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.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.SimpleGeneticCodeTable
  • org.biojava.bio.symbol.AbstractReversibleTranslationTable (implements org.biojava.bio.symbol.ReversibleTranslationTable)
    • org.biojava.bio.symbol.SimpleReversibleTranslationTable (implements java.io.Serializable)
  • 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.alignment.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.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