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## 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`

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