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.decomposition,
• net.maizegenetics.matrixalgebra.Matrix,
• net.maizegenetics.phenotype,
• net.maizegenetics.pipeline,
• net.maizegenetics.plugindef,
• net.maizegenetics.prefs,
• net.maizegenetics.progress,
• net.maizegenetics.stats.EMMA,
• net.maizegenetics.stats.linearmodels,
• net.maizegenetics.stats.math,
• net.maizegenetics.stats.PCA,
• 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

• java.lang.Object
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • net.maizegenetics.plugindef.AbstractPluginAction (implements net.maizegenetics.plugindef.PluginAction)
    • net.maizegenetics.gui.PrintHeapAction (implements java.lang.Runnable)
  • net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite (implements net.maizegenetics.analysis.modelfitter.AdditiveSite)
    • net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
    • net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
  • 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
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • net.maizegenetics.util.db.DefaultDBTuple (implements net.maizegenetics.util.db.DBTuple)
      • 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
  • org.jfree.data.general.AbstractDataset (implements java.lang.Cloneable, org.jfree.data.general.Dataset, java.io.ObjectInputValidation, java.io.Serializable)
    • org.jfree.data.general.AbstractSeriesDataset (implements java.io.Serializable, org.jfree.data.general.SeriesChangeListener, org.jfree.data.general.SeriesDataset)
      • org.jfree.data.xy.AbstractXYDataset (implements org.jfree.data.xy.XYDataset)
        • org.jfree.data.xy.AbstractIntervalXYDataset (implements org.jfree.data.xy.IntervalXYDataset)
          • org.jfree.data.xy.DefaultTableXYDataset (implements org.jfree.data.DomainInfo, org.jfree.data.xy.IntervalXYDataset, org.jfree.util.PublicCloneable, org.jfree.data.xy.TableXYDataset)
            • net.maizegenetics.analysis.chart.TableReportManhattanDataset
            • net.maizegenetics.analysis.chart.TableReportQQDataset
            • net.maizegenetics.analysis.chart.TableReportXYDataset
    • org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset (implements org.jfree.data.statistics.BoxAndWhiskerCategoryDataset, org.jfree.util.PublicCloneable, org.jfree.data.RangeInfo)
      • net.maizegenetics.analysis.chart.TableReportBoxWhiskerCatDataset
    • org.jfree.data.general.DefaultPieDataset (implements java.lang.Cloneable, org.jfree.data.general.PieDataset, org.jfree.util.PublicCloneable, java.io.Serializable)
      • net.maizegenetics.analysis.chart.TableReportPieDataset
    • org.jfree.data.statistics.DefaultStatisticalCategoryDataset (implements org.jfree.util.PublicCloneable, org.jfree.data.RangeInfo, org.jfree.data.statistics.StatisticalCategoryDataset)
      • net.maizegenetics.analysis.chart.TableReportStatCategoryDataset
  • 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.analysis.modelfitter.AbstractForwardRegression (implements net.maizegenetics.analysis.modelfitter.ForwardRegression)
    • net.maizegenetics.analysis.modelfitter.AdditiveModelForwardRegression
    • net.maizegenetics.analysis.modelfitter.AdditiveResidualForwardRegression
  • net.maizegenetics.gui.AbstractGenotypeTableMask (implements net.maizegenetics.gui.GenotypeTableMask)
    • net.maizegenetics.gui.GenotypeTableMaskBoolean
    • net.maizegenetics.gui.GenotypeTableMaskGeneticDistance
    • net.maizegenetics.gui.GenotypeTableMaskReference
  • javax.swing.AbstractListModel<E> (implements javax.swing.ListModel<E>, java.io.Serializable)
    • net.maizegenetics.gui.AbstractAvailableListModel
      • net.maizegenetics.gui.SiteNamesAvailableListModel
      • net.maizegenetics.gui.TaxaAvailableListModel
    • net.maizegenetics.gui.SelectFromAvailableDialog.SelectedListModel
    • net.maizegenetics.gui.TableRowHeaderListModel
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.concurrent.ConcurrentHashMap<K,V> (implements java.util.concurrent.ConcurrentMap<K,V>, java.io.Serializable)
      • net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin.TagCountQualityScoreMap
  • net.maizegenetics.dna.snp.AbstractMaskMatrix (implements net.maizegenetics.dna.snp.MaskMatrix)
    • net.maizegenetics.dna.snp.MaskGenotypeMatrix
    • net.maizegenetics.dna.snp.MaskGenotypeStatsMatrix
  • 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.plugindef.AbstractPlugin (implements net.maizegenetics.plugindef.Plugin)
    • 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.modelfitter.AdditiveSiteStorePlugin
    • net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
    • net.maizegenetics.analysis.data.AdjustPhasingPlugin
    • net.maizegenetics.analysis.distance.AMatrixPlugin
    • 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.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.association.FastMultithreadedAssociationPlugin
    • net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
    • net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
    • net.maizegenetics.analysis.gbs.FastqToTBTPlugin
    • net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
    • net.maizegenetics.analysis.data.FileLoadPlugin
    • net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
    • net.maizegenetics.analysis.imputation.FILLINImputationPlugin
    • 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.imputation.FSFHapImputationPlugin
    • net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
