dna.snp.score.DosageBuilder
• net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
• net.maizegenetics.dna.tag.AbstractTags (implements net.maizegenetics.dna.tag.Tags)
  • net.maizegenetics.dna.tag.AbstractTagsByTaxa (implements net.maizegenetics.dna.tag.TagsByTaxa)
    • net.maizegenetics.dna.tag.TagsByTaxaByte
    • net.maizegenetics.dna.tag.TagsByTaxaByteFileMap
    • net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq
    • net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups
    • net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups
    • net.maizegenetics.dna.tag.TagsByTaxaShort
  • net.maizegenetics.dna.tag.AbstractTagsHDF5
    • net.maizegenetics.dna.map.TagGWASMap
  • net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap (implements net.maizegenetics.dna.map.TOPMInterface)
    • net.maizegenetics.dna.map.TagsOnPhysMapHDF5 (implements net.maizegenetics.dna.map.TOPMInterface)
    • net.maizegenetics.dna.map.TagsOnPhysicalMap
    • net.maizegenetics.dna.map.TagsOnPhysicalMapV3 (implements net.maizegenetics.dna.map.TOPMInterface)
  • net.maizegenetics.dna.tag.TagCounts
    • net.maizegenetics.dna.tag.TagCountMutable
      • net.maizegenetics.dna.tag.UTagCountMutable
  • net.maizegenetics.dna.map.TagsOnGeneticMap
• net.maizegenetics.util.SuperByteMatrixSingleValue (implements net.maizegenetics.util.SuperByteMatrix)
• net.maizegenetics.analysis.gbs.neobio.FactorSequence
• net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
• net.maizegenetics.plugindef.AbstractPlugin (implements net.maizegenetics.plugindef.Plugin)
  • net.maizegenetics.analysis.distance.AMatrixPlugin
  • net.maizegenetics.analysis.chart.AbstractDisplayPlugin
    • net.maizegenetics.analysis.chart.ChartDisplayPlugin
    • net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
    • net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
    • net.maizegenetics.analysis.chart.QQDisplayPlugin
    • net.maizegenetics.analysis.chart.TableDisplayPlugin
  • net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
  • net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
  • net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
  • net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
  • net.maizegenetics.analysis.data.AdjustPhasingPlugin
  • net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
  • net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
  • net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
  • net.maizegenetics.analysis.gbs.BinaryToTextPlugin
  • net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
  • net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
  • net.maizegenetics.analysis.imputation.CallParentAllelesPlugin
  • net.maizegenetics.analysis.imputation.ClusterGenotypesPlugin
  • net.maizegenetics.analysis.monetdb.ColumnsToBinaryFullGenomeTablePlugin
  • net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
  • net.maizegenetics.analysis.data.CombineDataSetsPlugin
  • net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
  • net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
  • net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
  • net.maizegenetics.util.ConvertOldFastqToModernFormatPlugin
  • net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin
  • net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
  • net.maizegenetics.analysis.tree.CreateTreePlugin
  • net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
  • net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
  • net.maizegenetics.analysis.distance.DistanceMatrixPlugin
  • net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
  • net.maizegenetics.analysis.association.EqtlAssociationPlugin
  • net.maizegenetics.analysis.data.ExportMultiplePlugin
  • net.maizegenetics.analysis.data.ExportPlugin
  • net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
  • net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
  • net.maizegenetics.analysis.imputation.FILLINImputationPlugin
  • net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
  • net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
  • net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
  • net.maizegenetics.analysis.gbs.FastqToTBTPlugin
  • net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
  • net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
  • net.maizegenetics.analysis.data.FileLoadPlugin
  • net.maizegenetics.analysis.filter.FilterAlignmentPlugin
  • net.maizegenetics.analysis.filter.FilterDataSetPlugin
  • net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
  • net.maizegenetics.analysis.filter.FilterSiteNamePlugin
  • net.maizegenetics.analysis.filter.FilterSubsetPlugin
  • net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
  • net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
  • net.maizegenetics.analysis.filter.FilterTraitsPlugin
  • net.maizegenetics.analysis.data.FindInversionsPlugin
  • net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
  • net.maizegenetics.analysis.association.FixedEffectLMPlugin
  • net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
  • net.maizegenetics.analysis.gobii.GOBIIPlugin
  • net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
  • net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
  • net.maizegenetics.analysis.association.GenomicSelectionPlugin
  • net.maizegenetics.analysis.data.GenosToABHPlugin
  • net.maizegenetics.analysis.data.GenotypeSummaryPlugin
  • net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin
  • net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
  • net.maizegenetics.analysis.data.GetPositionListPlugin
  • net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
  • net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
  • net.maizegenetics.analysis.data.GetTaxaListPlugin
  • net.maizegenetics.analysis.data.HDF5SummaryPlugin
  • net.maizegenetics.analysis.distance.HMatrixPlugin
  • net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
  • net.maizegenetics.analysis.data.HetsToUnknownPlugin
  • net.maizegenetics.analysis.data.IdentityRecognitionPlugin
  • net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
  • net.maizegenetics.analysis.numericaltransform.ImputationPlugin
