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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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