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Packages that use ComplementableDiscreteAlphabet | |
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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 DifferentiableSequenceScore s that are mixtures of other DifferentiableSequenceScore s. |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ... |
Uses of ComplementableDiscreteAlphabet in de.jstacs.data.alphabets |
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Subclasses of ComplementableDiscreteAlphabet in de.jstacs.data.alphabets | |
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class |
DNAAlphabet
This class implements the discrete alphabet that is used for DNA. |
class |
GenericComplementableDiscreteAlphabet
This class implements an generic complementable discrete alphabet. |
Uses of ComplementableDiscreteAlphabet in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture with parameters of type ComplementableDiscreteAlphabet | |
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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 |
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Methods in de.jstacs.utils with parameters of type ComplementableDiscreteAlphabet | |
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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. |
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