  • net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
  • net.maizegenetics.analysis.data.IndelsToUnknownPlugin
  • net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
  • net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
  • net.maizegenetics.analysis.distance.KinshipPlugin
  • net.maizegenetics.analysis.data.KmerCountingPlugin
  • net.maizegenetics.analysis.gbs.KmerToTBTPlugin
  • net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
  • net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
  • net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
  • net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
  • net.maizegenetics.analysis.data.LIXPlugin
  • net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
  • net.maizegenetics.analysis.ListPluginParameters
  • net.maizegenetics.analysis.ListPlugins
  • net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
  • net.maizegenetics.analysis.association.MLMPlugin
    • net.maizegenetics.analysis.association.WeightedMLMPlugin
  • net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
  • net.maizegenetics.analysis.data.MaskGenotypePlugin
  • net.maizegenetics.analysis.data.MemoryUsagePlugin
  • net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
  • net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
  • net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
  • net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
  • net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
  • net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
  • net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
  • net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
  • net.maizegenetics.analysis.gbs.MergePETagCountPlugin
  • net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
  • net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
  • net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
  • net.maizegenetics.analysis.tree.MergeTreesPlugin
  • net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
  • net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
  • net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
  • net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
  • net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
  • net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
  • net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
  • net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
  • net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
  • net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
  • net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
  • net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
  • net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
  • net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
  • net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
  • net.maizegenetics.analysis.imputation.ParentPhasingPlugin
  • net.maizegenetics.analysis.data.PassThroughPlugin
  • net.maizegenetics.analysis.data.PlinkLoadPlugin
  • net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
  • net.maizegenetics.tassel.PreferencesDialog
  • net.maizegenetics.analysis.data.PrincipalComponentsPlugin
  • net.maizegenetics.analysis.gbs.ProductionPipeline
  • net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
  • net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
  • net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
  • net.maizegenetics.analysis.data.ProjectionLoadPlugin
  • net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
  • net.maizegenetics.analysis.gbs.QseqToTBTPlugin
  • net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
  • net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
  • net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
  • net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
  • net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
  • net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
  • net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
  • net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin
  • net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
  • net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
  • net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
  • net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
  • net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
  • net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
  • net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
  • net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
  • net.maizegenetics.analysis.gbs.SAMConverterPlugin
  • net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
  • net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
  • net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
  • net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
  • net.maizegenetics.analysis.data.SeparatePlugin
  • net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
  • net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
  • net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
  • net.maizegenetics.tassel.ShowParameterCachePlugin
  • net.maizegenetics.analysis.data.SortGenotypeFilePlugin
  • net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
  • net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
  • net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
  • net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
  • net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
  • net.maizegenetics.analysis.tree.SubsetTreePlugin
  • net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
  • net.maizegenetics.analysis.data.SubtractGenotypesPlugin
  • net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
  • net.maizegenetics.analysis.data.SynonymizerPlugin
  • net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
  • net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
  • net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
  • net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
  • net.maizegenetics.tassel.TasselLogging
  • net.maizegenetics.analysis.gbs.TextToBinaryPlugin
