Hierarchy For All Packages

Package Hierarchies:

• biolockj,
• biolockj.api,
• biolockj.exception,
• biolockj.launch,
• biolockj.module,
• biolockj.module.assembly,
• biolockj.module.classifier,
• biolockj.module.classifier.r16s,
• biolockj.module.classifier.wgs,
• biolockj.module.diversity,
• biolockj.module.diy,
• biolockj.module.getData,
• biolockj.module.getData.sra,
• biolockj.module.hello_world,
• biolockj.module.implicit,
• biolockj.module.implicit.parser,
• biolockj.module.implicit.parser.r16s,
• biolockj.module.implicit.parser.wgs,
• biolockj.module.implicit.qiime,
• biolockj.module.report,
• biolockj.module.report.humann2,
• biolockj.module.report.otu,
• biolockj.module.report.r,
• biolockj.module.report.taxa,
• biolockj.module.rnaseq,
• biolockj.module.seq,
• biolockj.node,
• biolockj.node.r16s,
• biolockj.node.wgs,
• biolockj.pipelines,
• biolockj.util,
• biolockj.util.paths

Class Hierarchy

• java.lang.Object
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • biolockj.module.report.taxa.TaxaLevelTable
  • biolockj.util.BashScriptBuilder
  • biolockj.util.paths.BasicDockerMapper (implements biolockj.util.paths.DockerMountMapper)
    • biolockj.util.paths.CommonDockerMapper
    • biolockj.util.paths.SimpleDockerMapper
  • biolockj.BioLockJ
  • biolockj.api.BioLockJ_API
  • biolockj.util.BioLockJUtil
  • biolockj.BioModuleFactory
  • biolockj.module.BioModuleImpl (implements biolockj.module.BioModule, java.lang.Comparable<T>)
    • biolockj.module.report.Email (implements biolockj.api.ApiModule)
    • biolockj.module.implicit.ImportMetadata (implements biolockj.api.ApiModule)
    • biolockj.module.ScriptModuleImpl (implements biolockj.module.ScriptModule)
      • biolockj.module.rnaseq.DESeq2 (implements biolockj.api.ApiModule)
      • biolockj.module.rnaseq.EdgeR (implements biolockj.api.ApiModule)
      • biolockj.module.diy.GenMod (implements biolockj.api.ApiModule, biolockj.module.getData.InputDataModule)
        • biolockj.module.diy.ForEachFile
        • biolockj.module.diy.ForEachLevel
        • biolockj.module.diy.ForEachLoop
        • biolockj.module.diy.ForEachSample
      • biolockj.module.hello_world.Hello_Friends (implements biolockj.api.ApiModule)
      • biolockj.module.hello_world.Hello_World (implements biolockj.api.ApiModule)
      • biolockj.module.JavaModuleImpl (implements biolockj.module.JavaModule)
        • biolockj.module.implicit.Demultiplexer (implements biolockj.api.ApiModule, biolockj.module.SeqModule)
        • biolockj.module.report.humann2.Humann2CountModule
          • biolockj.module.report.humann2.AddMetadataToPathwayTables
          • biolockj.module.report.humann2.RemoveLowPathwayCounts
          • biolockj.module.report.humann2.RemoveScarcePathwayCounts
        • biolockj.module.report.JsonReport
        • biolockj.module.seq.Multiplexer (implements biolockj.api.ApiModule, biolockj.module.SeqModule)
        • biolockj.module.report.otu.OtuCountModule
          • biolockj.module.report.taxa.BuildTaxaTables (implements biolockj.api.ApiModule)
          • biolockj.module.report.otu.CompileOtuCounts
          • biolockj.module.report.otu.RarefyOtuCounts (implements biolockj.api.ApiModule)
          • biolockj.module.report.otu.RemoveLowOtuCounts (implements biolockj.api.ApiModule)
          • biolockj.module.report.otu.RemoveScarceOtuCounts
        • biolockj.module.implicit.parser.ParserModuleImpl (implements biolockj.module.implicit.parser.ParserModule)
          • biolockj.module.implicit.parser.wgs.Humann2Parser (implements biolockj.api.ApiModule)
          • biolockj.module.implicit.parser.wgs.KrakenParser (implements biolockj.api.ApiModule)
            • biolockj.module.implicit.parser.wgs.Kraken2Parser
          • biolockj.module.implicit.parser.wgs.Metaphlan2Parser
          • biolockj.module.implicit.parser.r16s.QiimeParser
          • biolockj.module.implicit.parser.r16s.RdpParser (implements biolockj.api.ApiModule)
        • biolockj.module.seq.RarefySeqs (implements biolockj.api.ApiModule, biolockj.module.SeqModule)
        • biolockj.module.implicit.parser.r16s.RdpHierParser (implements biolockj.api.ApiModule)
        • biolockj.module.implicit.RegisterNumReads (implements biolockj.module.ReadCounter, biolockj.module.SeqModule)
