org.biojava.bio.symbol Class Hierarchy (BioJava-1.5-beta API)

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## Hierarchy For Package org.biojava.bio.symbol

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.symbol.AbstractAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
      - org.biojava.bio.symbol.IntegerAlphabet.SubIntegerAlphabet
      - org.biojava.bio.symbol.SimpleAlphabet (implements java.io.Serializable)
      - org.biojava.bio.symbol.SingletonAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet, java.io.Serializable)
    - org.biojava.bio.symbol.AbstractSymbol (implements org.biojava.bio.symbol.Symbol)
      - org.biojava.bio.symbol.FundamentalAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
      - org.biojava.bio.symbol.SimpleAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.AbstractSymbolList (implements org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.symbol.ChunkedSymbolList (implements java.io.Serializable)
      - org.biojava.bio.symbol.DummySymbolList (implements java.io.Serializable)
      - org.biojava.bio.symbol.PackedSymbolList (implements java.io.Serializable)
      - org.biojava.bio.symbol.SimpleAlignment (implements org.biojava.bio.symbol.Alignment, java.io.Serializable)
      - org.biojava.bio.symbol.SimpleGappedSymbolList (implements org.biojava.bio.symbol.GappedSymbolList, java.io.Serializable)
      - org.biojava.bio.symbol.SimpleSymbolList (implements org.biojava.utils.ChangeListener, java.io.Serializable)
    - org.biojava.bio.symbol.SimpleCodonPref (implements org.biojava.bio.symbol.CodonPref)
  - org.biojava.bio.symbol.AbstractLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
    - org.biojava.bio.symbol.AbstractRangeLocation
      - org.biojava.bio.symbol.FuzzyLocation (implements java.io.Serializable)
      - org.biojava.bio.symbol.PointLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
      - org.biojava.bio.symbol.RangeLocation (implements java.io.Serializable)
        - org.biojava.bio.symbol.MergeLocation
    - org.biojava.bio.symbol.FuzzyPointLocation
  - org.biojava.bio.symbol.AbstractLocationDecorator (implements org.biojava.bio.symbol.Location)
    - org.biojava.bio.symbol.BetweenLocation
    - org.biojava.bio.symbol.CircularLocation
  - org.biojava.bio.symbol.AbstractManyToOneTranslationTable (implements org.biojava.bio.symbol.ManyToOneTranslationTable)
    - org.biojava.bio.symbol.SimpleManyToOneTranslationTable (implements java.io.Serializable)
  - org.biojava.bio.symbol.AbstractReversibleTranslationTable (implements org.biojava.bio.symbol.ReversibleTranslationTable)
    - org.biojava.bio.symbol.SimpleReversibleTranslationTable (implements java.io.Serializable)
  - org.biojava.bio.symbol.Alignment.SymbolListIterator (implements java.util.Iterator)
  - org.biojava.bio.symbol.AlphabetManager
  - org.biojava.utils.ChangeForwarder (implements org.biojava.utils.ChangeListener)
    - org.biojava.bio.symbol.AbstractSymbolList.EditScreener
      - org.biojava.bio.symbol.AbstractSymbolList.EditTranslater
  - org.biojava.bio.symbol.CodonPrefFilter.AcceptAll (implements org.biojava.bio.symbol.CodonPrefFilter)
  - org.biojava.bio.symbol.CodonPrefFilter.ByName (implements org.biojava.bio.symbol.CodonPrefFilter)
  - org.biojava.bio.symbol.CodonPrefFilter.EverythingToXML (implements org.biojava.bio.symbol.CodonPrefFilter)
  - org.biojava.bio.symbol.CodonPrefTools
  - org.biojava.bio.symbol.DNAAmbPack (implements org.biojava.bio.symbol.Packing, java.io.Serializable)
  - org.biojava.bio.symbol.DNANoAmbPack (implements org.biojava.bio.symbol.Packing, java.io.Serializable)
  - org.biojava.bio.symbol.Edit (implements java.io.Serializable)
  - org.biojava.bio.symbol.LocationTools
  - org.biojava.bio.symbol.MotifTools
  - org.biojava.bio.symbol.PackedSymbolListFactory (implements org.biojava.bio.symbol.SymbolListFactory)
  - org.biojava.bio.symbol.PackingFactory
  - org.biojava.bio.symbol.SimpleGappedSymbolList.Block (implements java.io.Serializable)
  - org.biojava.bio.symbol.SimpleSymbolListFactory (implements org.biojava.bio.symbol.SymbolListFactory)
  - org.biojava.bio.symbol.SimpleSymbolPropertyTable (implements org.biojava.bio.symbol.SymbolPropertyTable)
  - org.biojava.bio.symbol.SimpleTranslationTable (implements java.io.Serializable)
  - org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector (implements org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector)
  - org.biojava.bio.symbol.SuffixTree (implements java.io.Serializable)
  - org.biojava.bio.symbol.SuffixTree.SuffixNode (implements java.io.Serializable)
  - org.biojava.bio.symbol.SymbolListViews
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - org.biojava.bio.BioException
        - org.biojava.bio.symbol.IllegalAlphabetException
        - org.biojava.bio.symbol.IllegalSymbolException
  - org.biojava.bio.symbol.UkkonenSuffixTree
  - org.biojava.bio.symbol.UkkonenSuffixTree.SuffixNode
  - org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.symbol.DoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - org.biojava.bio.symbol.DoubleAlphabet.DoubleRange (implements org.biojava.bio.symbol.BasisSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.DoubleAlphabet.DoubleSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.DoubleAlphabet.SubDoubleAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - org.biojava.bio.symbol.IntegerAlphabet (implements org.biojava.bio.symbol.Alphabet, java.io.Serializable)
    - org.biojava.bio.symbol.IntegerAlphabet.IntegerSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
    - org.biojava.bio.symbol.RelabeledAlignment (implements org.biojava.bio.symbol.Alignment)
    - org.biojava.bio.symbol.SoftMaskedAlphabet (implements org.biojava.bio.symbol.FiniteAlphabet)
    - org.biojava.bio.symbol.SoftMaskedAlphabet.CaseSensitiveTokenization (implements org.biojava.bio.seq.io.SymbolTokenization)

## Interface Hierarchy

- org.biojava.utils.Changeable
  - org.biojava.bio.symbol.AlphabetIndex
  - org.biojava.bio.Annotatable
    - org.biojava.bio.symbol.Alphabet
      - org.biojava.bio.symbol.FiniteAlphabet
    - org.biojava.bio.symbol.Symbol
      - org.biojava.bio.symbol.BasisSymbol
        - org.biojava.bio.symbol.AtomicSymbol
  - org.biojava.bio.symbol.SymbolList
    - org.biojava.bio.symbol.Alignment
    - org.biojava.bio.symbol.GappedSymbolList
- org.biojava.bio.symbol.CodonPref
- org.biojava.bio.symbol.CodonPrefFilter
- org.biojava.bio.symbol.FuzzyPointLocation.PointResolver
- org.biojava.bio.symbol.Location
- org.biojava.bio.symbol.Packing
- java.io.Serializable
  - org.biojava.bio.symbol.FuzzyLocation.RangeResolver
- org.biojava.bio.symbol.SoftMaskedAlphabet.MaskingDetector
- org.biojava.bio.symbol.SymbolListFactory
- org.biojava.bio.symbol.SymbolPropertyTable
- org.biojava.bio.symbol.TranslationTable
  - org.biojava.bio.symbol.ManyToOneTranslationTable
  - org.biojava.bio.symbol.ReversibleTranslationTable
- org.biojava.bio.symbol.WobbleDistribution

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