A B C D E F G H I J K L M N O P R S T U V W Y

A

a - Static variable in class jbil.sequence.DNAAlphabet

The atomic 'a' symbol

a() - Method in class jbil.sequence.DNAAlphabet

a - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The atomic 'a' symbol

a() - Method in class jbil.sequence.ExtendedDNAAlphabet

AbstractAlgorithm - Class in jbil.common

Stub implementation of the Algorithm interface.

AbstractAlgorithm() - Constructor for class jbil.common.AbstractAlgorithm

AbstractFixedLengthSequenceModel - Class in jbil.sequence

Abstract stub implementation of the FixedLengthSequenceModel interface.

AbstractFixedLengthSequenceModel() - Constructor for class jbil.sequence.AbstractFixedLengthSequenceModel

add(int, Symbol) - Method in class jbil.sequence.Alphabet

Adds a symbol to the alphabet at a given position.

addBaseSequence(Sequence) - Method in class jbil.sequence.FactorTrie

Adds a base sequence to the factor trie, i.e., add all factors of the adequate size of this sequence to the trie.

addMatch(AtomicSymbol) - Method in class jbil.sequence.HighOrderCharSymbol

addMatch(AtomicSymbol) - Method in interface jbil.sequence.HighOrderSymbol

Adds an atomic symbol to the alphabet of symbols matched by this symbol.

addMatches(List<AtomicSymbol>) - Method in class jbil.sequence.HighOrderCharSymbol

addMatches(List<AtomicSymbol>) - Method in interface jbil.sequence.HighOrderSymbol

Adds a list of atomic symbols to the alphabet of symbols matched by this symbol.

addSequence(Sequence) - Method in class jbil.sequence.Trie

Adds a sequence to the trie and returns its locus.

addSequence(Sequence, int, int) - Method in class jbil.sequence.Trie

Adds a sequence to the trie and returns its locus.

addTrie(Trie) - Method in class jbil.sequence.TrieForest

Add a trie to the forest.

Algorithm - Interface in jbil.common

Classes implementing this interface behave as algorithms.

Alphabet - Class in jbil.sequence

Class representing an alphabet of symbols.

Alphabet() - Constructor for class jbil.sequence.Alphabet

Creates an empty alphabet.

Alphabet(int) - Constructor for class jbil.sequence.Alphabet

Creates an empty alphabet with a given initial capacity.

Alphabet(List<? extends Symbol>) - Constructor for class jbil.sequence.Alphabet

Creates an alphabet from a list of symbols.

AlphabetRegistry - Class in jbil.sequence

Central (singleton) registry of alphabets.

append(Symbol) - Method in class jbil.sequence.ByteArraySequence

append(Sequence) - Method in class jbil.sequence.ByteArraySequence

append(ByteArraySequence) - Method in class jbil.sequence.ByteArraySequence

Optmised append operation for the case in which the operand is known to be of the same type.

append(Symbol) - Method in class jbil.sequence.Sequence

Appends a symbol to this sequence.

append(Sequence) - Method in class jbil.sequence.Sequence

Appends a sequence to this sequence.

append(Symbol) - Method in class jbil.sequence.SymbolArraySequence

append(Sequence) - Method in class jbil.sequence.SymbolArraySequence

arity() - Method in class jbil.sequence.CharSymbol

arity() - Method in interface jbil.sequence.Symbol

The arity of a Symbols corresponds to the number of symbols matching it.

ArrayPrinter - Class in jbil.util

Utility functions for printing arrays.

ArrayPrinter() - Constructor for class jbil.util.ArrayPrinter

ArrayUtilities - Class in jbil.util

Assorted array utility functions.

ArrayUtilities() - Constructor for class jbil.util.ArrayUtilities

asIndicatorVector(int, int[]) - Static method in class jbil.util.BooleanArrayUtilities

Creates an indicator array (boolean mask) from its size and the indexes of the true elements.

AtomicCharSymbol - Class in jbil.sequence

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

AtomicCharSymbol(char) - Constructor for class jbil.sequence.AtomicCharSymbol

Creates an atomic character symbol associated to a given char.

AtomicSymbol - Interface in jbil.sequence

A symbol that matches itself only.