    • net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
    • net.maizegenetics.analysis.association.GenomicSelectionPlugin
    • net.maizegenetics.analysis.data.GenosToABHPlugin
    • net.maizegenetics.analysis.data.GenotypeSummaryPlugin
    • 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.gobii.GOBIIPlugin
    • net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
    • net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
    • net.maizegenetics.analysis.data.HDF5SummaryPlugin
    • net.maizegenetics.analysis.data.HetsToUnknownPlugin
    • net.maizegenetics.analysis.distance.HMatrixPlugin
    • 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.gbs.KmerToTagCountPlugin
    • net.maizegenetics.analysis.gbs.KmerToTBTPlugin
    • net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
    • net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
    • net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
    • net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
    • net.maizegenetics.analysis.ListPlugins
    • net.maizegenetics.analysis.data.LIXPlugin
    • net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
    • 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.MergeMultipleTagCountPlugin
    • net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
    • net.maizegenetics.analysis.gbs.MergePETagCountPlugin
    • net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
    • net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
    • net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
    • net.maizegenetics.analysis.association.MLMPlugin
      • net.maizegenetics.analysis.association.WeightedMLMPlugin
    • 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.PanASplitTagBlockPosPlugin
    • net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
    • 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.tassel.PreferencesDialog
    • net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
    • 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.ProjectionLoadPlugin
    • net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
    • net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
    • net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
    • net.maizegenetics.analysis.gbs.QseqToTBTPlugin
    • net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
    • net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
    • net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
    • 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.gbs.repgen.RGBSProductionSNPCallerPlugin
    • net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
    • net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
    • net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
    • net.maizegenetics.analysis.gbs.SAMConverterPlugin
    • net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
    • net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
    • 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.gbs.v2.SNPCutPosTagVerificationPlugin
    • net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
    • 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.distance.SubtractDistanceMatrixPlugin
    • net.maizegenetics.analysis.data.SubtractGenotypesPlugin
    • net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
    • net.maizegenetics.analysis.data.SynonymizerPlugin
    • 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.gbs.TOPMSummaryPlugin
    • net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
    • net.maizegenetics.analysis.data.UnionAlignmentPlugin
      • net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
    • net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
    • net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
    • net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
    • net.maizegenetics.analysis.distance.VCAPScanPlugin
    • net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
    • net.maizegenetics.analysis.workflow.WorkflowPlugin
    • net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • net.maizegenetics.gui.AlignmentTableModel (implements javax.swing.event.ChangeListener)
    • net.maizegenetics.gui.TableReportNoPagingTableModel
  • net.maizegenetics.util.AbstractTableReport (implements net.maizegenetics.util.TableReport)
    • net.maizegenetics.analysis.popgen.DiversityAnalyses (implements java.io.Serializable, net.maizegenetics.util.TableReport)
    • net.maizegenetics.taxa.IdentifierSynonymizer (implements java.io.Serializable, net.maizegenetics.util.TableReport)
    • net.maizegenetics.util.SimpleTableReport (implements java.io.Serializable, net.maizegenetics.util.TableReport)
  • net.maizegenetics.dna.tag.AbstractTag (implements java.lang.Comparable<T>, net.maizegenetics.dna.tag.Tag)
  • 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.TagsOnPhysicalMap
      • net.maizegenetics.dna.map.TagsOnPhysicalMapV3 (implements net.maizegenetics.dna.map.TOPMInterface)
      • net.maizegenetics.dna.map.TagsOnPhysMapHDF5 (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
  • org.jfree.chart.labels.AbstractXYItemLabelGenerator (implements java.lang.Cloneable, java.io.Serializable)
    • net.maizegenetics.analysis.chart.XYAndLineToolTipGenerator (implements org.jfree.chart.labels.XYToolTipGenerator)
    • net.maizegenetics.analysis.chart.XYMultipleYToolTipGenerator (implements org.jfree.chart.labels.XYToolTipGenerator)
  • net.maizegenetics.analysis.imputation.AGPMap