  • net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
  • net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
  • net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
  • net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
  • net.maizegenetics.analysis.data.UnionAlignmentPlugin
    • net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
  • net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
  • net.maizegenetics.analysis.distance.VCAPScanPlugin
  • net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
  • net.maizegenetics.analysis.workflow.WorkflowPlugin
  • net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
• net.maizegenetics.dna.snp.Translate
  • net.maizegenetics.dna.snp.TranslateNegative
• net.maizegenetics.prefs.TasselPrefs
• net.maizegenetics.util.UndirectedGraph.UndirectedIterator
• net.maizegenetics.gui.TableRowHeaderListModel
• net.maizegenetics.stats.linearmodels.BasicLevel (implements net.maizegenetics.stats.linearmodels.Level)
• net.maizegenetics.util.ColumnMatrix.Builder
• net.maizegenetics.dna.map.GenomeFeatureMapBuilder
• net.maizegenetics.dna.map.GenomeSequenceBuilder
  • net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder
• net.maizegenetics.dna.snp.TOPMGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
• net.maizegenetics.plugindef.Datum
• net.maizegenetics.analysis.imputation.ViterbiAlgorithm
• net.maizegenetics.dna.snp.score.AlleleDepth (implements net.maizegenetics.dna.snp.score.SiteScore)
  • net.maizegenetics.dna.snp.score.FilterAlleleDepth
  • net.maizegenetics.dna.snp.score.FilterHDF5AlleleDepth
  • net.maizegenetics.dna.snp.score.HDF5AlleleDepth
  • net.maizegenetics.dna.snp.score.MaskAlleleDepth
• net.maizegenetics.dna.snp.byte2d.AbstractByte2D (implements net.maizegenetics.dna.snp.byte2d.Byte2D)
  • net.maizegenetics.dna.snp.byte2d.HDF5Byte2D
  • net.maizegenetics.dna.snp.byte2d.MemoryByte2D
• net.maizegenetics.dna.tag.AbstractPETags (implements net.maizegenetics.dna.tag.PETags)
  • net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
    • net.maizegenetics.dna.map.PETagsOnPhysicalMap
  • net.maizegenetics.dna.tag.PETagCounts
• net.maizegenetics.dna.snp.score.AlleleProbability (implements net.maizegenetics.dna.snp.score.SiteScore)
  • net.maizegenetics.dna.snp.score.FilterAlleleProbability
  • net.maizegenetics.dna.snp.score.MaskAlleleProbability
• net.maizegenetics.stats.linearmodels.CovariateModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
• net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
  • net.maizegenetics.analysis.modelfitter.ForwardStepAddDomSpliterator
  • net.maizegenetics.analysis.modelfitter.ForwardStepNestedAdditiveSpliterator
  • net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingAdditiveSpliterator
  • net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingNestedAdditiveSpliterator
• net.maizegenetics.dna.tag.AbstractTag (implements net.maizegenetics.dna.tag.Tag)
• net.maizegenetics.gui.AbstractGenotypeTableMask (implements net.maizegenetics.gui.GenotypeTableMask)
  • net.maizegenetics.gui.GenotypeTableMaskBoolean
  • net.maizegenetics.gui.GenotypeTableMaskGeneticDistance
  • net.maizegenetics.gui.GenotypeTableMaskReference
• net.maizegenetics.util.SuperByteMatrixMultiple (implements net.maizegenetics.util.SuperByteMatrix)
• net.maizegenetics.gui.TableReportNoPagingTableModel
• net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule (implements net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule)
• net.maizegenetics.phenotype.PhenotypeBuilder
• net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
• net.maizegenetics.gui.AbstractAvailableListModel
  • net.maizegenetics.gui.SiteNamesAvailableListModel
  • net.maizegenetics.gui.TaxaAvailableListModel
• net.maizegenetics.dna.snp.io.LineIndexBuilder
• net.maizegenetics.dna.snp.score.ReferenceProbability (implements net.maizegenetics.dna.snp.score.SiteScore)
  • net.maizegenetics.dna.snp.score.FilterReferenceProbability
  • net.maizegenetics.dna.snp.score.MaskReferenceProbability
• net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
• net.maizegenetics.dna.pd.PDAnnotation
• net.maizegenetics.dna.pd.SiteAnnotation
• net.maizegenetics.analysis.chart.BasicGraphFrame
• net.maizegenetics.analysis.chart.XYAndLineToolTipGenerator
• net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition)
• net.maizegenetics.dna.snp.CombineGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
• net.maizegenetics.analysis.gobii.GOBIIDbUtils
• net.maizegenetics.dna.snp.ExportUtils
• net.maizegenetics.analysis.monetdb.LittleEndianDataOutputStream
• net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
• net.maizegenetics.analysis.b4r.B4RPhenotypeUtils
• net.maizegenetics.analysis.association.AbstractFixedEffectLM (implements net.maizegenetics.analysis.association.FixedEffectLM)
  • net.maizegenetics.analysis.association.AlleleProbabilityFELM
  • net.maizegenetics.analysis.association.DiscreteSitesFELM
  • net.maizegenetics.analysis.association.ReferenceProbabilityFELM
• net.maizegenetics.stats.statistics.ContigencyTable
• net.maizegenetics.util.GraphUtils<T>
• net.maizegenetics.analysis.gbs.neobio.ScoringScheme
  • net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
  • net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
• net.maizegenetics.analysis.numericaltransform.TransformDataDialog
• net.maizegenetics.dna.snp.score.ReferenceProbabilityBuilder
• net.maizegenetics.dna.read.ReadUtils
• net.maizegenetics.analysis.chart.TableReportStatCategoryDataset
• net.maizegenetics.analysis.gbs.v2.GBSEnzyme
• net.maizegenetics.analysis.avro.GenericRecordPosition
• net.maizegenetics.dna.snp.io.ProjectionGenotypeIO
• net.maizegenetics.dna.pd.FolderParser
• net.maizegenetics.dna.pd.PDReport
• net.maizegenetics.taxa.tree.Parameterized.Utils
• net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite (implements net.maizegenetics.analysis.modelfitter.AdditiveSite)
  • net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
  • net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
• net.maizegenetics.matrixalgebra.decomposition.EJMLEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
• net.maizegenetics.analysis.association.AssociationConstants
