org.biojava.bio.symbol

Interfaces

• Alphabet
• AlphabetIndex
• AtomicSymbol
• BasisSymbol
• CodonPref
• CodonPrefFilter
• FiniteAlphabet
• FuzzyLocation.RangeResolver
• FuzzyPointLocation.PointResolver
• GappedSymbolList
• Location
• ManyToOneTranslationTable
• Packing
• ReversibleTranslationTable
• SoftMaskedAlphabet.MaskingDetector
• Symbol
• SymbolList
• SymbolListFactory
• SymbolPropertyTable
• TranslationTable
• WobbleDistribution

Classes

• AbstractAlphabet
• AbstractLocation
• AbstractLocationDecorator
• AbstractManyToOneTranslationTable
• AbstractRangeLocation
• AbstractReversibleTranslationTable
• AbstractSymbol
• AbstractSymbolList
• AlphabetManager
• BetweenLocation
• ChunkedSymbolList
• CircularLocation
• CodonPrefFilter.AcceptAll
• CodonPrefFilter.ByName
• CodonPrefFilter.EverythingToXML
• CodonPrefTools
• DNAAmbPack
• DNANoAmbPack
• DoubleAlphabet
• DoubleAlphabet.DoubleRange
• DoubleAlphabet.DoubleSymbol
• DoubleAlphabet.SubDoubleAlphabet
• DummySymbolList
• Edit
• FundamentalAtomicSymbol
• FuzzyLocation
• FuzzyPointLocation
• IntegerAlphabet
• IntegerAlphabet.IntegerSymbol
• IntegerAlphabet.SubIntegerAlphabet
• LocationTools
• MergeLocation
• MotifTools
• PackedSymbolList
• PackedSymbolListFactory
• PackingFactory
• PointLocation
• RangeLocation
• RelabeledAlignment
• SimpleAlphabet
• SimpleAtomicSymbol
• SimpleCodonPref
• SimpleGappedSymbolList
• SimpleGappedSymbolList.Block
• SimpleGeneticCodeTable
• SimpleManyToOneTranslationTable
• SimpleReversibleTranslationTable
• SimpleSymbolList
• SimpleSymbolListFactory
• SimpleSymbolPropertyTable
• SimpleTranslationTable
• SingletonAlphabet
• SoftMaskedAlphabet
• SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
• SuffixTree
• SuffixTree.SuffixNode
• SymbolListViews
• UkkonenSuffixTree
• UkkonenSuffixTree.SuffixNode

Exceptions

• IllegalAlphabetException
• IllegalSymbolException