  • net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
    • net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
  • net.maizegenetics.analysis.gbs.repgen.AlignmentInfo (implements java.lang.Comparable<T>)
  • 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.score.AlleleDepthBuilder
    • net.maizegenetics.dna.snp.score.HDF5AlleleDepthBuilder
  • net.maizegenetics.dna.snp.score.AlleleDepthUtil
  • net.maizegenetics.dna.snp.genotypecall.AlleleFreqCache
  • 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.dna.snp.score.AlleleProbabilityBuilder
  • net.maizegenetics.analysis.gbs.AnnotateTOPM
  • net.maizegenetics.util.ArgsEngine
  • net.maizegenetics.analysis.association.AssociationConstants
  • net.maizegenetics.analysis.association.AssociationUtils
  • net.maizegenetics.analysis.numericaltransform.AvgPhenotype
  • net.maizegenetics.analysis.avro.AvroConstants
  • net.maizegenetics.analysis.b4r.B4RPhenotypeUtils
  • net.maizegenetics.analysis.imputation.BackwardForwardAlgorithm
  • net.maizegenetics.analysis.imputation.BackwardForwardVariableStateNumber
  • net.maizegenetics.analysis.gbs.Barcode (implements java.lang.Comparable<T>)
  • net.maizegenetics.analysis.gbs.v2.BarcodeTrie
  • net.maizegenetics.dna.BaseEncoder
  • net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule (implements net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule)
  • net.maizegenetics.stats.linearmodels.BasicLevel (implements net.maizegenetics.stats.linearmodels.Level)
  • net.maizegenetics.stats.linearmodels.BasicShuffler
  • javax.swing.plaf.basic.BasicTableUI.MouseInputHandler (implements javax.swing.event.MouseInputListener)
    • net.maizegenetics.tassel.SeqViewerPanel.MyTableUI.MyMouseInputListener
  • net.maizegenetics.analysis.imputation.BiparentalHaplotypeFinder
  • net.maizegenetics.util.BitSet.BitSetListCollector (implements java.util.stream.Collector<T,A,R>)
  • net.maizegenetics.util.BitUtil
  • net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix (implements net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix)
  • net.maizegenetics.matrixalgebra.decomposition.BlasEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
  • net.maizegenetics.matrixalgebra.decomposition.BlasSingularValueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition)
  • net.maizegenetics.analysis.gobii.BMSConnection
  • net.maizegenetics.analysis.numericaltransform.BoxCoxTransformation
  • net.maizegenetics.dna.snp.io.BuilderFromGenotypeHDF5
  • net.maizegenetics.dna.snp.io.BuilderFromGVCF
  • net.maizegenetics.dna.snp.io.BuilderFromHapMap
  • net.maizegenetics.dna.snp.io.BuilderFromHapMapLIX
  • net.maizegenetics.dna.snp.io.BuilderFromPLINK
  • net.maizegenetics.dna.snp.io.BuilderFromVCF
  • net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK
  • net.maizegenetics.util.BuilderFromVCFUtil
  • net.maizegenetics.dna.snp.byte2d.Byte2DBuilder
  • net.maizegenetics.phenotype.CategoricalAttribute (implements net.maizegenetics.phenotype.PhenotypeAttribute)
  • net.maizegenetics.analysis.gbs.neobio.CharSequence
  • net.maizegenetics.util.CheckSum
  • net.maizegenetics.stats.statistics.ChiSquareTest
  • net.maizegenetics.dna.map.Chromosome (implements java.lang.Comparable<T>)
  • net.maizegenetics.taxa.tree.CladeSystem
  • net.maizegenetics.stats.PCA.ClassicMds
  • net.maizegenetics.analysis.gbs.Clusters
  • net.maizegenetics.matrixalgebra.Matrix.ColtDoubleMatrix (implements net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix)
  • net.maizegenetics.matrixalgebra.decomposition.ColtEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
  • net.maizegenetics.matrixalgebra.decomposition.ColtSingularValueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition)
  • net.maizegenetics.analysis.monetdb.ColumnsToBinaryUtils
  • net.maizegenetics.dna.snp.genotypecall.CombineGenotypeCallTable
  • net.maizegenetics.dna.snp.CombineGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • javax.swing.table.DefaultTableCellRenderer (implements java.io.Serializable, javax.swing.table.TableCellRenderer)
            • net.maizegenetics.gui.AlignmentTableCellRenderer
              • net.maizegenetics.gui.TOPMGenotypeTableCellRenderer
          • net.maizegenetics.gui.RowHeaderRenderer (implements javax.swing.ListCellRenderer<E>)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • 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.tassel.DataTreePanel (implements net.maizegenetics.plugindef.PluginListener)
          • net.maizegenetics.progress.PluginProgressUnit (implements net.maizegenetics.plugindef.PluginListener)
          • net.maizegenetics.progress.ProgressPanel
          • net.maizegenetics.tassel.SeqViewerPanel (implements java.awt.event.ComponentListener, javax.swing.event.TableModelListener)
          • net.maizegenetics.tassel.TableReportPanel
        • net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
        • net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • net.maizegenetics.tassel.AboutBox (implements java.awt.event.ActionListener)
            • net.maizegenetics.analysis.filter.FilterTraitsDialog (implements java.awt.event.ActionListener, javax.swing.event.TableModelListener)
            • net.maizegenetics.tassel.HelpDialog
            • net.maizegenetics.gui.ReportDestinationDialog
            • net.maizegenetics.gui.SelectFromAvailableDialog
              • net.maizegenetics.gui.SelectFromAvailableSitesDialog
            • net.maizegenetics.pipeline.TasselPipelineStepsDialog (implements net.maizegenetics.plugindef.PluginListener)
