## Hierarchy For All Packages

Package Hierarchies:
  edu.msu.cme.rdp.classifier.comparison, edu.msu.cme.rdp.classifier.readseqwrapper, edu.msu.cme.rdp.classifier.rrnaclassifier, edu.msu.cme.rdp.classifier.train

## 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.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.comparison.AbstractNode.LineageIterator (implements java.util.Iterator<E>)
  - edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator (implements java.util.Iterator<E>)
  - junit.framework.Assert
    - junit.framework.TestCase (implements junit.framework.Test)
      - edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierTest
      - edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBeanTest
      - edu.msu.cme.rdp.classifier.comparison.ComparisonSuite
      - edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
      - edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTreeTest
      - edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
      - edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
      - edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
      - edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserTest
      - edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
      - edu.msu.cme.rdp.classifier.comparison.TaxonTreeTest
      - edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
      - edu.msu.cme.rdp.classifier.train.TrainSuite
      - edu.msu.cme.rdp.classifier.train.TreeFactoryTest
      - edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
      - edu.msu.cme.rdp.classifier.comparison.UncNodeTest
      - edu.msu.cme.rdp.classifier.comparison.ZtableTest
  - edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult
  - edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
  - edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  - edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
  - edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  - edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker
  - 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>)
  - 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.rrnaclassifier.TreeFileParser
  - edu.msu.cme.rdp.classifier.rrnaclassifier.GenusWordConditionalProb
  - edu.msu.cme.rdp.classifier.rrnaclassifier.GenusWordProbFileParser
  - edu.msu.cme.rdp.classifier.train.GoodWordIterator
  - edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
  - edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
  - edu.msu.cme.rdp.classifier.rrnaclassifier.LogWordPriorFileParser
  - edu.msu.cme.rdp.classifier.train.ParsedRawSequence
  - edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence (implements edu.msu.cme.rdp.classifier.readseqwrapper.Sequence)
  - edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
  - edu.msu.cme.rdp.classifier.rrnaclassifier.ProbIndexFileParser
  - edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  - edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
  - edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  - edu.msu.cme.rdp.classifier.train.RawSequenceParser
  - 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.classifier.comparison.SeqInfo.ScoreIterator (implements java.util.Iterator<E>)
  - edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  - edu.msu.cme.rdp.classifier.comparison.SigCalculator
  - edu.msu.cme.rdp.classifier.train.Taxonomy
  - edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator (implements java.util.Iterator<E>)
  - edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator (implements java.util.Iterator<E>)
  - java.lang.Thread (implements java.lang.Runnable)
    - edu.msu.cme.rdp.classifier.comparison.ComparisonManager
    - edu.msu.cme.rdp.classifier.comparison.ComparisonManager.Timer
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - java.lang.RuntimeException
        - java.lang.IllegalArgumentException
          - edu.msu.cme.rdp.classifier.rrnaclassifier.ShortSequenceException
      - edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserException
      - edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingDataException
  - edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  - edu.msu.cme.rdp.classifier.train.TreeFactory
  - edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator (implements java.util.Iterator<E>)
  - edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator (implements java.util.Iterator<E>)
  - edu.msu.cme.rdp.classifier.comparison.Ztable

## Interface Hierarchy

- edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
- edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
- edu.msu.cme.rdp.classifier.comparison.Taxon

## Enum Hierarchy

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