Uses of Class
calhoun.analysis.crf.AbstractFeatureManager

Packages that use AbstractFeatureManager

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 AbstractFeatureManager in calhoun.analysis.crf

Subclasses of AbstractFeatureManager in calhoun.analysis.crf

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.

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

Subclasses of AbstractFeatureManager in calhoun.analysis.crf.features.generic

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 AbstractFeatureManager in calhoun.analysis.crf.features.interval13

Subclasses of AbstractFeatureManager in calhoun.analysis.crf.features.interval13

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	StateTransitionsInterval13

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

Subclasses of AbstractFeatureManager in calhoun.analysis.crf.features.interval29

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	StateTransitionsInterval29

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

Subclasses of AbstractFeatureManager in calhoun.analysis.crf.features.tricycle13

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 AbstractFeatureManager in calhoun.analysis.crf.test

Subclasses of AbstractFeatureManager in calhoun.analysis.crf.test

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