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

M

m - Static variable in class jbil.sequence.ExtendedDNAAlphabet

The high order m={a,c} symbol

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

main(String[]) - Static method in class jbil.sequence.test.GibbsMotifSiteSamplerTest

main(String[]) - Static method in class jbil.sequence.test.MarkovMotifPvalueTest

MarkovFixedLengthSequenceModel - Class in jbil.sequence

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).

MarkovFixedLengthSequenceModel(Alphabet, int, int, KMerCounter) - Constructor for class jbil.sequence.MarkovFixedLengthSequenceModel

Constructs a new K-order Markov sequence model.

MarkovMotifPvalueTest - Class in jbil.sequence.test

Example of the p-value algorithms for K-order Markov motif models.

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

max(int[]) - Static method in class jbil.util.ArrayUtilities

Returns the maximum of an int array.

MAX_RESTARTS - Static variable in class jbil.sequence.GibbsMotifSiteSampler

min(int[]) - Static method in class jbil.util.ArrayUtilities

Returns the minimum of an int array.

MOTIF_LENGTH - Static variable in class jbil.sequence.GibbsMotifSiteSampler

MOTIF_MODEL - Static variable in class jbil.sequence.GibbsMotifSiteSampler

MOTIF_ORDER - Static variable in class jbil.sequence.GibbsMotifSiteSampler