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## 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`

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