            • net.maizegenetics.analysis.numericaltransform.TransformDataDialog (implements java.awt.event.ActionListener)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • net.maizegenetics.analysis.chart.BasicGraphFrame
            • net.maizegenetics.tassel.TASSELMainFrame (implements java.awt.event.ActionListener)
  • javax.swing.plaf.ComponentUI
    • javax.swing.plaf.LabelUI
      • javax.swing.plaf.basic.BasicLabelUI (implements java.beans.PropertyChangeListener)
        • net.maizegenetics.gui.VerticalLabelUI
    • javax.swing.plaf.TableUI
      • javax.swing.plaf.basic.BasicTableUI
        • net.maizegenetics.tassel.SeqViewerPanel.MyTableUI
  • net.maizegenetics.analysis.association.CompressedDoubleMatrix
  • net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
  • net.maizegenetics.stats.statistics.ContigencyTable
  • net.maizegenetics.dna.snp.CoreGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
  • net.maizegenetics.phenotype.CorePhenotype (implements net.maizegenetics.phenotype.Phenotype)
  • net.maizegenetics.stats.linearmodels.CovariateModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
  • net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator (implements java.util.Spliterator<T>)
  • net.maizegenetics.plugindef.DataSet (implements java.io.Serializable)
  • net.maizegenetics.plugindef.Datum (implements java.io.Serializable)
  • net.maizegenetics.plugindef.DefaultPluginListener (implements net.maizegenetics.plugindef.PluginListener)
  • net.maizegenetics.gui.DialogUtils
  • net.maizegenetics.dna.snp.genotypecall.DifferenceGenotypeCallTable
  • net.maizegenetics.util.DirectedGraph<T> (implements net.maizegenetics.util.Graph<T>)
  • net.maizegenetics.util.DirectoryCrawler
  • net.maizegenetics.taxa.distance.DistanceMatrix (implements net.maizegenetics.util.TableReport)
    • net.maizegenetics.taxa.distance.DistanceMatrixWithCounts
  • net.maizegenetics.taxa.distance.DistanceMatrixBuilder
  • net.maizegenetics.taxa.distance.DistanceMatrixUtils
  • net.maizegenetics.analysis.distance.DominanceNormalizedIBSMatrix
  • net.maizegenetics.analysis.distance.DominanceRelationshipMatrix
  • net.maizegenetics.dna.map.DonorHaplotypes (implements java.lang.Comparable<T>)
  • net.maizegenetics.analysis.popgen.DonorHypoth (implements java.lang.Comparable<T>)
  • 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.dna.snp.score.DosageBuilder
  • net.maizegenetics.util.DoubleFormat
  • net.maizegenetics.matrixalgebra.Matrix.DoubleMatrixFactory
  • net.maizegenetics.dna.snp.bit.DynamicBitStorage (implements net.maizegenetics.dna.snp.bit.BitStorage)
  • net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix (implements net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix)
  • net.maizegenetics.matrixalgebra.decomposition.EJMLEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
  • net.maizegenetics.matrixalgebra.decomposition.EJMLSingularValueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition)
  • net.maizegenetics.analysis.imputation.EmissionProbability
    • net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
  • net.maizegenetics.stats.EMMA.EMMAforDoubleMatrix
  • net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
  • net.maizegenetics.stats.math.ErrorFunction
  • java.util.EventObject (implements java.io.Serializable)
    • net.maizegenetics.plugindef.PluginEvent
  • net.maizegenetics.util.ExceptionUtils
  • net.maizegenetics.analysis.avro.ExportAvro
  • net.maizegenetics.dna.snp.ExportUtils
  • net.maizegenetics.analysis.gbs.neobio.Factor
  • net.maizegenetics.stats.linearmodels.FactorModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
  • net.maizegenetics.analysis.gbs.neobio.FactorSequence
  • net.maizegenetics.dna.read.FastqChunk
  • net.maizegenetics.dna.tag.FastqReader
  • net.maizegenetics.gui.FileBrowserUtils
  • javax.swing.filechooser.FileFilter
    • net.maizegenetics.util.BasicFileFilter
  • net.maizegenetics.analysis.imputation.FILLINDonorGenotypeUtils
  • net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
  • net.maizegenetics.analysis.imputation.FILLINImputationUtils
  • net.maizegenetics.dna.snp.FilterAndMaskGVCFGenomeSequence
  • net.maizegenetics.analysis.filter.FilterBySites
  • net.maizegenetics.analysis.filter.FilterByTaxa
  • net.maizegenetics.dna.snp.FilterGenotypeTable
  • net.maizegenetics.dna.snp.io.FilterJSONUtils
  • net.maizegenetics.dna.snp.FilterList (implements java.util.List<E>)
  • net.maizegenetics.phenotype.FilterPhenotype (implements net.maizegenetics.phenotype.Phenotype)
  • net.maizegenetics.dna.snp.FilterSite (implements net.maizegenetics.dna.snp.Filter)
  • net.maizegenetics.dna.snp.FilterTableReport (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.dna.snp.FilterTaxa (implements net.maizegenetics.dna.snp.Filter)
  • net.maizegenetics.analysis.rna.FindMatchByWordHash
  • net.maizegenetics.analysis.rna.FindMatchByWordHash.Builder
  • net.maizegenetics.analysis.rna.FindMatchByWordHash.Match
  • net.maizegenetics.stats.statistics.FisherExact
  • net.maizegenetics.dna.pd.FolderParser
  • java.text.Format (implements java.lang.Cloneable, java.io.Serializable)
    • java.text.NumberFormat
      • net.maizegenetics.analysis.chart.ManhattanNumberFormat
  • net.maizegenetics.util.FormattedInput (implements java.io.Serializable)
  • net.maizegenetics.util.FormattedOutput
  • net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator (implements java.util.Spliterator<T>)
