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## Uses of Interface
calhoun.analysis.crf.FeatureList

Packages that use FeatureList
calhoun.analysis.crf | the interface, main `Conrad` class, and solver for the Conrad engine.
calhoun.analysis.crf.features.generic | features useful across different models
calhoun.analysis.crf.features.interval13 | mdoel definition and setup for the interval13 model
calhoun.analysis.crf.features.interval29 |
calhoun.analysis.crf.features.tricycle13 | basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.test |

Uses of FeatureList in calhoun.analysis.crf

Methods in calhoun.analysis.crf with parameters of type FeatureList
`void` | `FeatureManagerEdge.evaluateEdge(InputSequence<? extends InputType> seq, int pos, int prevState, int state, FeatureList result)` Evaluates the set of features managed by this object for the given arguments.
`void` | `CompositeFeatureManager.evaluateEdge(InputSequence seq, int pos, int prevState, int state, FeatureList result)`
`void` | `FeatureManagerEdgeExplicitLength.evaluateEdgeLength(InputSequence<? extends InputType> seq, int pos, int length, int prevState, int state, FeatureList result)`
`void` | `CompositeFeatureManager.evaluateEdgeLength(InputSequence seq, int pos, int length, int prevState, int state, FeatureList result)`
`void` | `FeatureManagerNode.evaluateNode(InputSequence<? extends InputType> seq, int pos, int state, FeatureList result)` Evaluates the set of features managed by this object for the given arguments.
`void` | `CompositeFeatureManager.evaluateNode(InputSequence seq, int pos, int state, FeatureList result)`
`void` | `FeatureManagerNodeExplicitLength.evaluateNodeLength(InputSequence<? extends InputType> seq, int pos, int length, int state, FeatureList result)`
`void` | `CompositeFeatureManager.evaluateNodeLength(InputSequence seq, int pos, int length, int state, FeatureList result)`

Uses of FeatureList in calhoun.analysis.crf.features.generic

Methods in calhoun.analysis.crf.features.generic with parameters of type FeatureList
`void` | `WeightedStateChanges.evaluateEdge(InputSequence<?> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `WeightedEdges.evaluateEdge(InputSequence<?> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `IndicatorEdges.evaluateEdge(InputSequence seq, int pos, int prevState, int state, FeatureList result)`
`void` | `StartFeatures.evaluateNode(InputSequence<?> seq, int pos, int state, FeatureList result)`
`void` | `EndFeatures.evaluateNode(InputSequence<?> seq, int pos, int state, FeatureList result)`

Uses of FeatureList in calhoun.analysis.crf.features.interval13

Methods in calhoun.analysis.crf.features.interval13 with parameters of type FeatureList
`void` | `StateTransitionsInterval13.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `PWMInterval13.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)`
`void` | `GeneConstraintsInterval13.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `ESTInterval13.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `ReferenceBasePredictorInterval13Base.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `GeneConstraintsInterval13.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `ESTInterval13.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`void` | `BlastInterval13.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`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` | `StateLengthLogprobInterval13.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)`

Uses of FeatureList in calhoun.analysis.crf.features.interval29

Methods in calhoun.analysis.crf.features.interval29 with parameters of type FeatureList
`void` | `StateTransitionsInterval29.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `PWMInterval29.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)`
`void` | `GeneConstraintsInterval29.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `ESTInterval29.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `ReferenceBasePredictorInterval29Base.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `GeneConstraintsInterval29.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `ESTInterval29.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`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` | `StateLengthLogprobInterval29.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)`

Uses of FeatureList in calhoun.analysis.crf.features.tricycle13

Methods in calhoun.analysis.crf.features.tricycle13 with parameters of type FeatureList
`void` | `PositionWeightMatrixFeatures.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)`
`void` | `MaxentMotifFeatures.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int previousState, int state, FeatureList result)`
`void` | `GeneConstraints.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `CodingStopFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int ix, int prevState, int state, FeatureList result)`
`void` | `PWM_evolution.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int previousState, int state, FeatureList result)`
`void` | `ESTEdge.evaluateEdge(InputSequence<? extends CompositeInput> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `KmerFeatures.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `EmissionMarkovFeature.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `PfamPhase.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`void` | `PfamGenic.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`void` | `ESTIntron.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`void` | `ESTExon.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`void` | `ESTEdge.evaluateNode(InputSequence<? extends CompositeInput> seq, int pos, int state, FeatureList result)`
`void` | `IntervalPresenceFeatures.evaluateNode(InputSequence<? extends IntervalInputSequence.IntervalPosition> seq, int pos, int state, FeatureList result)`
`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` | `IntronLengthFeature.evaluateNodeLength(InputSequence seq, int pos, int length, int state, FeatureList result)`

Uses of FeatureList in calhoun.analysis.crf.test

Methods in calhoun.analysis.crf.test with parameters of type FeatureList
`void` | `TestFeatures.ExplicitHalfExponentialLengthFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `TestFeatures.ExponentialLengthFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `TestFeatures.HalfExponentialLengthFeature.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `GeneConstraintsToy.evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result)`
`void` | `ConstraintTest.FixedEdges.evaluateEdge(InputSequence seq, int pos, int prevState, int state, FeatureList result)`
`void` | `TestFeatures.EmissionFeature.evaluateNode(InputSequence<? extends java.lang.Character> seq, int pos, int state, FeatureList result)`
`void` | `TestFeatures.GaussianLengthFeature.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)`
`void` | `TestFeatures.ExplicitHalfExponentialLengthFeature.evaluateNodeLength(InputSequence<? extends java.lang.Character> seq, int pos, int length, int state, FeatureList result)`

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