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| Packages that use jbil.sequence | |
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| jbil.sequence | |
| Classes in jbil.sequence used by jbil.sequence | |
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| AbstractFixedLengthSequenceModel
Abstract stub implementation of the FixedLengthSequenceModel interface. |
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| Alphabet
Class representing an alphabet of symbols. |
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| AlphabetRegistry
Central (singleton) registry of alphabets. |
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| AtomicCharSymbol
An atomic char symbol is an atomic symbol associated to a character 'image'. |
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| AtomicSymbol
A symbol that matches itself only. |
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| ByteArraySequence
Implementation of Sequence in which the sequence of symbols is translated into an array of bytes s.t. |
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| CharSymbol
Abstract class for symbols associated to a character (either atomic or higher order). |
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| DNAAlphabet
Class representing the basic DNA nucleotide alphabet {a,g,c,t}. |
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| ExtendedDNAAlphabet
Class representing the extended DNA nucleotide alphabet. |
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| FixedLengthSequenceModel
Specialises the SequenceModel interface for sets of sequences of a fixed length. |
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| HighOrderCharSymbol
A high order symbol that is associated to a character 'image'. |
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| HighOrderSymbol
A high order symbol is a symbol that matches zero or more atomic symbols. |
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| KMerCounter
Contains methods for counting kmers in sets of sequences. |
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| Sequence
Abstract class representing a sequence of symbols from a fixed alphabet. |
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| SequenceFactory
Singleton sequence factory. |
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| SequenceModel
Generic interface for a sequence model. |
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| Symbol
The unit component of sequences. |
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| Trie
Class representing an extended character trie over a given alphabet. |
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