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| 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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