    • net.maizegenetics.analysis.modelfitter.ForwardStepNestedAdditiveSpliterator
    • net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingAdditiveSpliterator
    • net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingNestedAdditiveSpliterator
  • net.maizegenetics.stats.statistics.GammaDistribution
    • net.maizegenetics.stats.statistics.ApproxFastChiSquareDistribution
    • net.maizegenetics.stats.statistics.ChiSquareDistribution
    • net.maizegenetics.stats.statistics.ExponentialDistribution
  • net.maizegenetics.stats.math.GammaFunction
  • net.maizegenetics.analysis.gbs.v2.GBSEnzyme
  • net.maizegenetics.dna.tag.GBSHDF5Constants
  • net.maizegenetics.analysis.gbs.v2.GBSUtils
  • net.maizegenetics.analysis.distance.GCTADistanceMatrix
  • net.maizegenetics.util.GeneralAnnotationStorage (implements net.maizegenetics.util.GeneralAnnotation)
  • net.maizegenetics.util.GeneralAnnotationStorage.Builder
  • net.maizegenetics.dna.map.GeneralPosition (implements net.maizegenetics.dna.map.Position)
  • net.maizegenetics.dna.map.GeneralPosition.Builder
  • net.maizegenetics.plugindef.GeneratePluginCode
  • net.maizegenetics.analysis.avro.GenericArrayPositions (implements org.apache.avro.generic.GenericArray<T>)
  • net.maizegenetics.analysis.avro.GenericArrayTaxa (implements org.apache.avro.generic.GenericArray<T>)
  • net.maizegenetics.analysis.avro.GenericMapAnnotations (implements java.util.Map<K,V>)
  • net.maizegenetics.analysis.avro.GenericRecordChromosome (implements org.apache.avro.generic.GenericRecord)
  • net.maizegenetics.analysis.avro.GenericRecordGenotype (implements org.apache.avro.generic.GenericRecord)
  • net.maizegenetics.analysis.avro.GenericRecordGenotypeTable (implements org.apache.avro.generic.GenericRecord)
  • net.maizegenetics.analysis.avro.GenericRecordPosition (implements org.apache.avro.generic.GenericRecord)
  • net.maizegenetics.analysis.avro.GenericRecordTaxon (implements org.apache.avro.generic.GenericRecord)
  • net.maizegenetics.dna.map.GenomeFeature
  • net.maizegenetics.dna.map.GenomeFeatureBuilder
  • net.maizegenetics.dna.map.GenomeFeatureMap
  • net.maizegenetics.dna.map.GenomeFeatureMapBuilder
  • net.maizegenetics.dna.map.GenomeSequenceBuilder
    • net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder
  • net.maizegenetics.dna.snp.genotypecall.GenotypeCallTableBuilder
  • net.maizegenetics.phenotype.GenotypePhenotype (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.phenotype.GenotypePhenotypeBuilder
  • net.maizegenetics.dna.snp.GenotypeTableBuilder
  • net.maizegenetics.dna.snp.GenotypeTableUtils
  • net.maizegenetics.analysis.gobii.GOBII_IFLUtils
  • net.maizegenetics.dna.snp.genotypecall.GOBIIAvroGenotypeCallTable
  • net.maizegenetics.analysis.gobii.GOBIIDbUtils
  • net.maizegenetics.dna.snp.genotypecall.GOBIIGenotypeCallTable
  • net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
  • net.maizegenetics.util.GraphBuilder<T>
  • net.maizegenetics.util.GraphUtils<T>
  • net.maizegenetics.analysis.clustering.Haplotype (implements java.lang.Comparable<T>)
  • net.maizegenetics.analysis.clustering.HaplotypeCluster (implements java.lang.Comparable<T>)
  • net.maizegenetics.analysis.clustering.HaplotypeClusterer
  • net.maizegenetics.dna.snp.HapMapHDF5Constants
  • net.maizegenetics.util.HDF5TableReport (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.util.HDF5Utils
  • net.maizegenetics.dna.snp.genotypecall.HighestDepthGenotypeMergeRule (implements net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule)
  • net.maizegenetics.dna.snp.genotypecall.HybridGenotypeCallTable
  • net.maizegenetics.analysis.distance.IBSDistanceMatrix
  • net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
  • net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
  • net.maizegenetics.analysis.distance.IBSDistanceMatrixOneByAll
  • net.maizegenetics.analysis.avro.ImportAvro
  • net.maizegenetics.dna.snp.ImportUtils
  • net.maizegenetics.analysis.numericaltransform.ImputationByMean
  • net.maizegenetics.analysis.imputation.ImputationUtils
  • net.maizegenetics.analysis.imputation.ImputeCrossProgeny
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • java.util.zip.InflaterInputStream
        • java.util.zip.GZIPInputStream
          • net.maizegenetics.util.MultiMemberGZIPInputStream
  • net.maizegenetics.dna.snp.io.JSONUtils
  • net.maizegenetics.analysis.distance.Kinship
  • net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
  • net.maizegenetics.taxa.tree.LabelMapping (implements java.io.Serializable)
  • net.maizegenetics.util.db.LambdaTuplesContext
  • net.maizegenetics.analysis.popgen.LDResult
  • net.maizegenetics.analysis.popgen.LDResult.Builder
  • net.maizegenetics.stats.statistics.LikelihoodRatioTest
  • net.maizegenetics.stats.linearmodels.LinearModelForStepwiseRegression
  • net.maizegenetics.stats.linearmodels.LinearModelUtils
  • net.maizegenetics.dna.snp.io.LineIndex
  • net.maizegenetics.dna.snp.io.LineIndexBuilder
  • net.maizegenetics.dna.snp.genotypecall.LineIndexHapmapGenotypeCallTable
  • net.maizegenetics.util.LoggingUtils
  • net.maizegenetics.analysis.data.LowLevelCopyOfHDF5
  • net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin.HmpTaxaData
  • net.maizegenetics.dna.snp.genotypecall.MaskedGenotypes
  • net.maizegenetics.dna.snp.genotypecall.MaskGenotypeCallTable
  • net.maizegenetics.dna.snp.MaskMatrixBuilder
  • net.maizegenetics.dna.snp.MaskSiteMatrix (implements net.maizegenetics.dna.snp.MaskMatrix)