• net.maizegenetics.taxa.Taxon
• net.maizegenetics.analysis.avro.AvroConstants
• net.maizegenetics.dna.tag.GBSHDF5Constants
• net.maizegenetics.dna.read.Read
• net.maizegenetics.dna.map.GenomeFeatureMap
• net.maizegenetics.tassel.SeqViewerPanel
• net.maizegenetics.analysis.tree.MergeTreesPluginKt
• net.maizegenetics.taxa.tree.TreeClusters
• net.maizegenetics.analysis.avro.GenericArrayPositions
• net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule (implements net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule)
• net.maizegenetics.analysis.gbs.TerryPipelines
• net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
• net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
• net.maizegenetics.util.BuilderFromVCFUtil
• net.maizegenetics.dna.map.Chromosome
• net.maizegenetics.util.SuperByteMatrixBuilder
• net.maizegenetics.tassel.MyTableUI.MyMouseInputListener
• net.maizegenetics.dna.tag.SAMUtils
• net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
• net.maizegenetics.analysis.avro.GenericRecordGenotype
• net.maizegenetics.util.UndirectedGraph.UndirectedSet<E>
• net.maizegenetics.analysis.gbs.UTagPairFinder
• net.maizegenetics.plugindef.GenerateRCode.PositionVectors
• net.maizegenetics.plugindef.ParameterCache
• net.maizegenetics.dna.snp.AbstractMaskMatrix (implements net.maizegenetics.dna.snp.MaskMatrix)
  • net.maizegenetics.dna.snp.MaskGenotypeMatrix
  • net.maizegenetics.dna.snp.MaskGenotypeStatsMatrix
• net.maizegenetics.analysis.gbs.PolymorphismFinder
• net.maizegenetics.dna.map.GeneralPosition (implements net.maizegenetics.dna.map.Position)
• net.maizegenetics.phenotype.FilterPhenotype (implements net.maizegenetics.phenotype.Phenotype)
• net.maizegenetics.taxa.distance.DistanceMatrixUtils
• net.maizegenetics.analysis.popgen.LinkageDisequilibrium (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
  • net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
• net.maizegenetics.analysis.chart.BasicChartPanel
  • net.maizegenetics.analysis.chart.BarChartPanel
  • net.maizegenetics.analysis.chart.HistogramPanel
  • net.maizegenetics.analysis.chart.PieChartPanel
  • net.maizegenetics.analysis.chart.XYScatterAndLinePanel
  • net.maizegenetics.analysis.chart.XYScatterMultipleYPanel
  • net.maizegenetics.analysis.chart.XYScatterPanel
• net.maizegenetics.util.db.Pair<T,K>
• net.maizegenetics.dna.map.GenomeFeature
• net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
• net.maizegenetics.analysis.avro.ExportAvro
• net.maizegenetics.taxa.distance.WriteDistanceMatrix
• net.maizegenetics.util.BitSet.BitSetListCollector
• net.maizegenetics.taxa.tree.SimpleTree (implements net.maizegenetics.taxa.tree.Tree)
  • net.maizegenetics.taxa.tree.NeighborJoiningTree
  • net.maizegenetics.taxa.tree.UPGMATree
• net.maizegenetics.analysis.chart.ManhattanNumberFormat
• net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
• net.maizegenetics.tassel.TASSELMainApp
• net.maizegenetics.dna.map.PositionList.PositionListCollector
• net.maizegenetics.stats.math.GammaFunction
• net.maizegenetics.taxa.tree.TreeUtils
• net.maizegenetics.util.DirectoryCrawler
• net.maizegenetics.taxa.tree.NewickUtils
• net.maizegenetics.stats.linearmodels.LinearModelUtils
• net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
• net.maizegenetics.analysis.popgen.LDResult
• net.maizegenetics.gui.AlignmentTableCellRenderer
  • net.maizegenetics.gui.TOPMGenotypeTableCellRenderer
• net.maizegenetics.dna.snp.io.JSONUtils
• net.maizegenetics.dna.snp.genotypecall.ListStats
  • net.maizegenetics.dna.snp.genotypecall.ListStatsFilterSite
  • net.maizegenetics.dna.snp.genotypecall.ListStatsFilterTaxa
  • net.maizegenetics.dna.snp.genotypecall.ListStatsSite
  • net.maizegenetics.dna.snp.genotypecall.ListStatsTaxa
• net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
• net.maizegenetics.analysis.gobii.BMSConnection
• net.maizegenetics.plugindef.AbstractPluginAction (implements net.maizegenetics.plugindef.PluginAction)
• net.maizegenetics.analysis.imputation.PopulationData
• net.maizegenetics.util.CheckSum
• net.maizegenetics.dna.snp.FilterTableReport (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.gui.RowHeaderRenderer
• net.maizegenetics.taxa.TaxaListTableReport (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.dna.map.GenomeFeatureBuilder
• net.maizegenetics.analysis.chart.XYMultipleYToolTipGenerator
• net.maizegenetics.dna.read.PEFastqChunk
• net.maizegenetics.dna.tag.TagsByTaxaUtils
• net.maizegenetics.taxa.TaxaListBuilder
• net.maizegenetics.analysis.association.PhenotypeLM
• net.maizegenetics.dna.map.PositionListTableReport (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
• net.maizegenetics.util.db.ResultSetIterator
• net.maizegenetics.dna.snp.genotypecall.Stats
• net.maizegenetics.dna.snp.TranslateBuilder
• net.maizegenetics.util.AbstractTableReport (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.analysis.popgen.DiversityAnalyses (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.taxa.IdentifierSynonymizer (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.util.SimpleTableReport (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.dna.map.PositionListBuilder
• net.maizegenetics.analysis.numericaltransform.BoxCoxTransformation
• net.maizegenetics.analysis.phg.ParseGVCF
• net.maizegenetics.analysis.ListPluginParametersKt
• net.maizegenetics.gui.PrintHeapAction
• net.maizegenetics.plugindef.GeneratePluginCode
• net.maizegenetics.analysis.data.LowLevelCopyOfHDF5
• net.maizegenetics.analysis.association.AssociationUtils
• net.maizegenetics.dna.snp.score.AlleleProbabilityBuilder
• net.maizegenetics.dna.read.PERead
• net.maizegenetics.analysis.imputation.TransitionProbability
  • net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
• net.maizegenetics.analysis.modelfitter.AbstractForwardRegression (implements net.maizegenetics.analysis.modelfitter.ForwardRegression)
  • net.maizegenetics.analysis.modelfitter.AdditiveModelForwardRegression
  • net.maizegenetics.analysis.modelfitter.AdditiveResidualForwardRegression
• net.maizegenetics.stats.statistics.PenalizedLikelihood
• net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix (implements net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix)
