Uses of Interface
calhoun.analysis.crf.FeatureManagerEdge

Packages that use FeatureManagerEdge

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 FeatureManagerEdge in calhoun.analysis.crf

Subinterfaces of FeatureManagerEdge in calhoun.analysis.crf

interface

ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf that implement FeatureManagerEdge

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 FeatureManagerEdge in calhoun.analysis.crf.features.generic

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

class	IndicatorEdges a set of indicator features for the valid transitions in the model.
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 FeatureManagerEdge in calhoun.analysis.crf.features.interval13

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

class	ESTInterval13
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	PWMInterval13
class	StateTransitionsInterval13

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

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

class	ESTInterval29
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	StateTransitionsInterval29

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

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

class	CodingStopFeature
class	ESTEdge
class	GeneConstraints lmplements basic constraints on gene calls.
class	MaxentMotifFeatures
class	PositionWeightMatrixFeatures
class	PWM_evolution

Uses of FeatureManagerEdge in calhoun.analysis.crf.test

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

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.ExplicitHalfExponentialLengthFeature
static class	TestFeatures.ExponentialLengthFeature
static class	TestFeatures.HalfExponentialLengthFeature
class	ZeroOrderManager
class	ZeroOrderModel