  • net.maizegenetics.dna.snp.MaskTaxaMatrix (implements net.maizegenetics.dna.snp.MaskMatrix)
  • net.maizegenetics.dna.snp.genotypecall.MergedGenotypeCallTable
  • net.maizegenetics.dna.snp.MergedGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
  • net.maizegenetics.stats.math.MersenneTwisterFast (implements java.io.Serializable)
  • net.maizegenetics.analysis.data.MigrateHDF5FromT4T5
  • net.maizegenetics.stats.linearmodels.ModelEffectUtils
  • net.maizegenetics.taxa.tree.MultiParameterized (implements net.maizegenetics.taxa.tree.Parameterized)
  • net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect (implements net.maizegenetics.stats.linearmodels.ModelEffect)
  • net.maizegenetics.analysis.modelfitter.NestedCovariatePermutationTestSpliterator (implements java.util.Spliterator<T>)
  • net.maizegenetics.taxa.tree.NodeFactory
  • net.maizegenetics.taxa.tree.NodeUtils
  • net.maizegenetics.stats.statistics.NormalDistribution
  • net.maizegenetics.dna.snp.NucleotideAlignmentConstants
  • net.maizegenetics.analysis.imputation.NucleotideImputationUtils
  • net.maizegenetics.phenotype.NumericAttribute (implements net.maizegenetics.phenotype.PhenotypeAttribute)
  • net.maizegenetics.util.OpenBitSet (implements net.maizegenetics.util.BitSet, java.lang.Cloneable, java.io.Serializable)
  • net.maizegenetics.stats.math.OrderEnumerator.Utils
  • net.maizegenetics.stats.math.OrthogonalHints.Utils
  • net.maizegenetics.analysis.gbs.neobio.OutMatrix (implements net.maizegenetics.analysis.gbs.neobio.Matrix)
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.FilterOutputStream
      • net.maizegenetics.analysis.monetdb.LittleEndianDataOutputStream
  • net.maizegenetics.util.db.Pair<T,K>
  • net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment (implements java.io.Serializable)
  • 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.analysis.gbs.pana.PanAUsageExample
  • net.maizegenetics.plugindef.ParameterCache
  • net.maizegenetics.taxa.tree.Parameterized.Null (implements net.maizegenetics.taxa.tree.Parameterized)
  • net.maizegenetics.taxa.tree.Parameterized.ParameterizedBase
  • net.maizegenetics.taxa.tree.Parameterized.ParameterizedUser
  • net.maizegenetics.taxa.tree.Parameterized.Utils
  • net.maizegenetics.stats.statistics.ParetoDistribution
  • net.maizegenetics.analysis.gbs.ParseBarcodeRead
    • net.maizegenetics.analysis.gbs.PEParseBarcodeRead
  • net.maizegenetics.analysis.phg.ParseGVCF
  • net.maizegenetics.analysis.phg.ParseGVCF.GVCFLine
  • net.maizegenetics.analysis.phg.ParseGVCF.ProcessLines (implements java.util.concurrent.Callable<V>)
  • net.maizegenetics.stats.linearmodels.PartitionedLinearModel
  • net.maizegenetics.dna.pd.PDAnnotation
  • net.maizegenetics.dna.pd.PDReport
  • net.maizegenetics.dna.read.PEFastqChunk
  • net.maizegenetics.stats.statistics.PenalizedLikelihood
  • net.maizegenetics.dna.read.PERead
  • net.maizegenetics.analysis.gbs.PEReadBarcodeResult
  • net.maizegenetics.dna.map.PETagsOnPhysicalMapV3 (implements net.maizegenetics.dna.tag.Tags)
  • net.maizegenetics.analysis.imputation.PhaseHighCoverage
  • net.maizegenetics.phenotype.PhenotypeBuilder
  • net.maizegenetics.analysis.association.PhenotypeLM
  • net.maizegenetics.phenotype.PhenotypeUtils
  • net.maizegenetics.plugindef.PluginParameter<T>
  • net.maizegenetics.plugindef.PluginParameter.Builder<T>
  • net.maizegenetics.analysis.popgen.PolymorphismDistribution (implements java.io.Serializable)
  • net.maizegenetics.analysis.gbs.PolymorphismFinder
  • net.maizegenetics.analysis.imputation.PopulationData
  • net.maizegenetics.dna.map.PositionList.PositionListCollector (implements java.util.stream.Collector<T,A,R>)
  • net.maizegenetics.dna.map.PositionListBuilder
  • net.maizegenetics.dna.map.PositionListIOUtils
  • net.maizegenetics.dna.map.PositionListTableReport (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.stats.PCA.PrinComp
  • net.maizegenetics.gui.PrintTextArea
  • net.maizegenetics.analysis.gbs.ProductionPipelineMain
  • net.maizegenetics.dna.snp.ProjectionBuilder
  • net.maizegenetics.dna.snp.genotypecall.ProjectionGenotypeCallTable
  • net.maizegenetics.dna.snp.io.ProjectionGenotypeIO
  • net.maizegenetics.dna.read.Read
  • net.maizegenetics.analysis.gbs.ReadBarcodeResult
  • net.maizegenetics.dna.snp.io.ReadBedfile
  • net.maizegenetics.dna.snp.io.ReadBedfile.BedFileRange (implements java.lang.Comparable<T>)
  • net.maizegenetics.taxa.distance.ReadDistanceMatrix
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.FilterReader
      • java.io.PushbackReader
        • net.maizegenetics.util.InputSource
  • net.maizegenetics.dna.snp.io.ReadNumericMarkerUtils
  • net.maizegenetics.dna.tag.ReadsByTaxa (implements net.maizegenetics.dna.tag.Reads)
  • net.maizegenetics.dna.snp.ReadSequenceAlignmentUtils
  • net.maizegenetics.dna.read.ReadUtils
  • 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.dna.snp.score.ReferenceProbabilityBuilder
  • net.maizegenetics.analysis.gbs.repgen.RefTagData
  • net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
  • net.maizegenetics.dna.tag.RepGenSQLite (implements java.lang.AutoCloseable, net.maizegenetics.dna.tag.RepGenDataWriter)
  • net.maizegenetics.analysis.imputation.RephaseParents
  • net.maizegenetics.util.db.ResultSetIterator (implements java.util.Iterator<E>)
  • net.maizegenetics.taxa.tree.RootedTreeUtils
  • net.maizegenetics.dna.tag.SAMUtils
  • net.maizegenetics.analysis.gbs.neobio.ScoringScheme
    • net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