        • biolockj.module.seq.SeqFileValidator (implements biolockj.api.ApiModule, biolockj.module.ReadCounter, biolockj.module.SeqModule)
        • biolockj.module.report.taxa.TaxaCountModule
          • biolockj.module.report.taxa.AddMetadataToTaxaTables (implements biolockj.api.ApiModule)
          • biolockj.module.report.taxa.TransformTaxaTables
            • biolockj.module.report.taxa.AddPseudoCount (implements biolockj.api.ApiModule)
            • biolockj.module.report.taxa.LogTransformTaxaTables (implements biolockj.api.ApiModule)
            • biolockj.module.report.taxa.NormalizeByReadsPerMillion (implements biolockj.api.ApiModule)
            • biolockj.module.report.taxa.NormalizeTaxaTables (implements biolockj.api.ApiModule)
            • biolockj.module.diversity.ShannonDiversity (implements biolockj.api.ApiModule)
        • biolockj.module.seq.TrimPrimers (implements biolockj.api.ApiModule, biolockj.module.ReadCounter, biolockj.module.SeqModule)
      • biolockj.module.implicit.qiime.MergeQiimeOtuTables
      • biolockj.module.report.r.R_Module
        • biolockj.module.report.r.R_CalculateStats (implements biolockj.api.ApiModule)
        • biolockj.module.report.r.R_PlotEffectSize (implements biolockj.api.ApiModule)
        • biolockj.module.report.r.R_PlotMds (implements biolockj.api.ApiModule)
        • biolockj.module.report.r.R_PlotOtus (implements biolockj.api.ApiModule)
        • biolockj.module.report.r.R_PlotPvalHistograms (implements biolockj.api.ApiModule)
      • biolockj.module.diy.Rmarkdown (implements biolockj.api.ApiModule)
      • biolockj.module.SeqModuleImpl (implements biolockj.module.SeqModule)
        • biolockj.module.seq.AwkFastaConverter (implements biolockj.api.ApiModule)
        • biolockj.module.implicit.qiime.BuildQiimeMapping
        • biolockj.module.classifier.ClassifierModuleImpl (implements biolockj.module.classifier.ClassifierModule, biolockj.module.DatabaseModule)
          • biolockj.module.classifier.wgs.Humann2Classifier (implements biolockj.api.ApiModule)
          • biolockj.module.classifier.wgs.Kraken2Classifier (implements biolockj.api.ApiModule)
          • biolockj.module.classifier.wgs.KrakenClassifier (implements biolockj.api.ApiModule)
          • biolockj.module.classifier.wgs.Metaphlan2Classifier (implements biolockj.api.ApiModule)
          • biolockj.module.implicit.qiime.QiimeClassifier
            • biolockj.module.classifier.r16s.QiimeClosedRefClassifier (implements biolockj.api.ApiModule)
            • biolockj.module.classifier.r16s.QiimeDeNovoClassifier (implements biolockj.api.ApiModule)
            • biolockj.module.classifier.r16s.QiimeOpenRefClassifier (implements biolockj.api.ApiModule)
          • biolockj.module.classifier.r16s.RdpClassifier (implements biolockj.api.ApiModule)
        • biolockj.module.assembly.GenomeAssembly (implements biolockj.api.ApiModule)
        • biolockj.module.seq.Gunzipper (implements biolockj.api.ApiModule)
        • biolockj.module.seq.KneadData (implements biolockj.api.ApiModule, biolockj.module.DatabaseModule)
        • biolockj.module.seq.PearMergeReads (implements biolockj.api.ApiModule, biolockj.module.ReadCounter)
      • biolockj.module.getData.sra.SequenceReadArchive
        • biolockj.module.getData.sra.SraDownload (implements biolockj.api.ApiModule, biolockj.module.getData.InputDataModule, biolockj.module.OutsidePipelineWriter)
        • biolockj.module.getData.sra.SraMetaData (implements biolockj.api.ApiModule, biolockj.module.getData.InputDataModule)
        • biolockj.module.getData.sra.SraMetaDB (implements biolockj.api.ApiModule, biolockj.module.OutsidePipelineWriter)
        • biolockj.module.getData.sra.SrpSrrConverter (implements biolockj.api.ApiModule)
      • biolockj.module.hello_world.Step1
        • biolockj.module.hello_world.Step2 (implements biolockj.api.ApiModule)
          • biolockj.module.hello_world.Step3
            • biolockj.module.hello_world.Step4
              • biolockj.module.hello_world.Step5
    • biolockj.module.Stop (implements biolockj.api.ApiModule)
  • biolockj.api.BuildDocs
  • biolockj.Config
  • biolockj.Constants
  • biolockj.util.DemuxUtil
  • java.util.Dictionary<K,V>
    • java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • java.util.Properties
        • biolockj.Properties
  • biolockj.util.DockerUtil
