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

G

g - Static variable in class jbil.sequence.DNAAlphabet

The atomic 'g' symbol

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

g - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The atomic 'a' symbol

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

get(int) - Method in class jbil.common.Pair

Gets an element from its index: 0=first, 1=second.

get(int) - Method in class jbil.sequence.Alphabet

Return a symbol at a given position in the alphabet.

get(char) - Method in class jbil.sequence.DNAAlphabet

Gets a symbol from its character representation.

get(char) - Method in class jbil.sequence.ExtendedDNAAlphabet

Gets a symbol from its character representation.

getAlphabet(String) - Method in class jbil.sequence.AlphabetRegistry

Gets the alphabet associated to a given name.

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

getAlphabet() - Method in class jbil.sequence.MarkovFixedLengthSequenceModel

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

getAlphabet() - Method in interface jbil.sequence.SequenceModel

Returns the base alphabet of the modelled sequences.

getAlphabet() - Method in class jbil.sequence.SymbolArraySequence

getAlphabet() - Method in class jbil.sequence.Trie

Returns the base alphabet of the tire.

getAlphabet() - Method in class jbil.sequence.UniformFixedLengthSequenceModel

getDNAAlphabet() - Method in class jbil.sequence.AlphabetRegistry

getExtendedDNAAlphabet() - Method in class jbil.sequence.AlphabetRegistry

getHeight() - Method in class jbil.sequence.Trie

Gets the height of this trie, i.e., the maximum height of a leaf.

getInput(String) - Method in class jbil.common.AbstractAlgorithm

getInput(String) - Method in interface jbil.common.Algorithm

Get the input value associated to a name.

getInstance() - Static method in class jbil.sequence.AlphabetRegistry

getInstance() - Static method in class jbil.sequence.SequenceFactory

getInstance() - Static method in class jbil.util.RandomManager

Gets the singleton instance of this class.

getMatches() - Method in class jbil.sequence.AtomicCharSymbol

getMatches() - Method in class jbil.sequence.HighOrderCharSymbol

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

getMean() - Method in class jbil.rv.IntIntervalDist

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

getOutput(String) - Method in class jbil.common.AbstractAlgorithm

getOutput(String) - Method in interface jbil.common.Algorithm

Gets an output of the algorithm from its name.

getParams() - Method in class jbil.rv.IntIntervalDist

Returns the array {lowerLimit, weights[0],...,weights[W-1]}

getPvalueMode() - Method in class jbil.sequence.MarkovFixedLengthSequenceModel

Gets the p-value computation mode.

getRandomStream() - Method in class jbil.util.RandomManager

Returns the system-wide RNG.

getSequenceList() - Method in class jbil.sequence.Trie

Returns the list of sequences represented by this trie.

getStandardDeviation() - Method in class jbil.rv.IntIntervalDist

getVariance() - Method in class jbil.rv.IntIntervalDist

GibbsMotifSiteSampler - Class in jbil.sequence

Implementation of the simple Gibbs motif site sampler using motif trie-based K-order Markov models.

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

GibbsMotifSiteSamplerTest - Class in jbil.sequence.test

Demo of the motif site sampler for K-order markov models.

GibbsMotifSiteSamplerTest() - Constructor for class jbil.sequence.test.GibbsMotifSiteSamplerTest