Uses of Package
jbil.sequence

Packages that use jbil.sequence

jbil.sequence

Classes in jbil.sequence used by jbil.sequence

AbstractFixedLengthSequenceModel
Abstract stub implementation of the FixedLengthSequenceModel interface.

Alphabet
Class representing an alphabet of symbols.

AlphabetRegistry
Central (singleton) registry of alphabets.

AtomicCharSymbol
An atomic char symbol is an atomic symbol associated to a character 'image'.

AtomicSymbol
A symbol that matches itself only.

ByteArraySequence
Implementation of Sequence in which the sequence of symbols is translated into an array of bytes s.t.

CharSymbol
Abstract class for symbols associated to a character (either atomic or higher order).

DNAAlphabet
Class representing the basic DNA nucleotide alphabet {a,g,c,t}.

ExtendedDNAAlphabet
Class representing the extended DNA nucleotide alphabet.

FixedLengthSequenceModel
Specialises the SequenceModel interface for sets of sequences of a fixed length.

HighOrderCharSymbol
A high order symbol that is associated to a character 'image'.

HighOrderSymbol
A high order symbol is a symbol that matches zero or more atomic symbols.

KMerCounter
Contains methods for counting kmers in sets of sequences.

Sequence
Abstract class representing a sequence of symbols from a fixed alphabet.

SequenceFactory
Singleton sequence factory.

SequenceModel
Generic interface for a sequence model.

Symbol
The unit component of sequences.

Trie
Class representing an extended character trie over a given alphabet.