Uses of Class
calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn

Packages that use MultipleAlignmentInputSequence.MultipleAlignmentColumn

calhoun.analysis.crf.features.interval13	mdoel definition and setup for the interval13 model
calhoun.analysis.crf.features.interval29
calhoun.analysis.crf.features.supporting.phylogenetic	utility classes for phylogenetic analysis
calhoun.analysis.crf.features.tricycle13	basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.io	handles input and output of gene calling formats

Uses of MultipleAlignmentInputSequence.MultipleAlignmentColumn in calhoun.analysis.crf.features.interval13

Method parameters in calhoun.analysis.crf.features.interval13 with type arguments of type MultipleAlignmentInputSequence.MultipleAlignmentColumn

void	PhylogeneticLogprobInterval13.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	GapFeaturesInterval13.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	FootprintsInterval13.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	PhylogeneticLogprobInterval13.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)
void	GapFeaturesInterval13.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)
void	FootprintsInterval13.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)

Uses of MultipleAlignmentInputSequence.MultipleAlignmentColumn in calhoun.analysis.crf.features.interval29

Method parameters in calhoun.analysis.crf.features.interval29 with type arguments of type MultipleAlignmentInputSequence.MultipleAlignmentColumn

void	GapFeaturesInterval29.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	FootprintsInterval29.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	GapFeaturesInterval29.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)
void	FootprintsInterval29.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)

Uses of MultipleAlignmentInputSequence.MultipleAlignmentColumn in calhoun.analysis.crf.features.supporting.phylogenetic

Methods in calhoun.analysis.crf.features.supporting.phylogenetic with parameters of type MultipleAlignmentInputSequence.MultipleAlignmentColumn

double	EvolutionaryModel.logprob(MultipleAlignmentInputSequence.MultipleAlignmentColumn col, boolean conditionref)
double	EvolutionaryModel.logprobRC(MultipleAlignmentInputSequence.MultipleAlignmentColumn col, boolean conditionref)

Method parameters in calhoun.analysis.crf.features.supporting.phylogenetic with type arguments of type MultipleAlignmentInputSequence.MultipleAlignmentColumn

double	ColumnConditionalLogProbability.condLogProb(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state)
void	ColumnConditionalLogProbability.train(ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)

Uses of MultipleAlignmentInputSequence.MultipleAlignmentColumn in calhoun.analysis.crf.features.tricycle13

Method parameters in calhoun.analysis.crf.features.tricycle13 with type arguments of type MultipleAlignmentInputSequence.MultipleAlignmentColumn

void	GapConjunctionFeatures.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	FelsensteinFeatures.evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn> seq, int pos, int state, FeatureList result)
void	GapConjunctionFeatures.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)
void	FelsensteinFeatures.train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>> data)

Uses of MultipleAlignmentInputSequence.MultipleAlignmentColumn in calhoun.analysis.crf.io

Methods in calhoun.analysis.crf.io that return MultipleAlignmentInputSequence.MultipleAlignmentColumn

MultipleAlignmentInputSequence.MultipleAlignmentColumn

MultipleAlignmentInputSequence.getX(int ix)

Methods in calhoun.analysis.crf.io that return types with arguments of type MultipleAlignmentInputSequence.MultipleAlignmentColumn

InputSequence<MultipleAlignmentInputSequence.MultipleAlignmentColumn>

MultipleAlignmentInputSequence.subSequence(int start, int end)