Uses of Class
de.jstacs.data.alphabets.ComplementableDiscreteAlphabet

Packages that use ComplementableDiscreteAlphabet

Package	Description
de.jstacs.data.alphabets	Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Uses of ComplementableDiscreteAlphabet in de.jstacs.data.alphabets

Subclasses of ComplementableDiscreteAlphabet in de.jstacs.data.alphabets

Modifier and Type	Class and Description
class	DNAAlphabet This class implements the discrete alphabet that is used for DNA.
class	GenericComplementableDiscreteAlphabet This class implements an generic complementable discrete alphabet.
class	IUPACDNAAlphabet This class implements a discrete alphabet for the IUPAC DNA code.

Uses of ComplementableDiscreteAlphabet in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture with parameters of type ComplementableDiscreteAlphabet

Modifier and Type	Method and Description
static double[][][]	StrandDiffSM.getReverseComplementDistributions(ComplementableDiscreteAlphabet abc, double[][][] condDistr) This method computes the reverse complement distributions for given conditional distributions.

Uses of ComplementableDiscreteAlphabet in de.jstacs.utils

Methods in de.jstacs.utils with parameters of type ComplementableDiscreteAlphabet

Modifier and Type	Method and Description
static ComparableElement<String,Double>[]	PFMComparator.find(ComplementableDiscreteAlphabet abc, double[][] pfm, ArrayList<AbstractMap.SimpleEntry<String,double[][]>> knownPFMs, PFMComparator.PFMDistance distance, int minOverlap, int allowMiniShift, boolean pValues, double threshold) This methods finds for a user specified PFM pfm similar PFMs in a list of known PFMs.
static double[][]	PFMComparator.getReverseComplement(ComplementableDiscreteAlphabet abc, double[][] pfm) This method returns the PFM that is the reverse complement of the given PFM.