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public interface FixedLengthSequenceModel
Specialises the SequenceModel interface for sets of sequences of a fixed length.
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 |
|---|
int length()
Sequence sample()
Sequence[] sampleN(int sampleSize)
sampleSize - The number of sampled sequences.
double likelihood(Sequence word,
int beginIndex)
double pvalue(Sequence word,
int beginIndex)
SequenceModel.pvalue(Sequence, SequenceModel)
double pvalue(Sequence word,
int beginIndex,
SequenceModel nullModel)
SequenceModel.pvalue(Sequence, SequenceModel)
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