Uses of Interface
jbil.sequence.SequenceModel

Packages that use SequenceModel

jbil.sequence

Uses of SequenceModel in jbil.sequence

Subinterfaces of SequenceModel in jbil.sequence

interface

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

Classes in jbil.sequence that implement SequenceModel

class	AbstractFixedLengthSequenceModel Abstract stub implementation of the FixedLengthSequenceModel interface.
class	MarkovFixedLengthSequenceModel Probabilistic model for sequences of a fixed length W, in which they are assumed to be generated from a non-homogeneous Markov chain of order K, that is Pr(x1...xW) = prod_{i=1}^W Pr(xi|xi-1...xi-K).
class	UniformFixedLengthSequenceModel This class represents a uniform model for words of a fixed length W over a given alphabet A.

Methods in jbil.sequence with parameters of type SequenceModel

double	UniformFixedLengthSequenceModel.likelihoodThreshold(double significance, SequenceModel nullModel)
double	SequenceModel.likelihoodThreshold(double significance, SequenceModel nullModel) Given p in [0,1], we define the p-value of p as the as the probability under a null model for a sequence to have a likelihood greater or equal to p.
double	MarkovFixedLengthSequenceModel.likelihoodThreshold(double significance, SequenceModel nullModel)
double	SequenceModel.pvalue(Sequence word, int beginIndex, int endIndex, SequenceModel nullModel) Returns the p-value of the subword of the given word starting at beginIndex and ending at endIndex-1.
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, int endIndex, SequenceModel nullModel)
double	UniformFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, SequenceModel nullModel)
double	MarkovFixedLengthSequenceModel.pvalue(Sequence word, int beginIndex, SequenceModel nullModel)
double	FixedLengthSequenceModel.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.
double	SequenceModel.pvalue(Sequence word, SequenceModel nullModel) The p-value of a given sequence is defined as the probability under a null model for a sequence to have a likelihood greater or equal to the likelihood of the given sequence under this model.
double	AbstractFixedLengthSequenceModel.pvalue(Sequence word, SequenceModel nullModel)