• net.maizegenetics.dna.snp.io.SiteScoresIO
• net.maizegenetics.util.TableReportUtils
• net.maizegenetics.analysis.gbs.PEReadBarcodeResult
• net.maizegenetics.gui.DialogUtils
• net.maizegenetics.analysis.gbs.pana.PanAUsageExample
• net.maizegenetics.taxa.tree.MultiParameterized (implements net.maizegenetics.taxa.tree.Parameterized)
• net.maizegenetics.taxa.TaxaTissueDist
• net.maizegenetics.gui.VerticalLabelUI
• net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
• net.maizegenetics.tassel.TASSELMainFrame
• net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
• net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
  • net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
• net.maizegenetics.taxa.tree.RootedTreeUtils
• net.maizegenetics.util.SuperByteMatrixTranspose (implements net.maizegenetics.util.SuperByteMatrix)
• net.maizegenetics.util.DirectedGraph<T> (implements net.maizegenetics.util.Graph<T>)
• net.maizegenetics.analysis.distance.DominanceRelationshipMatrix
• net.maizegenetics.taxa.tree.SimpleNode (implements net.maizegenetics.taxa.tree.AttributeNode)
• net.maizegenetics.analysis.numericaltransform.SubtractPhenotype
• net.maizegenetics.analysis.tree.RemoveBranchLengthsPluginKt
• net.maizegenetics.dna.snp.score.AlleleDepthBuilder
  • net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder
• net.maizegenetics.analysis.gbs.ProductionPipelineMain
• net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
• net.maizegenetics.analysis.popgen.DonorHypoth
• net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
• net.maizegenetics.dna.snp.io.BuilderFromGVCF
• net.maizegenetics.stats.linearmodels.PartitionedLinearModel
• net.maizegenetics.util.db.Transformations
• net.maizegenetics.dna.snp.score.AlleleDepthUtil
• net.maizegenetics.analysis.imputation.EmissionProbability
  • net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
• net.maizegenetics.stats.statistics.LikelihoodRatioTest
• net.maizegenetics.dna.snp.ImportUtils
• net.maizegenetics.analysis.gbs.repgen.RefTagData
• net.maizegenetics.dna.snp.TranslateIndex
  • net.maizegenetics.dna.snp.TranslateIndexRange
  • net.maizegenetics.dna.snp.TranslateIndexRedirect
    • net.maizegenetics.dna.snp.TranslateIndexRedirectUnordered
• net.maizegenetics.progress.ProgressPanel
• net.maizegenetics.taxa.distance.ReadDistanceMatrix
• net.maizegenetics.stats.linearmodels.SweepFastNestedModel
• net.maizegenetics.analysis.imputation.SubpopulationFinder
• net.maizegenetics.analysis.tree.SubsetTreePluginKt
• net.maizegenetics.dna.map.PositionListIOUtils
• net.maizegenetics.taxa.TaxaListIOUtils
• net.maizegenetics.plugindef.ThreadedPluginListener
• net.maizegenetics.phenotype.CorePhenotype (implements net.maizegenetics.phenotype.Phenotype)
• net.maizegenetics.analysis.avro.ImportAvro
• net.maizegenetics.util.LoggingUtils
• net.maizegenetics.analysis.chart.TableReportManhattanDataset
• net.maizegenetics.dna.snp.io.BuilderFromHapMapLIX
• net.maizegenetics.pipeline.TasselPipeline (implements net.maizegenetics.plugindef.PluginListener)
• net.maizegenetics.dna.tag.RepGenSQLite (implements net.maizegenetics.dna.tag.RepGenDataWriter)
• net.maizegenetics.analysis.gbs.Barcode
• net.maizegenetics.dna.tag.TagDataSQLite (implements net.maizegenetics.dna.tag.TagDataWriter)
• net.maizegenetics.analysis.gbs.neobio.Smawk
• net.maizegenetics.util.OpenBitSet (implements net.maizegenetics.util.BitSet)
• net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
• net.maizegenetics.tassel.HelpDialog
• net.maizegenetics.dna.snp.io.FilterJSONUtils
• net.maizegenetics.analysis.gbs.TagBlockPosition
• net.maizegenetics.analysis.imputation.NucleotideImputationUtils
• net.maizegenetics.util.GraphBuilder<T>
• net.maizegenetics.util.FormattedOutput
• net.maizegenetics.dna.tag.UTagPairs
• net.maizegenetics.pipeline.TasselPipelineXMLUtil
• net.maizegenetics.analysis.popgen.LDResult.Builder
• net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap
• net.maizegenetics.tassel.AboutBox
• net.maizegenetics.dna.snp.genotypecall.MaskedGenotypes
• net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines
• net.maizegenetics.analysis.avro.GenericMapAnnotations
• net.maizegenetics.analysis.data.KmerCountingPluginKt
• net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
  • net.maizegenetics.analysis.modelfitter.AddDomPermutationTestSpliterator
• net.maizegenetics.dna.snp.io.BuilderFromPLINK
• net.maizegenetics.dna.map.DonorHaplotypes
• net.maizegenetics.analysis.filter.FilterBySites
• net.maizegenetics.phenotype.TaxaAttribute (implements net.maizegenetics.phenotype.PhenotypeAttribute)
• net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
• net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix (implements net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix)
• net.maizegenetics.gui.SelectFromAvailableDialog
  • net.maizegenetics.gui.SelectFromAvailableSitesDialog
• net.maizegenetics.stats.math.MersenneTwisterFast
• net.maizegenetics.dna.snp.bit.DynamicBitStorage (implements net.maizegenetics.dna.snp.bit.BitStorage)
• net.maizegenetics.dna.map.UpdateTOPMWithGeneticMapping
• net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix (implements net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix)
• net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
  • net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
    • net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
    • net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
  • net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
  • net.maizegenetics.analysis.gbs.neobio.SmithWaterman
• net.maizegenetics.plugindef.DefaultPluginListener (implements net.maizegenetics.plugindef.PluginListener)
• net.maizegenetics.dna.snp.MaskSiteMatrix (implements net.maizegenetics.dna.snp.MaskMatrix)
• net.maizegenetics.dna.map.TagGeneticMappingInfo
• net.maizegenetics.util.UndirectedGraph<T> (implements net.maizegenetics.util.Graph<T>)
• net.maizegenetics.util.DoubleFormat
• net.maizegenetics.taxa.tree.CladeSystem
• net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
• net.maizegenetics.util.db.TransformerService
• net.maizegenetics.phenotype.GenotypePhenotype (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.util.ArgsEngine
