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## Uses of Interface
calhoun.analysis.crf.FeatureManagerNode

Packages that use FeatureManagerNode
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 FeatureManagerNode in calhoun.analysis.crf

Subinterfaces of FeatureManagerNode in calhoun.analysis.crf
`interface` | `FeatureManagerNodeBoundaries<InputType>` An extension of FeatureManagerNode for situations where the nodes use in semi-markov models is non-standard.
`interface` | `ModelManager` overall itnerface for an entire model.

Classes in calhoun.analysis.crf that implement FeatureManagerNode
`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 FeatureManagerNode in calhoun.analysis.crf.features.generic

Classes in calhoun.analysis.crf.features.generic that implement FeatureManagerNode
`class` | `EndFeatures` indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.
`class` | `StartFeatures` indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.

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

Classes in calhoun.analysis.crf.features.interval13 that implement FeatureManagerNode
`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` | `ReferenceBasePredictorInterval13`
`class` | `ReferenceBasePredictorNodeOnlyInterval13`
`class` | `ReferenceBasePredictorZeroPadInterval13`

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

Classes in calhoun.analysis.crf.features.interval29 that implement FeatureManagerNode
`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` | `ReferenceBasePredictorInterval29`
`class` | `ReferenceBasePredictorNodeOnlyInterval29`
`class` | `ReferenceBasePredictorZeroPadInterval29`

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

Classes in calhoun.analysis.crf.features.tricycle13 that implement FeatureManagerNode
`class` | `EmissionMarkovFeature`
`class` | `ESTEdge`
`class` | `ESTExon`
`class` | `ESTIntron`
`class` | `FelsensteinFeatures`
`class` | `GapConjunctionFeatures`
`class` | `IntervalPresenceFeatures`
`class` | `KmerFeatures` trains on the data and then evaluates to P(state | label) for given Kmers.
`class` | `PfamGenic`
`class` | `PfamPhase`

Uses of FeatureManagerNode in calhoun.analysis.crf.test

Classes in calhoun.analysis.crf.test that implement FeatureManagerNode
`static class` | `TestFeatures.EmissionFeature`
`class` | `ZeroOrderManager`
`class` | `ZeroOrderModel`

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