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## Hierarchy For Package calhoun.analysis.crf.io

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - calhoun.analysis.crf.io.AlignmentTree (implements calhoun.analysis.crf.io.InputComponentIO)
  - calhoun.analysis.crf.io.AllIntergenicHiddenStateReader (implements calhoun.analysis.crf.io.TrainingSequenceIO)
  - calhoun.analysis.crf.io.CompositeInput (implements java.io.Serializable)
  - calhoun.analysis.crf.io.CompositeInput.InputComponent (implements java.io.Serializable)
  - calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler (implements calhoun.analysis.crf.io.InputHandler)
  - calhoun.analysis.crf.io.ExtensionMapper (implements calhoun.analysis.crf.io.FilenameMapper)
  - calhoun.analysis.crf.io.FastaAlignmentInput (implements calhoun.analysis.crf.io.InputComponentIO)
  - calhoun.analysis.crf.io.FastaInput (implements calhoun.analysis.crf.io.InputComponentIO)
  - calhoun.analysis.crf.io.GTFInputInterval13 (implements calhoun.analysis.crf.io.TrainingSequenceIO)
    - calhoun.analysis.crf.io.GTFInputInterval29
  - calhoun.analysis.crf.io.InputHandlerBase (implements calhoun.analysis.crf.io.InputHandler)
    - calhoun.analysis.crf.io.InputHandlerDirectory
    - calhoun.analysis.crf.io.InputHandlerFile
  - calhoun.analysis.crf.io.InputHandlerInterleaved (implements calhoun.analysis.crf.io.InputHandler)
  - calhoun.analysis.crf.io.InputSequenceBoolean (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceCharacter (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceComposite (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceInt (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InputSequenceObject<T> (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.InterleavedInputComponentBase (implements calhoun.analysis.crf.io.InterleavedInputComponent)
    - calhoun.analysis.crf.io.BooleanInput
    - calhoun.analysis.crf.io.IntervalInput
    - calhoun.analysis.crf.io.IntInput (implements calhoun.analysis.crf.io.TrainingSequenceIO)
      - calhoun.analysis.crf.io.Interval21HiddenSequenceTranslator
      - calhoun.analysis.crf.io.IntInputInterval29
    - calhoun.analysis.crf.io.MultipleAlignmentInput
    - calhoun.analysis.crf.io.NameInput
    - calhoun.analysis.crf.io.StringInput
  - calhoun.analysis.crf.io.IntervalInputSequence (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.IntervalInputSequence.IntervalPosition
  - calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
  - calhoun.analysis.crf.io.IteratorAdapterInputComponent (implements java.util.Iterator<E>)
  - calhoun.analysis.crf.io.IteratorAdapterTrainingSequenceInput<T> (implements java.util.Iterator<E>)
  - calhoun.analysis.crf.io.MultipleAlignmentInputSequence (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  - calhoun.analysis.crf.io.NameInputSequence (implements calhoun.analysis.crf.io.InputSequence<A>)
  - calhoun.analysis.crf.io.OutputHandlerComposite (implements calhoun.analysis.crf.io.OutputHandler)
  - calhoun.analysis.crf.io.OutputHandlerGeneCallPredict (implements calhoun.analysis.crf.io.OutputHandler)
  - calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results (implements java.io.Serializable)
  - calhoun.analysis.crf.io.OutputHandlerGeneCallStats (implements calhoun.analysis.crf.io.OutputHandler)
    - calhoun.analysis.crf.io.OutputHandlerGeneCallStatsInterval29
  - calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results (implements java.io.Serializable)
  - calhoun.analysis.crf.io.OutputHandlerWriter (implements calhoun.analysis.crf.io.OutputHandler)
  - calhoun.analysis.crf.io.SequenceConverter
  - calhoun.analysis.crf.io.TrainingSequence<A> (implements calhoun.analysis.crf.io.InputSequence<A>)

## Interface Hierarchy

- calhoun.analysis.crf.io.FilenameMapper
- calhoun.analysis.crf.io.InputSequence<A>
- java.io.Serializable
  - calhoun.analysis.crf.io.InputComponentIO
    - calhoun.analysis.crf.io.InterleavedInputComponent
  - calhoun.analysis.crf.io.InputHandler
  - calhoun.analysis.crf.io.OutputHandler
  - calhoun.analysis.crf.io.TrainingSequenceIO

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