    • net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
  • net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
  • net.maizegenetics.dna.snp.genotypecall.SetToNGenotypeMergeRule (implements net.maizegenetics.dna.snp.genotypecall.GenotypeMergeRule)
  • net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
  • net.maizegenetics.dna.snp.SimpleAllele (implements net.maizegenetics.dna.snp.Allele)
  • net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
  • net.maizegenetics.taxa.tree.SimpleNode (implements net.maizegenetics.taxa.tree.AttributeNode)
  • net.maizegenetics.taxa.tree.SimpleTree (implements java.io.Serializable, net.maizegenetics.taxa.tree.Tree)
    • net.maizegenetics.taxa.tree.NeighborJoiningTree
    • net.maizegenetics.taxa.tree.UPGMATree
  • net.maizegenetics.dna.pd.SiteAnnotation
  • net.maizegenetics.dna.snp.io.SiteScoresIO
  • net.maizegenetics.dna.snp.score.SiteScoreUtil
  • net.maizegenetics.util.Sizeof
  • net.maizegenetics.analysis.gbs.neobio.Smawk
  • net.maizegenetics.analysis.gbs.SmithWaterman
  • net.maizegenetics.util.SMTPClient
  • net.maizegenetics.analysis.modelfitter.SNP
  • net.maizegenetics.analysis.gbs.SNPLogging
  • net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing
  • net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing.Marker
  • net.maizegenetics.taxa.tree.SplitSystem
  • net.maizegenetics.taxa.tree.SplitUtils
  • net.maizegenetics.util.db.SQL
  • net.maizegenetics.dna.snp.genotypecall.Stats
  • net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
  • net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
  • net.maizegenetics.util.StringNumberComparator (implements java.util.Comparator<T>)
  • net.maizegenetics.analysis.imputation.SubpopulationFinder
  • net.maizegenetics.analysis.numericaltransform.SubtractPhenotype
  • net.maizegenetics.util.SuperByteMatrixBuilder
  • net.maizegenetics.util.SuperByteMatrixMultiple (implements net.maizegenetics.util.SuperByteMatrix)
  • net.maizegenetics.util.SuperByteMatrixSingle (implements net.maizegenetics.util.SuperByteMatrix)
  • net.maizegenetics.util.SuperByteMatrixSingleValue (implements net.maizegenetics.util.SuperByteMatrix)
  • net.maizegenetics.util.SuperByteMatrixTranspose (implements net.maizegenetics.util.SuperByteMatrix)
  • net.maizegenetics.stats.linearmodels.SweepFast
  • net.maizegenetics.stats.linearmodels.SweepFastLinearModel
  • net.maizegenetics.stats.linearmodels.SweepFastNestedModel
  • net.maizegenetics.matrixalgebra.decomposition.SymmetricEigenvalueDecomposition (implements net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition)
  • net.maizegenetics.stats.linearmodels.SymmetricMatrixInverterDM
  • net.maizegenetics.util.TableReportBuilder
  • net.maizegenetics.util.TableReportUtils
  • net.maizegenetics.analysis.gbs.TagAgainstAnchor
  • net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
  • net.maizegenetics.analysis.gbs.TagBlockPosition
  • net.maizegenetics.dna.tag.TagBuilder
  • net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
  • net.maizegenetics.dna.tag.TagDataSQLite (implements java.lang.AutoCloseable, net.maizegenetics.dna.tag.TagDataWriter)
  • net.maizegenetics.dna.map.TagGeneticMappingInfo
  • net.maizegenetics.dna.map.TagGWASMapInfo
  • net.maizegenetics.dna.map.TagLocus
  • net.maizegenetics.dna.map.TagMappingInfo
  • net.maizegenetics.dna.map.TagMappingInfoV3
  • net.maizegenetics.analysis.gbs.TagMatchFinder
  • net.maizegenetics.dna.tag.TagsByTaxaUtils
  • net.maizegenetics.util.Tassel5HDF5Constants
  • net.maizegenetics.tassel.TASSELMainApp
  • net.maizegenetics.pipeline.TasselPipeline (implements net.maizegenetics.plugindef.PluginListener)
  • net.maizegenetics.pipeline.TasselPipelineXMLUtil
  • net.maizegenetics.prefs.TasselPrefs
  • net.maizegenetics.phenotype.TaxaAttribute (implements net.maizegenetics.phenotype.PhenotypeAttribute)
  • net.maizegenetics.dna.tag.TaxaDistBuilder
  • net.maizegenetics.taxa.TaxaList.TaxaListCollector (implements java.util.stream.Collector<T,A,R>)
  • net.maizegenetics.taxa.TaxaListBuilder
  • net.maizegenetics.taxa.TaxaListIOUtils
  • net.maizegenetics.taxa.TaxaListTableReport (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.taxa.TaxaListUtils
  • net.maizegenetics.taxa.TaxaTissueDist
  • net.maizegenetics.taxa.Taxon (implements java.lang.Comparable<T>)
  • net.maizegenetics.taxa.Taxon.Builder
  • net.maizegenetics.analysis.gbs.TerryPipelines
  • java.lang.Thread (implements java.lang.Runnable)
    • net.maizegenetics.analysis.popgen.LinkageDisequilibrium (implements java.io.Serializable, net.maizegenetics.util.TableReport)
    • net.maizegenetics.plugindef.ThreadedPluginListener
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • net.maizegenetics.analysis.gbs.neobio.IncompatibleScoringSchemeException
      • net.maizegenetics.analysis.gbs.neobio.InvalidScoringMatrixException
      • net.maizegenetics.analysis.gbs.neobio.InvalidSequenceException
      • java.lang.RuntimeException
        • net.maizegenetics.util.db.DataAccessException
      • net.maizegenetics.taxa.tree.TreeParseException
  • net.maizegenetics.dna.snp.TOPMGenotypeTable (implements net.maizegenetics.dna.snp.GenotypeTable)
  • net.maizegenetics.dna.map.TOPMTableReport (implements net.maizegenetics.util.TableReport)
  • net.maizegenetics.dna.map.TOPMUtils
  • net.maizegenetics.util.db.Transformations
  • net.maizegenetics.util.db.TransformerService
  • net.maizegenetics.analysis.imputation.TransitionProbability
