Uses of Interface
calhoun.analysis.crf.FeatureManager

Packages that use FeatureManager

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 FeatureManager in calhoun.analysis.crf

Subinterfaces of FeatureManager in calhoun.analysis.crf

interface	FeatureManagerEdge<InputType> holds features whose value depends on the current state and the previous state.
interface	FeatureManagerEdgeExplicitLength<InputType> Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
interface	FeatureManagerNode<InputType> holds features whose value only depends on the current state, and not the previous state.
interface	FeatureManagerNodeBoundaries<InputType> An extension of FeatureManagerNode for situations where the nodes use in semi-markov models is non-standard.
interface	FeatureManagerNodeExplicitLength<InputType> Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
interface	ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf that implement FeatureManager

class	AbstractFeatureManager<InputType> base class for feature implementations.
class	BeanModel a useful base class for creating model beans.
class	CompositeFeatureManager a feature manager that combines feature types together.
class	ConstrainedFeatureManager a feature manager that combines it's composite feature types together into a single feature.

Methods in calhoun.analysis.crf that return types with arguments of type FeatureManager

java.util.List<FeatureManager>

CompositeFeatureManager.getComponentFeatures()

Methods in calhoun.analysis.crf with parameters of type FeatureManager

void	CompositeFeatureManager.addFeatureManager(FeatureManager fm)
void	CompositeFeatureManager.addFeatureManager(java.lang.String name, java.lang.String inputParams, FeatureManager fm)

Method parameters in calhoun.analysis.crf with type arguments of type FeatureManager

void	CompositeFeatureManager.setComponentFeatures(java.util.List<FeatureManager> components)

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

Classes in calhoun.analysis.crf.features.generic that implement FeatureManager

class	EndFeatures indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.
class	IndicatorEdges a set of indicator features for the valid transitions in the model.
class	StartFeatures indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.
class	WeightedEdges learns transition probabilities from the data and then creates a single feature for all edge transitions.
class	WeightedStateChanges learns transition probabilities from the data and then creates a single feature for all edge transitions out of a given state.

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

Classes in calhoun.analysis.crf.features.interval13 that implement FeatureManager

class	BlastInterval13
class	ESTInterval13
class	FootprintsInterval13
class	GapFeaturesInterval13
class	GeneConstraintsInterval13 Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
class	Interval13Model
class	PhylogeneticLogprobInterval13
class	PWMInterval13
class	ReferenceBasePredictorInterval13
class	ReferenceBasePredictorInterval13Base
class	ReferenceBasePredictorNodeOnlyInterval13
class	ReferenceBasePredictorZeroPadInterval13
class	StateLengthLogprobInterval13
class	StateTransitionsInterval13

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

Classes in calhoun.analysis.crf.features.interval29 that implement FeatureManager

class	ESTInterval29
class	FootprintsInterval29
class	GapFeaturesInterval29
class	GeneConstraintsInterval29 Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
class	Interval29Model
class	PWMInterval29
class	ReferenceBasePredictorInterval29
class	ReferenceBasePredictorInterval29Base
class	ReferenceBasePredictorNodeOnlyInterval29
class	ReferenceBasePredictorZeroPadInterval29
class	StateLengthLogprobInterval29
class	StateTransitionsInterval29

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

Classes in calhoun.analysis.crf.features.tricycle13 that implement FeatureManager

class	CodingStopFeature
class	EmissionMarkovFeature
class	ESTEdge
class	ESTExon
class	ESTIntron
class	FelsensteinFeatures
class	GapConjunctionFeatures
class	GeneConstraints lmplements basic constraints on gene calls.
class	IntervalPresenceFeatures
class	IntronLengthFeature Learns from data an explicit length distribution for introns, and also subtracts out what it would have gotten from just the exponential distribution given by DenseWeightedEdgeFeatures.
class	KmerFeatures trains on the data and then evaluates to P(state | label) for given Kmers.
class	MaxentMotifFeatures
class	PfamGenic
class	PfamPhase
class	PositionWeightMatrixFeatures
class	PWM_evolution

Uses of FeatureManager in calhoun.analysis.crf.test

Classes in calhoun.analysis.crf.test that implement FeatureManager

static class	ConstraintTest.FixedEdges Edge class used for testing that favors changing states whenever possible.
class	GeneConstraintsToy Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
static class	TestFeatures.EmissionFeature
static class	TestFeatures.ExplicitHalfExponentialLengthFeature
static class	TestFeatures.ExponentialLengthFeature
static class	TestFeatures.GaussianLengthFeature
static class	TestFeatures.HalfExponentialLengthFeature
static class	TestFeatures.TestFeature
class	ZeroOrderManager
class	ZeroOrderModel