Uses of Class
jbil.sequence.Alphabet

Packages that use Alphabet

jbil.sequence

Uses of Alphabet in jbil.sequence

Subclasses of Alphabet in jbil.sequence

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

Methods in jbil.sequence that return Alphabet

Alphabet	UniformFixedLengthSequenceModel.getAlphabet()
Alphabet	Trie.getAlphabet() Returns the base alphabet of the tire.
Alphabet	SymbolArraySequence.getAlphabet()
Alphabet	SequenceModel.getAlphabet() Returns the base alphabet of the modelled sequences.
abstract Alphabet	Sequence.getAlphabet()
Alphabet	MarkovFixedLengthSequenceModel.getAlphabet()
Alphabet	ByteArraySequence.getAlphabet()
Alphabet	AlphabetRegistry.getAlphabet(java.lang.String alphabetName) Gets the alphabet associated to a given name.
Alphabet	Symbol.getMatches()
Alphabet	HighOrderCharSymbol.getMatches()
Alphabet	AtomicCharSymbol.getMatches()
Alphabet	Alphabet.intersection(Alphabet other) Computes the intersection between this alphabet and a given alphabet.
Alphabet	AlphabetRegistry.registerAlphabet(java.lang.String name, Alphabet alphabet) Registers an alphabet, associating it to unique name.

Methods in jbil.sequence with parameters of type Alphabet

Alphabet	Alphabet.intersection(Alphabet other) Computes the intersection between this alphabet and a given alphabet.
Sequence	SequenceFactory.newSequence(Alphabet alphabet) Creates a new empty sequence over the specified base alphabet.
Alphabet	AlphabetRegistry.registerAlphabet(java.lang.String name, Alphabet alphabet) Registers an alphabet, associating it to unique name.

Constructors in jbil.sequence with parameters of type Alphabet

ByteArraySequence(Alphabet alphabet)
Creates an empty sequence over a given alphabet.

ByteArraySequence(Alphabet alphabet, int initialCapacity)
Creates an empty sequence with a given initial capacity over a given alphabet.

FactorTrie(Alphabet alphabet, int factorLength)
Creates an empty factor trie.

MarkovFixedLengthSequenceModel(Alphabet alphabet, int length, int order, KMerCounter transitionsTree)
Constructs a new K-order Markov sequence model.

SymbolArraySequence(Alphabet alphabet)
Creates an empty sequence over a given alphabet.

SymbolArraySequence(Alphabet alphabet, int initialCapacity)
Creates an empty sequence with a given initial capacity over a given alphabet.

Trie(Alphabet alphabet)
Constructs a new trie for representing strings over a given alphabet.

UniformFixedLengthSequenceModel(Alphabet alphabet, int length)
Creates a new fixed length uniform model.