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## 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)`

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