jbil.sequence
Interface FixedLengthSequenceModel

All Superinterfaces:

SequenceModel

All Known Implementing Classes:

AbstractFixedLengthSequenceModel, MarkovFixedLengthSequenceModel, UniformFixedLengthSequenceModel

public interface FixedLengthSequenceModel
extends SequenceModel

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

Author:

Paulo G. S. da Fonseca

See Also:

SequenceModel

Method Summary

int	length() Returns the length of the modelled sequences.
double	likelihood(Sequence word, int beginIndex) Returns the likelihod of the subword of the given word starting at beginIndex and with the appropriate length.
double	pvalue(Sequence word, int beginIndex) Returns the p-value of the subword of the given word starting at beginIndex and of the appropriate length with a default null model (typically the uniform model).
double	pvalue(Sequence word, int beginIndex, SequenceModel nullModel) Returns the p-value of the subword of the given word starting at beginIndex and with the appropriate length.
Sequence	sample() Samples a sequence with the apropriate length from this model.
Sequence[]	sampleN(int sampleSize) Samples a set of i.i.d.

Methods inherited from interface jbil.sequence.SequenceModel

getAlphabet, likelihood, likelihood, likelihoodThreshold, likelihoodThreshold, positionProbability, prefixLikelihood, prefixLikelihood, pvalue, pvalue, pvalue, pvalue, sample, sampleN

Method Detail

length

int length()

Returns the length of the modelled sequences.

sample

Sequence sample()

Samples a sequence with the apropriate length from this model.

sampleN

Sequence[] sampleN(int sampleSize)

Samples a set of i.i.d. sequences with the apropriate length from this model.

Parameters:

sampleSize - The number of sampled sequences.

likelihood

double likelihood(Sequence word,
                  int beginIndex)

Returns the likelihod of the subword of the given word starting at beginIndex and with the appropriate length.

pvalue

double pvalue(Sequence word,
              int beginIndex)

Returns the p-value of the subword of the given word starting at beginIndex and of the appropriate length with a default null model (typically the uniform model).

See Also:

SequenceModel.pvalue(Sequence, SequenceModel)

pvalue

double pvalue(Sequence word,
              int beginIndex,
              SequenceModel nullModel)

Returns the p-value of the subword of the given word starting at beginIndex and with the appropriate length.

See Also:

SequenceModel.pvalue(Sequence, SequenceModel)