• net.maizegenetics.analysis.distance.GCTADistanceMatrix
• net.maizegenetics.analysis.gobii.GOBII_IFLUtils
• net.maizegenetics.util.UnmodifiableBitSet (implements net.maizegenetics.util.BitSet)
• net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
• net.maizegenetics.plugindef.PluginEvent
• net.maizegenetics.analysis.chart.TableReportQQDataset
• net.maizegenetics.dna.map.TagGWASMapInfo
• net.maizegenetics.analysis.avro.GenericArrayTaxa
• net.maizegenetics.util.BasicFileFilter
• net.maizegenetics.dna.BaseEncoder
• net.maizegenetics.analysis.ListPluginParameters.Companion
• net.maizegenetics.analysis.popgen.PolymorphismDistribution
• net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
• net.maizegenetics.analysis.distance.Kinship
• net.maizegenetics.analysis.gbs.ParseBarcodeRead
  • net.maizegenetics.analysis.gbs.PEParseBarcodeRead
• net.maizegenetics.util.StringNumberComparator
• net.maizegenetics.dna.snp.ReadSequenceAlignmentUtils
• net.maizegenetics.taxa.tree.Parameterized.Null (implements net.maizegenetics.taxa.tree.Parameterized)
• net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
• net.maizegenetics.util.db.LambdaTuplesContext
• net.maizegenetics.dna.map.PETagsOnPhysicalMapV3 (implements net.maizegenetics.dna.tag.Tags)
• net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
• net.maizegenetics.phenotype.CategoricalAttribute (implements net.maizegenetics.phenotype.PhenotypeAttribute)
• net.maizegenetics.progress.PluginProgressUnit (implements net.maizegenetics.plugindef.PluginListener)
• net.maizegenetics.taxa.tree.SplitSystem
• net.maizegenetics.analysis.chart.TableReportPieDataset
• net.maizegenetics.dna.map.TOPMUtils
• net.maizegenetics.util.InputSource
• net.maizegenetics.taxa.tree.LabelMapping
• net.maizegenetics.stats.linearmodels.FactorModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
• net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
• net.maizegenetics.analysis.rna.FindMatchByWordHash
• net.maizegenetics.dna.snp.HapMapHDF5Constants
• net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
• net.maizegenetics.util.Utils
• net.maizegenetics.stats.statistics.GammaDistribution
  • net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
  • net.maizegenetics.stats.statistics.ChiSquareDistribution
  • net.maizegenetics.stats.statistics.ExponentialDistribution
• net.maizegenetics.analysis.gbs.SmithWaterman
• net.maizegenetics.analysis.tree.ConvertTreeNamesPluginKt
• net.maizegenetics.dna.snp.FilterTaxa (implements net.maizegenetics.dna.snp.Filter)
• net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition)
• net.maizegenetics.dna.tag.TaxaDistBuilder
• net.maizegenetics.dna.snp.MaskMatrixBuilder
• net.maizegenetics.dna.snp.NucleotideAlignmentConstants
• net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
• net.maizegenetics.util.ChangeLog
• net.maizegenetics.analysis.gbs.AnnotateTOPM
• net.maizegenetics.stats.math.OrderEnumerator.Utils
• net.maizegenetics.stats.linearmodels.WithinPopulationPermuter
• net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
• net.maizegenetics.analysis.gbs.v2.BarcodeTrie
• net.maizegenetics.analysis.gbs.TagMatchFinder
• net.maizegenetics.dna.tag.FastqReader
• net.maizegenetics.dna.map.TagLocus
• net.maizegenetics.stats.linearmodels.SweepFastLinearModel
• net.maizegenetics.dna.map.GeneralPosition.Builder
• net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
• net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
• net.maizegenetics.dna.snp.io.BuilderFromVCF
• net.maizegenetics.util.HDF5TableReport (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.dna.tag.ReadsByTaxa (implements net.maizegenetics.dna.tag.Reads)
• net.maizegenetics.analysis.gbs.neobio.OutMatrix (implements net.maizegenetics.analysis.gbs.neobio.Matrix)
• net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
• net.maizegenetics.dna.snp.FilterAndMaskGVCFGenomeSequence
• net.maizegenetics.stats.statistics.FisherExact
• net.maizegenetics.analysis.imputation.ImputationUtils
• net.maizegenetics.dna.snp.score.Dosage (implements net.maizegenetics.dna.snp.score.SiteScore)
  • net.maizegenetics.dna.snp.score.FilterDosage
  • net.maizegenetics.dna.snp.score.MaskDosage
• net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
• net.maizegenetics.pipeline.TasselPipelineStepsDialog (implements net.maizegenetics.plugindef.PluginListener)
• net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
• net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
• net.maizegenetics.taxa.distance.DistanceMatrix (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.taxa.distance.DistanceMatrixWithCounts
• net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
• net.maizegenetics.analysis.imputation.ImputeCrossProgeny
• net.maizegenetics.analysis.gbs.SNPLogging
• net.maizegenetics.util.TableReportBuilder
• net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
• net.maizegenetics.dna.map.TOPMTableReport (implements net.maizegenetics.util.TableReport)
• net.maizegenetics.dna.snp.io.LineIndex
• net.maizegenetics.dna.snp.FilterSite (implements net.maizegenetics.dna.snp.Filter)
• net.maizegenetics.analysis.modelfitter.AddPlusDomModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
• net.maizegenetics.util.Tuple<X,Y>
• net.maizegenetics.gui.AlignmentTableModel
• net.maizegenetics.dna.snp.io.FlapjackUtils
• net.maizegenetics.util.GeneralAnnotationStorage.Builder
• net.maizegenetics.analysis.clustering.Haplotype
• net.maizegenetics.dna.snp.io.ReadBedfile
• net.maizegenetics.analysis.filter.FilterTraitsDialog
• net.maizegenetics.taxa.TaxaListUtils
• net.maizegenetics.analysis.imputation.FILLINDonorGenotypeUtils
• net.maizegenetics.dna.tag.TagBuilder
• net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
• net.maizegenetics.analysis.avro.GenericRecordTaxon
• net.maizegenetics.analysis.filter.FilterByTaxa
• net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
• net.maizegenetics.dna.read.FastqChunk
• net.maizegenetics.dna.snp.TranslateIndexBuilder
• net.maizegenetics.dna.snp.io.ReadBedfile.BedFileRange
• net.maizegenetics.util.SuperByteMatrixSingle (implements net.maizegenetics.util.SuperByteMatrix)
