Hierarchy For All Packages

Package Hierarchies:

• net.maizegenetics.pangenome,
• net.maizegenetics.pangenome.api,
• net.maizegenetics.pangenome.db_loading,
• net.maizegenetics.pangenome.fastaExtraction,
• net.maizegenetics.pangenome.gui,
• net.maizegenetics.pangenome.gvcfFiltering,
• net.maizegenetics.pangenome.hapCalling,
• net.maizegenetics.pangenome.hapcollapse,
• net.maizegenetics.pangenome.multiSequenceAlignment,
• net.maizegenetics.pangenome.pipelineTests,
• net.maizegenetics.pangenome.processAssemblyGenomes,
• net.maizegenetics.pangenome.trimAnchors,
• net.maizegenetics.pangenome.Utils

Class Hierarchy

• java.lang.Object
  • net.maizegenetics.plugindef.AbstractPlugin (implements net.maizegenetics.plugindef.Plugin)
    • net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
    • net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
    • net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
    • net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
    • net.maizegenetics.pangenome.pipelineTests.CountConsensusTaxaAtRefRange
    • net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
    • net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
    • net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
    • net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
    • net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
    • net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
    • net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
    • net.maizegenetics.pangenome.hapCalling.FastqToHapCountPlugin
    • net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
    • net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
    • net.maizegenetics.pangenome.api.FilterGraphPlugin
    • net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
    • net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
    • net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
    • net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
    • net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
    • net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
    • net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
    • net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
    • net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
    • net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
    • net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin
    • net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin
    • net.maizegenetics.pangenome.db_loading.LoadHaplotypeCountsTablePlugin
    • net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin
    • net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin
    • net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
    • net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
    • net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
    • net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
    • net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
    • net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
    • net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
    • net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
    • net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
    • net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
    • net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
    • net.maizegenetics.pangenome.gui.ViewGraphPlugin
    • net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
  • net.maizegenetics.pangenome.db_loading.AnchorDataPHG (implements java.lang.Comparable<T>)
  • net.maizegenetics.pangenome.trimAnchors.AnchorInfo
  • net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
  • net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
  • net.maizegenetics.pangenome.CompareFastaToReference
  • net.maizegenetics.pangenome.CompareHaplotypesToAssembly
  • net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
  • net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
  • net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
  • net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
  • net.maizegenetics.pangenome.hapCalling.ConvertGBSToSNPs
  • net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils
  • net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
  • net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
  • net.maizegenetics.pangenome.db_loading.CreateBiggerIntervals
  • net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
  • net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts
  • net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
  • net.maizegenetics.pangenome.api.CreateGraphUtils
  • net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
  • net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
  • net.maizegenetics.pangenome.Utils.CreateHashForFiles
  • net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
  • net.maizegenetics.pangenome.gui.CreateStreamGraph
  • net.maizegenetics.pangenome.db_loading.DBLoadingUtils
  • net.maizegenetics.analysis.imputation.EmissionProbability
    • net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
  • net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest
  • net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFbyKnownSNPTest2
  • net.maizegenetics.pangenome.pipelineTests.EvaluateGVCFWithIBDTest
  • net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
  • net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU
  • net.maizegenetics.pangenome.fastaExtraction.ExtractFastaUtils
  • net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus
  • net.maizegenetics.pangenome.pipelineTests.FindProteomeGenesInAssembly
  • net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
  • net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
  • net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
  • net.maizegenetics.pangenome.db_loading.GeneGFFData (implements java.lang.Comparable<T>)
  • net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
  • net.maizegenetics.pangenome.db_loading.GenoHaploData
  • net.maizegenetics.pangenome.GetFastaSequenceLengths
  • net.maizegenetics.pangenome.api.GraphIO
  • net.maizegenetics.pangenome.api.GraphUtils
  • net.maizegenetics.pangenome.fastaExtraction.GVCFSequence (implements net.maizegenetics.dna.map.GenomeSequence)
    • net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
  • net.maizegenetics.pangenome.GVCFStats
  • net.maizegenetics.pangenome.hapcollapse.GVCFUtils
  • net.maizegenetics.pangenome.hapCalling.HapCallingUtils
  • net.maizegenetics.pangenome.api.HaplotypeEdge
  • net.maizegenetics.pangenome.api.HaplotypeGraph
  • net.maizegenetics.pangenome.api.HaplotypeNode (implements java.lang.Comparable<T>)
  • net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
  • net.maizegenetics.pangenome.api.HaplotypePath
  • net.maizegenetics.pangenome.api.HaplotypeSequence
  • net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
  • net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
  • net.maizegenetics.pangenome.db_loading.PHGdbAccess (implements java.lang.AutoCloseable, net.maizegenetics.pangenome.db_loading.PHGDataWriter)
  • net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
  • net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
  • net.maizegenetics.pangenome.processAssemblyGenomes.RedirectStreams
  • net.maizegenetics.pangenome.api.ReferenceRange (implements java.lang.Comparable<T>)
  • net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
  • net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs
  • net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper
  • net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
  • net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader
  • net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
  • net.maizegenetics.pangenome.db_loading.TestPHGStuff
  • net.maizegenetics.analysis.imputation.TransitionProbability
    • net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
  • net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors

Interface Hierarchy

• net.maizegenetics.pangenome.db_loading.PHGData
  • net.maizegenetics.pangenome.db_loading.PHGDataWriter

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.METHOD
    • net.maizegenetics.pangenome.db_loading.DBLoadingUtils.AnchorType
    • net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType
    • net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus.INDEL_MERGE_RULE
    • net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin.CLUSTER_METHOD
    • net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin.EMIT_MODE