  • biolockj.util.DownloadUtil
  • biolockj.exception.FatalExceptionHandler
  • biolockj.node.JsonNode (implements java.lang.Comparable<T>, java.io.Serializable)
  • biolockj.launch.Launcher
  • biolockj.launch.LaunchProcess
    • biolockj.launch.DockerLaunchProcess
    • biolockj.launch.JavaLaunchProcess
  • biolockj.Log
  • biolockj.util.LogUtil
  • biolockj.util.MasterConfigUtil
  • biolockj.util.MemoryUtil
  • biolockj.util.MetaUtil
  • biolockj.util.ModuleUtil
  • biolockj.util.NextflowUtil
  • biolockj.pipelines.OtherPipelineFactory
  • biolockj.pipelines.OtherPipelineImpl (implements biolockj.pipelines.OtherPipeline)
  • biolockj.node.OtuNodeImpl (implements java.lang.Comparable<T>, biolockj.node.OtuNode)
    • biolockj.node.wgs.Kraken2Node
    • biolockj.node.wgs.KrakenNode
    • biolockj.node.wgs.MetaphlanNode
    • biolockj.node.r16s.QiimeNode
    • biolockj.node.r16s.RdpNode
  • biolockj.util.OtuUtil
  • biolockj.util.OtuUtil.OtuCountLine
  • biolockj.node.ParsedSample (implements java.lang.Comparable<T>, java.io.Serializable)
  • biolockj.util.PathwayUtil
  • biolockj.Pipeline
  • biolockj.pipelines.PipelineUtil
  • biolockj.Processor
  • biolockj.Processor.Subprocess (implements java.lang.Runnable)
  • biolockj.launch.ProgressMsgDemo
  • biolockj.launch.ProgressUtil
  • biolockj.launch.Reset
  • biolockj.util.RMetaUtil
  • biolockj.util.RuntimeParamUtil
  • biolockj.util.SeqUtil
  • biolockj.util.SummaryUtil
  • biolockj.util.TaxaUtil
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • biolockj.api.API_Exception
      • biolockj.exception.BioLockJException
        • biolockj.exception.BioLockJStatusException
        • biolockj.exception.ConfigException
          • biolockj.exception.ConfigConflictException
          • biolockj.exception.ConfigFormatException
          • biolockj.exception.ConfigNotFoundException
          • biolockj.exception.ConfigPathException
          • biolockj.exception.ConfigViolationException
          • biolockj.exception.SpecialPropertiesException
        • biolockj.exception.DirectModuleException
        • biolockj.exception.DockerImageException
        • biolockj.exception.DockerVolumeException
          • biolockj.exception.DockerVolCreationException
        • biolockj.exception.ExpectationFileFormatException
        • biolockj.exception.IntentionalStop
          • biolockj.exception.StopAfterPrecheck
          • biolockj.exception.StopModuleException
        • biolockj.exception.InvalidPipelineException
        • biolockj.exception.MetadataException
          • biolockj.exception.FileWithoutMetadataException
          • biolockj.exception.MetadataWithoutFileException
        • biolockj.exception.OtuFileException
        • biolockj.exception.PipelineFormationException
        • biolockj.exception.PipelineScriptException
        • biolockj.exception.RequiredRPackageException
        • biolockj.exception.RuntimeParamException
        • biolockj.exception.SequnceFormatException
        • biolockj.exception.ValidationException
        • biolockj.exception.ValidationExecutionException
        • biolockj.exception.ValidationUtilityException
      • biolockj.launch.EndLaunch
  • java.util.TimerTask (implements java.lang.Runnable)
    • biolockj.launch.JavaLaunchProcess.InterruptTimerTask
    • biolockj.launch.LabeledSpinner
  • biolockj.util.UpdateJavaDocs
  • biolockj.util.ValidationUtil

Interface Hierarchy

• biolockj.module.BioModule
  • biolockj.api.ApiModule
  • biolockj.module.classifier.ClassifierModule
  • biolockj.module.DatabaseModule
  • biolockj.module.JavaModule
    • biolockj.module.implicit.parser.ParserModule
  • biolockj.module.OutsidePipelineWriter
  • biolockj.module.implicit.parser.ParserModule
  • biolockj.module.ReadCounter
  • biolockj.module.ScriptModule
    • biolockj.module.classifier.ClassifierModule
    • biolockj.module.JavaModule
      • biolockj.module.implicit.parser.ParserModule
    • biolockj.module.implicit.parser.ParserModule
    • biolockj.module.SeqModule
      • biolockj.module.classifier.ClassifierModule
  • biolockj.module.SeqModule
    • biolockj.module.classifier.ClassifierModule
• biolockj.module.getData.InputDataModule
• biolockj.pipelines.OtherPipeline
• biolockj.node.OtuNode
• biolockj.util.paths.PathMapper
  • biolockj.util.paths.DockerMountMapper