• net.maizegenetics.tassel.TableReportPanel
• net.maizegenetics.analysis.imputation.PhaseHighCoverage
• net.maizegenetics.analysis.gbs.UNetworkFilter
• net.maizegenetics.analysis.clustering.HaplotypeClusterer
• net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
• net.maizegenetics.analysis.data.MigrateHDF5FromT4T5
• net.maizegenetics.gui.FileBrowserUtils
• net.maizegenetics.gui.PrintTextArea
• net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
• net.maizegenetics.dna.snp.ProjectionBuilder
• net.maizegenetics.stats.statistics.ParetoDistribution
• net.maizegenetics.dna.snp.CoreGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
• net.maizegenetics.stats.linearmodels.SweepFast
• net.maizegenetics.stats.statistics.NormalDistribution
• net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
• net.maizegenetics.util.SMTPClient
• net.maizegenetics.analysis.distance.IBSDistanceMatrix
• net.maizegenetics.analysis.modelfitter.NestedCovariatePermutationTestSpliterator
• net.maizegenetics.plugindef.PluginParameter<T>
• net.maizegenetics.util.ColumnMatrix
• net.maizegenetics.analysis.avro.GenericRecordChromosome
• net.maizegenetics.dna.snp.GenotypeTableBuilder
• net.maizegenetics.analysis.monetdb.ColumnsToBinaryUtils
• net.maizegenetics.dna.snp.io.ReadNumericMarkerUtils
• net.maizegenetics.stats.PCA.PrinComp
• net.maizegenetics.analysis.modelfitter.SNP
• net.maizegenetics.analysis.gbs.Clusters
• net.maizegenetics.analysis.imputation.RephaseParents
• net.maizegenetics.analysis.imputation.AGPMap
• net.maizegenetics.dna.snp.MaskTaxaMatrix (implements net.maizegenetics.dna.snp.MaskMatrix)
• net.maizegenetics.taxa.TaxaList.TaxaListCollector
• net.maizegenetics.stats.math.ErrorFunction
• net.maizegenetics.analysis.gbs.neobio.Trie
• net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
• net.maizegenetics.plugindef.GenerateRCode.TableReportVectors
• net.maizegenetics.stats.linearmodels.SymmetricMatrixInverterDM
• net.maizegenetics.analysis.gbs.TagAgainstAnchor
• net.maizegenetics.analysis.gbs.neobio.Factor
• net.maizegenetics.dna.snp.io.VCFUtil
• net.maizegenetics.gui.ReportDestinationDialog
• net.maizegenetics.phenotype.NumericAttribute (implements net.maizegenetics.phenotype.PhenotypeAttribute)
• net.maizegenetics.phenotype.PhenotypeUtils
• net.maizegenetics.stats.PCA.ClassicMds
• net.maizegenetics.util.db.DefaultDBTuple (implements net.maizegenetics.util.db.DBTuple)
• net.maizegenetics.taxa.tree.SplitUtils
• net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
• net.maizegenetics.dna.snp.score.SiteScoreUtil
• net.maizegenetics.taxa.Taxon.Builder
• net.maizegenetics.dna.snp.io.BuilderFromGenotypeHDF5
• net.maizegenetics.analysis.association.CompressedDoubleMatrix
• net.maizegenetics.analysis.gbs.v2.GBSUtils
• net.maizegenetics.util.db.SQL
• net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
• net.maizegenetics.util.Tassel5HDF5Constants
• net.maizegenetics.plugindef.PluginParameter.Builder<T>
• net.maizegenetics.stats.linearmodels.BasicShuffler
• net.maizegenetics.util.Sizeof
• net.maizegenetics.util.GeneralAnnotationStorage (implements net.maizegenetics.util.GeneralAnnotation)
• net.maizegenetics.taxa.distance.DistanceMatrixBuilder
• net.maizegenetics.analysis.clustering.HaplotypeCluster
• net.maizegenetics.analysis.gobii.UpdateMarkerAndDNA_idxes
• net.maizegenetics.util.HDF5Utils
• net.maizegenetics.taxa.tree.NodeFactory
• net.maizegenetics.analysis.imputation.UseParentHaplotypes
• net.maizegenetics.util.MultiMemberGZIPInputStream
• net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
• net.maizegenetics.dna.snp.FilterList
• net.maizegenetics.tassel.DataTreePanel (implements net.maizegenetics.plugindef.PluginListener)
• net.maizegenetics.analysis.imputation.FILLINImputationUtils
• net.maizegenetics.plugindef.DataSet
• net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
• net.maizegenetics.phenotype.GenotypePhenotypeBuilder
• net.maizegenetics.dna.snp.io.BuilderFromHapMap
• net.maizegenetics.dna.map.TagMappingInfo
• net.maizegenetics.dna.snp.SimpleAllele (implements net.maizegenetics.dna.snp.Allele)
• net.maizegenetics.analysis.distance.DominanceNormalizedIBSMatrix
• net.maizegenetics.stats.statistics.ChiSquareTest
• net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
• net.maizegenetics.util.ExceptionUtils
• net.maizegenetics.analysis.chart.TableReportBoxWhiskerCatDataset
• net.maizegenetics.stats.linearmodels.ModelEffectUtils
• net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
• net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
• net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition)
• net.maizegenetics.analysis.chart.TableReportXYDataset
• net.maizegenetics.tassel.SeqViewerPanel.MyTableUI
• net.maizegenetics.util.BitUtil
• net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
• net.maizegenetics.dna.snp.MergedGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
• net.maizegenetics.analysis.rna.FindMatchByWordHash.Builder
• net.maizegenetics.analysis.numericaltransform.ImputationByMean
• net.maizegenetics.dna.snp.FilterGenotypeTable
• net.maizegenetics.dna.map.TagMappingInfoV3
• net.maizegenetics.analysis.gbs.ReadBarcodeResult
• net.maizegenetics.analysis.gbs.neobio.CharSequence
• net.maizegenetics.dna.snp.GenotypeTableUtils
• net.maizegenetics.util.FormattedInput
• net.maizegenetics.plugindef.GenerateRCode
• net.maizegenetics.stats.math.OrthogonalHints.Utils
• net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
• net.maizegenetics.analysis.distance.IBSDistanceMatrixOneByAll
• net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule (implements net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule)
• net.maizegenetics.taxa.tree.NodeUtils

Interface Hierarchy

• net.maizegenetics.analysis.modelfitter.AdditiveSite
• net.maizegenetics.dna.snp.Allele
• net.maizegenetics.util.BitSet
• net.maizegenetics.dna.snp.bit.BitStorage
• net.maizegenetics.taxa.tree.BranchLimits
• net.maizegenetics.dna.snp.byte2d.Byte2D
• net.maizegenetics.util.db.DBTuple
• net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
• net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition
• net.maizegenetics.dna.snp.Filter
• net.maizegenetics.analysis.association.FixedEffectLM
