# Hierarchy For All Packages

Package Hierarchies:

- edu.msu.cme.rdp.classifier,
- edu.msu.cme.rdp.classifier.cli,
- edu.msu.cme.rdp.classifier.comparison,
- edu.msu.cme.rdp.classifier.io,
- edu.msu.cme.rdp.classifier.rrnaclassifier,
- edu.msu.cme.rdp.classifier.train,
- edu.msu.cme.rdp.classifier.train.validation,
- edu.msu.cme.rdp.classifier.train.validation.crossvalidate,
- edu.msu.cme.rdp.classifier.train.validation.distance,
- edu.msu.cme.rdp.classifier.train.validation.leaveoneout,
- edu.msu.cme.rdp.classifier.train.validation.movingwindow,
- edu.msu.cme.rdp.classifier.utils,
- edu.msu.cme.rdp.multicompare,
- edu.msu.cme.rdp.multicompare.gridware,
- edu.msu.cme.rdp.multicompare.taxon,
- edu.msu.cme.rdp.multicompare.visitors,
- edu.msu.cme.rdp.taxatree,
- edu.msu.cme.rdp.taxatree.utils,
- edu.msu.cme.rdp.unifrac

## Class Hierarchy

- java.lang.Object
  - java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    - java.util.AbstractSet<E> (implements java.util.Set<E>)
      - java.util.TreeSet<E> (implements java.lang.Cloneable, java.util.NavigableSet<E>, java.io.Serializable)
        - edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet
        - edu.msu.cme.rdp.classifier.train.validation.SortedROCSet
  - edu.msu.cme.rdp.classifier.comparison.AbstractNode (implements edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode, edu.msu.cme.rdp.classifier.comparison.Taxon)
    - edu.msu.cme.rdp.classifier.comparison.TaxonTree
    - edu.msu.cme.rdp.classifier.comparison.UncNode
  - edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils
  - edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
  - edu.msu.cme.rdp.classifier.ClassificationResult
  - edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
  - edu.msu.cme.rdp.classifier.Classifier
  - edu.msu.cme.rdp.classifier.ClassifierCmd
  - edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  - edu.msu.cme.rdp.multicompare.gridware.ClassifierGridware
  - edu.msu.cme.rdp.classifier.cli.ClassifierMain
  - edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker
  - edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder<E>
  - edu.msu.cme.rdp.classifier.cli.CmdOptions
  - edu.msu.cme.rdp.classifier.train.validation.leaveoneout.CompareMisclassified
  - edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets
  - edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets.HierarchyTreeExtend
  - edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
  - edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
  - edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet.ComparisonResultComparator (implements java.util.Comparator<T>)
  - edu.msu.cme.rdp.taxatree.ConcretRoot<E>
    - edu.msu.cme.rdp.taxatree.UnifracTree
  - edu.msu.cme.rdp.classifier.train.CopyNumberParser
  - edu.msu.cme.rdp.classifier.train.CopyNumberParser.TaxonCopyNumber
  - edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
  - edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate
  - edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidateMain
  - edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
  - org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    - edu.msu.cme.rdp.classifier.io.TreeFileParser
  - edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor (implements edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor<E>)
  - edu.msu.cme.rdp.multicompare.visitors.EstimateSPrintVisitor (implements edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor<E>)
  - edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrame
  - edu.msu.cme.rdp.classifier.GenusWordConditionalProb
  - edu.msu.cme.rdp.classifier.io.GenusWordProbFileParser
  - edu.msu.cme.rdp.classifier.HierarchyTree
  - edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  - edu.msu.cme.rdp.classifier.utils.HierarchyVersion
  - edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester
  - edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
  - edu.msu.cme.rdp.classifier.train.LineageSequenceParser
  - edu.msu.cme.rdp.classifier.io.LogWordPriorFileParser
  - edu.msu.cme.rdp.multicompare.Main
  - edu.msu.cme.rdp.classifier.train.validation.movingwindow.MainMovingWindow
  - edu.msu.cme.rdp.multicompare.MCSample
    - edu.msu.cme.rdp.multicompare.MCSampleResult
  - edu.msu.cme.rdp.multicompare.MCSamplePrintUtil
  - edu.msu.cme.rdp.multicompare.MergeTaxonCount
  - edu.msu.cme.rdp.multicompare.MultiClassifier
  - edu.msu.cme.rdp.multicompare.MultiClassifierResult
  - edu.msu.cme.rdp.classifier.train.validation.NBClassifier
  - edu.msu.cme.rdp.taxatree.Node
    - edu.msu.cme.rdp.taxatree.Taxon
      - edu.msu.cme.rdp.multicompare.taxon.MCTaxon
        - edu.msu.cme.rdp.unifrac.UnifracTaxon
  - edu.msu.cme.rdp.classifier.train.validation.distance.PairwiseSeqDistance
  - edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
  - edu.msu.cme.rdp.classifier.io.ProbIndexFileParser
  - edu.msu.cme.rdp.classifier.RankAssignment
  - edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
  - edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  - edu.msu.cme.rdp.classifier.train.validation.crossvalidate.RdmSelectTaxon
  - edu.msu.cme.rdp.multicompare.Reprocess
  - edu.msu.cme.rdp.classifier.comparison.Score
  - edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
  - edu.msu.cme.rdp.classifier.comparison.SeqInfo
  - edu.msu.cme.rdp.readseq.readers.Sequence (implements java.io.Serializable)
    - edu.msu.cme.rdp.classifier.utils.ClassifierSequence
    - edu.msu.cme.rdp.classifier.train.LineageSequence
  - edu.msu.cme.rdp.classifier.comparison.SigCalculator
  - edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.PredictionCount
  - edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.ResultComparator (implements java.util.Comparator<T>)
  - edu.msu.cme.rdp.classifier.train.validation.StatusCount
  - edu.msu.cme.rdp.classifier.train.validation.StatusCountUtils
  - edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
  - edu.msu.cme.rdp.classifier.train.Taxonomy
  - edu.msu.cme.rdp.classifier.train.validation.Taxonomy
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - edu.msu.cme.rdp.classifier.train.NameRankDupException
      - java.lang.RuntimeException
        - java.lang.IllegalArgumentException
          - edu.msu.cme.rdp.classifier.ShortSequenceException
      - edu.msu.cme.rdp.classifier.TrainingDataException
  - edu.msu.cme.rdp.classifier.TrainingInfo
  - edu.msu.cme.rdp.classifier.train.TreeFactory
  - edu.msu.cme.rdp.classifier.train.validation.TreeFactory
  - edu.msu.cme.rdp.unifrac.Unifrac
  - edu.msu.cme.rdp.taxatree.UnifracTree.UnifracResult
  - edu.msu.cme.rdp.unifrac.UnifracTreeBuilder
  - edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample
  - edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
  - edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
  - edu.msu.cme.rdp.classifier.train.validation.movingwindow.Window
  - edu.msu.cme.rdp.classifier.train.validation.movingwindow.WindowTester
  - edu.msu.cme.rdp.classifier.comparison.Ztable

## Interface Hierarchy

- edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder.ClassifierTaxonFactory<E>
- edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
- edu.msu.cme.rdp.classifier.comparison.Taxon

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    - edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter.FORMAT