    • net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
  • net.maizegenetics.dna.snp.Translate
    • net.maizegenetics.dna.snp.TranslateNegative
  • net.maizegenetics.dna.snp.TranslateBuilder
  • net.maizegenetics.dna.snp.TranslateIndex
    • net.maizegenetics.dna.snp.TranslateIndexRange
    • net.maizegenetics.dna.snp.TranslateIndexRedirect
      • net.maizegenetics.dna.snp.TranslateIndexRedirectUnordered
  • net.maizegenetics.dna.snp.TranslateIndexBuilder
  • net.maizegenetics.taxa.tree.TreeClusters
  • net.maizegenetics.taxa.tree.TreeUtils
  • net.maizegenetics.analysis.gbs.neobio.Trie
  • net.maizegenetics.util.Tuple<X,Y> (implements java.lang.Comparable<T>)
  • net.maizegenetics.util.UndirectedGraph<T> (implements net.maizegenetics.util.Graph<T>)
  • net.maizegenetics.analysis.gbs.UNetworkFilter
  • net.maizegenetics.util.UnmodifiableBitSet (implements net.maizegenetics.util.BitSet)
  • net.maizegenetics.analysis.gobii.UpdateMarkerAndDNA_idxes
  • net.maizegenetics.dna.map.UpdateTOPMWithGeneticMapping
  • net.maizegenetics.analysis.imputation.UseParentHaplotypes
  • net.maizegenetics.analysis.gbs.UTagPairFinder
  • net.maizegenetics.dna.tag.UTagPairs
  • net.maizegenetics.util.Utils
  • net.maizegenetics.dna.snp.io.VCFUtil
  • net.maizegenetics.analysis.imputation.ViterbiAlgorithm
  • net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
  • net.maizegenetics.stats.linearmodels.WithinPopulationPermuter
  • net.maizegenetics.taxa.distance.WriteDistanceMatrix

Interface Hierarchy

• 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
• java.lang.Comparable<T>
  • net.maizegenetics.analysis.modelfitter.AdditiveSite (also extends java.io.Serializable)
  • net.maizegenetics.stats.linearmodels.Level
  • net.maizegenetics.dna.map.Position
• net.maizegenetics.matrixalgebra.Matrix.DoubleMatrix
• net.maizegenetics.matrixalgebra.decomposition.EigenvalueDecomposition
• java.util.EventListener
  • javax.swing.Action
    • net.maizegenetics.plugindef.PluginAction
  • java.awt.event.ActionListener
    • javax.swing.Action
      • net.maizegenetics.plugindef.PluginAction
    • net.maizegenetics.plugindef.PluginAction
  • net.maizegenetics.plugindef.PluginAction
• 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.util.Graph<T>
• cern.colt.function.IntComparator
  • net.maizegenetics.dna.tag.PETags (also extends cern.colt.Swapper)
  • net.maizegenetics.dna.tag.Tags (also extends cern.colt.Swapper)
    • net.maizegenetics.dna.tag.TagsByTaxa
    • net.maizegenetics.dna.map.TOPMInterface
  • net.maizegenetics.dna.tag.TagsByTaxa
  • net.maizegenetics.dna.map.TOPMInterface
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • net.maizegenetics.util.db.DBTuple
    • java.util.List<E>
      • net.maizegenetics.dna.map.PositionList
      • net.maizegenetics.taxa.TaxaList
    • net.maizegenetics.dna.map.PositionList
    • net.maizegenetics.taxa.TaxaList
  • net.maizegenetics.util.db.DBTuple
  • java.util.List<E>
    • net.maizegenetics.dna.map.PositionList
    • net.maizegenetics.taxa.TaxaList
  • net.maizegenetics.dna.map.PositionList
  • net.maizegenetics.taxa.TaxaList
• net.maizegenetics.dna.snp.MaskMatrix
• net.maizegenetics.analysis.gbs.neobio.Matrix
• net.maizegenetics.stats.linearmodels.ModelEffect
• net.maizegenetics.taxa.tree.MultiParameterized.ParameterAccessWatcher
• net.maizegenetics.stats.math.OrderEnumerator
• net.maizegenetics.stats.math.OrderEnumerator.OEFactory
• net.maizegenetics.stats.math.OrthogonalHints
• net.maizegenetics.taxa.tree.Parameterized
• net.maizegenetics.phenotype.PhenotypeAttribute
• net.maizegenetics.plugindef.PluginListener
  • net.maizegenetics.plugindef.Plugin (also extends net.maizegenetics.util.ProgressListener, java.lang.Runnable)
• net.maizegenetics.util.ProgressListener
  • net.maizegenetics.plugindef.Plugin (also extends net.maizegenetics.plugindef.PluginListener, java.lang.Runnable)
• 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
• java.lang.Runnable
  • net.maizegenetics.plugindef.Plugin (also extends net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener)
• java.io.Serializable
  • net.maizegenetics.analysis.modelfitter.AdditiveSite (also extends java.lang.Comparable<T>)
  • net.maizegenetics.taxa.tree.AttributeNode
  • net.maizegenetics.gui.GenotypeTableMask
  • net.maizegenetics.taxa.tree.Node
    • net.maizegenetics.taxa.tree.AttributeNode
  • net.maizegenetics.taxa.tree.Tree (also extends net.maizegenetics.taxa.tree.UnitsProvider)
• net.maizegenetics.matrixalgebra.decomposition.SingularValueDecomposition
• net.maizegenetics.dna.snp.score.SiteScore
• net.maizegenetics.util.db.SQLAction<T>
• net.maizegenetics.util.SuperByteMatrix
• cern.colt.Swapper
  • net.maizegenetics.dna.tag.PETags (also extends cern.colt.function.IntComparator)
  • net.maizegenetics.dna.tag.Tags (also extends cern.colt.function.IntComparator)
    • net.maizegenetics.dna.tag.TagsByTaxa
    • net.maizegenetics.dna.map.TOPMInterface
  • net.maizegenetics.dna.tag.TagsByTaxa
  • net.maizegenetics.dna.map.TOPMInterface
• 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.TaxaDistribution
• net.maizegenetics.util.db.TypeTransformer<T,K>
• net.maizegenetics.taxa.tree.Units
  • net.maizegenetics.taxa.tree.Tree (also extends java.io.Serializable, net.maizegenetics.taxa.tree.UnitsProvider)
  • net.maizegenetics.taxa.tree.UnitsProvider
    • net.maizegenetics.taxa.tree.Tree (also extends java.io.Serializable)

Enum Hierarchy

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