• net.maizegenetics.analysis.modelfitter.ForwardRegression
• net.maizegenetics.util.GeneralAnnotation
• net.maizegenetics.dna.map.GenomeSequence
  • net.maizegenetics.dna.map.GVCFGenomeSequence
• net.maizegenetics.dna.snp.genotypecall.GenotypeCallTable
• net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule
• net.maizegenetics.dna.snp.GenotypeTable
• net.maizegenetics.gui.GenotypeTableMask
• net.maizegenetics.util.Graph<T>
• net.maizegenetics.stats.linearmodels.Level
• net.maizegenetics.dna.snp.MaskMatrix
• net.maizegenetics.analysis.gbs.neobio.Matrix
• net.maizegenetics.stats.linearmodels.ModelEffect
• net.maizegenetics.taxa.tree.Node
  • net.maizegenetics.taxa.tree.AttributeNode
• net.maizegenetics.stats.math.OrderEnumerator.OEFactory
• net.maizegenetics.stats.math.OrderEnumerator
• net.maizegenetics.stats.math.OrthogonalHints
• net.maizegenetics.dna.tag.PETags
• net.maizegenetics.taxa.tree.MultiParameterized.ParameterAccessWatcher
• net.maizegenetics.taxa.tree.Parameterized
• net.maizegenetics.phenotype.PhenotypeAttribute
• net.maizegenetics.plugindef.PluginAction
• net.maizegenetics.plugindef.PluginListener
  • net.maizegenetics.plugindef.Plugin (also extends net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener)
• net.maizegenetics.dna.map.Position
• net.maizegenetics.dna.map.PositionList
• net.maizegenetics.util.ProgressListener
  • net.maizegenetics.plugindef.Plugin (also extends net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener)
• net.maizegenetics.matrixalgebra.decomposition.QRDecomposition
• net.maizegenetics.dna.tag.Reads
• net.maizegenetics.dna.tag.RepGenData
  • net.maizegenetics.dna.tag.RepGenDataWriter
• net.maizegenetics.util.db.ResultSetProcessor
• net.maizegenetics.util.db.SQLAction<T>
• net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
• net.maizegenetics.dna.snp.score.SiteScore
• net.maizegenetics.util.SuperByteMatrix
• net.maizegenetics.util.TableReport
  • net.maizegenetics.phenotype.Phenotype
• net.maizegenetics.dna.tag.Tag
• net.maizegenetics.dna.tag.TagData
  • net.maizegenetics.dna.tag.TagDataWriter
• net.maizegenetics.dna.tag.Tags
  • net.maizegenetics.dna.map.TOPMInterface
  • net.maizegenetics.dna.tag.TagsByTaxa
• net.maizegenetics.dna.tag.TaxaDistribution
• net.maizegenetics.taxa.TaxaList
• net.maizegenetics.util.db.TypeTransformer<T,K>
• net.maizegenetics.taxa.tree.Units
  • net.maizegenetics.taxa.tree.Tree
  • net.maizegenetics.taxa.tree.UnitsProvider
    • net.maizegenetics.taxa.tree.Tree

Enum Hierarchy

• net.maizegenetics.dna.snp.FilterSite.FILTER_SITES_ATTRIBUTES
• net.maizegenetics.stats.PCA.PrinComp.PC_TYPE
• net.maizegenetics.gui.AlignmentTableCellRenderer.RENDERING_TYPE
• net.maizegenetics.util.Graph.GraphType
• net.maizegenetics.plugindef.Plugin.PARAMETER_PROPERTIES
• net.maizegenetics.analysis.distance.KinshipPlugin.KINSHIP_METHOD
• net.maizegenetics.analysis.data.GenosToABHPlugin.OUTPUT_CHECK
• net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION
• net.maizegenetics.dna.map.TagMappingInfoV3.Aligner
• net.maizegenetics.dna.read.ReadUtils.ReadFormat
• net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2.CALL_MERGE
• net.maizegenetics.dna.snp.FilterTaxa.FILTER_TAXA_ATTRIBUTES
• net.maizegenetics.analysis.data.PrincipalComponentsPlugin.PCA_LIMIT
• net.maizegenetics.analysis.association.CompressedDoubleMatrix.kinshipMethod
• net.maizegenetics.analysis.chart.AbstractDisplayPlugin.Outformat
• net.maizegenetics.analysis.rna.FindMatchByWordHash.MatchType
• net.maizegenetics.analysis.clustering.HaplotypeCluster.TYPE
• net.maizegenetics.analysis.association.MLMPlugin.CompressionType
• net.maizegenetics.analysis.data.FindInversionsPlugin.WINDOW_UNIT
• net.maizegenetics.analysis.data.FileLoadPlugin.TasselFileType
• net.maizegenetics.analysis.distance.VCAPScanPlugin.SCAN_METHOD
• net.maizegenetics.analysis.gbs.AnnotateTOPM.EvidenceType
• net.maizegenetics.plugindef.PluginParameter.PARAMETER_TYPE
• net.maizegenetics.dna.WHICH_ALLELE
• net.maizegenetics.analysis.numericaltransform.TransformDataPlugin.BASE
• net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin.BestScore
• net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap.PETagType
• net.maizegenetics.analysis.association.WeightedMLMPlugin.CompressionType
• net.maizegenetics.dna.snp.GenotypeTable.ALLELE_SORT_TYPE
• net.maizegenetics.analysis.clustering.HaplotypeClusterer.TYPE
• net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin.SiteCompareType
• net.maizegenetics.gui.GenotypeTableMask.MaskType
• net.maizegenetics.analysis.distance.KinshipPlugin.ALGORITHM_VARIATION
• net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory.FactoryType
• net.maizegenetics.dna.snp.score.SiteScore.SITE_SCORE_TYPE
• net.maizegenetics.dna.map.TagsOnPhysicalMap.SAMFormat
• net.maizegenetics.analysis.avro.AvroConstants.POSITION_INDICES
• net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin.TRANSFORM_TYPE
• net.maizegenetics.analysis.data.SortGenotypeFilePlugin.SupportedFileTypes
• net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter.VIF_TYPE
• net.maizegenetics.dna.tag.TagsByTaxa.FilePacking
• net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter.MODEL_TYPE
• net.maizegenetics.analysis.distance.Kinship.KINSHIP_TYPE
• net.maizegenetics.analysis.avro.AvroConstants.CHROMOSOME_INDICES
• net.maizegenetics.analysis.popgen.LinkageDisequilibrium.HetTreatment
• net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2.DEPTH_MERGE
• net.maizegenetics.analysis.tree.CreateTreePlugin.CLUSTERING_METHOD
• net.maizegenetics.analysis.gbs.BinaryToTextPlugin.FILE_TYPES
• net.maizegenetics.analysis.avro.AvroConstants.GENOTYPE_TABLE_COMPONENTS
• net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT
• net.maizegenetics.analysis.popgen.LinkageDisequilibrium.testDesign
• net.maizegenetics.pipeline.TasselPipeline.FLAGS
• net.maizegenetics.analysis.chart.ChartDisplayPlugin.ChartType
• net.maizegenetics.gui.AlignmentTableModel.COLUMN_NAME_TYPE
• net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2.MERGE_TYPES
• net.maizegenetics.phenotype.Phenotype.ATTRIBUTE_TYPE
• net.maizegenetics.dna.snp.FilterSite.SITE_RANGE_FILTER_TYPES
• net.maizegenetics.analysis.avro.AvroConstants.TAXON_INDICES