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## Uses of Package
calhoun.analysis.crf

Packages that use calhoun.analysis.crf
calhoun.analysis.crf | the interface, main `Conrad` class, and solver for the Conrad engine.
calhoun.analysis.crf.executables.viewer | prototype of a viewing utility for examiining the results of inference.
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.supporting.phylogenetic | utility classes for phylogenetic analysis
calhoun.analysis.crf.features.tricycle13 | basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.io | handles input and output of gene calling formats
calhoun.analysis.crf.scoring | local similarity functions used in gene calling models
calhoun.analysis.crf.solver | training and inference algorithms used in the CRF engine
calhoun.analysis.crf.solver.semimarkov |
calhoun.analysis.crf.test |

Classes in calhoun.analysis.crf used by calhoun.analysis.crf
AbstractFeatureManager base class for feature implementations.
BeanModel.Edge an edge in the hidden state diagram.
BeanModel.Node a hidden state.
CacheStrategySpec
CacheStrategySpec.CacheStrategy
CacheStrategySpec.DenseBoundaryEntry
CompositeFeatureManager a feature manager that combines feature types together.
Conrad the central class for the Conrad engine.
CRFInference an interface to inference algorithms for CRFs.
CRFInference.InferenceResult holder which contains the results of an inference run.
CRFTraining an interface to numerical solvers for optimizing the CRF objective function.
FeatureList used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager evaluates CRF feature functions on the model.
FeatureManagerEdge holds features whose value depends on the current state and the previous state.
FeatureManagerEdgeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
FeatureManagerNode holds features whose value only depends on the current state, and not the previous state.
FeatureManagerNodeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.executables.viewer
Conrad the central class for the Conrad engine.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.features.generic
AbstractFeatureManager base class for feature implementations.
CacheStrategySpec
FeatureList used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager evaluates CRF feature functions on the model.
FeatureManagerEdge holds features whose value depends on the current state and the previous state.
FeatureManagerNode holds features whose value only depends on the current state, and not the previous state.
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.features.interval13
AbstractFeatureManager base class for feature implementations.
BeanModel a useful base class for creating model beans.
CacheStrategySpec
CompositeFeatureManager a feature manager that combines feature types together.
FeatureList used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager evaluates CRF feature functions on the model.
FeatureManagerEdge holds features whose value depends on the current state and the previous state.
FeatureManagerEdgeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
FeatureManagerNode holds features whose value only depends on the current state, and not the previous state.
FeatureManagerNodeBoundaries An extension of FeatureManagerNode for situations where the nodes use in semi-markov models is non-standard.
FeatureManagerNodeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.features.interval29
AbstractFeatureManager base class for feature implementations.
BeanModel a useful base class for creating model beans.
CacheStrategySpec
CompositeFeatureManager a feature manager that combines feature types together.
FeatureList used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager evaluates CRF feature functions on the model.
FeatureManagerEdge holds features whose value depends on the current state and the previous state.
FeatureManagerEdgeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
FeatureManagerNode holds features whose value only depends on the current state, and not the previous state.
FeatureManagerNodeBoundaries An extension of FeatureManagerNode for situations where the nodes use in semi-markov models is non-standard.
FeatureManagerNodeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.features.supporting.phylogenetic
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.features.tricycle13
AbstractFeatureManager base class for feature implementations.
BeanModel.Node a hidden state.
CacheStrategySpec
FeatureList used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager evaluates CRF feature functions on the model.
FeatureManagerEdge holds features whose value depends on the current state and the previous state.
FeatureManagerNode holds features whose value only depends on the current state, and not the previous state.
FeatureManagerNodeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.io
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.scoring
LocalPathSimilarityScore interface for local scoring functions used by the local score gradient functions.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.solver
CacheStrategySpec.CacheStrategy
CRFInference an interface to inference algorithms for CRFs.
CRFInference.InferenceResult holder which contains the results of an inference run.
CRFObjectiveFunctionGradient an interface to algorithms that compute an objective function and its gradient for CRFs.
CRFTraining an interface to numerical solvers for optimizing the CRF objective function.
ModelManager overall itnerface for an entire model.
SemiMarkovSetup holds additional configuration information used in semi-Markov CRFs.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.solver.semimarkov
CRFObjectiveFunctionGradient an interface to algorithms that compute an objective function and its gradient for CRFs.
LocalPathSimilarityScore interface for local scoring functions used by the local score gradient functions.
ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf used by calhoun.analysis.crf.test
AbstractFeatureManager base class for feature implementations.
BeanModel a useful base class for creating model beans.
CacheStrategySpec
CompositeFeatureManager a feature manager that combines feature types together.
Conrad the central class for the Conrad engine.
FeatureList used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager evaluates CRF feature functions on the model.
FeatureManagerEdge holds features whose value depends on the current state and the previous state.
FeatureManagerEdgeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
FeatureManagerNode holds features whose value only depends on the current state, and not the previous state.
FeatureManagerNodeExplicitLength Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
ModelManager overall itnerface for an entire model.

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