calhoun.analysis.crf
Class BeanModel

java.lang.Object
  calhoun.analysis.crf.AbstractFeatureManager
      calhoun.analysis.crf.CompositeFeatureManager
          calhoun.analysis.crf.BeanModel

All Implemented Interfaces:

FeatureManager, FeatureManagerEdge, FeatureManagerEdgeExplicitLength, FeatureManagerNode, FeatureManagerNodeExplicitLength, ModelManager, java.io.Serializable

Direct Known Subclasses:

Interval13Model, Interval29Model, ZeroOrderModel

public class BeanModel
extends CompositeFeatureManager
implements ModelManager

a useful base class for creating model beans. Defines internal Node and Edge class that can be used to define a hidden state model for the CRF. The actual state diagram could be implemented through a derived class or through setup of the model in the XML model file. Because XML configuration of a state model is verbose and because the state diagram is central to most models, we recommend using a derived class to set up the model, as we have done with gene calling.

See Also:

Serialized Form

Nested Class Summary

static class	BeanModel.Edge an edge in the hidden state diagram.
static class	BeanModel.Node a hidden state.

Constructor Summary

BeanModel()

Method Summary

DenseBooleanMatrix2D	getLegalTransitions() returns a boolean matrix where each (row, column) entry contains true if the model has a legal transition between state row and state column.
int	getNumStates() the number of hidden states.
int	getStateIndex(java.lang.String name) looks up a hidden state's index given it's human readable name.
java.lang.String	getStateName(int state) looks up the human readable name of a hidden state given it's index.
void	setEdges(java.util.List<BeanModel.Edge> edges) sets the list of legal state transitions in this model.
void	setNodes(java.util.List<BeanModel.Node> nodes) sets the list of hidden states in this model.

Methods inherited from class calhoun.analysis.crf.CompositeFeatureManager

addFeatureManager, addFeatureManager, evaluateEdge, evaluateEdgeLength, evaluateNode, evaluateNodeLength, getCacheStrategy, getComponentFeatures, getFeatureName, getFeatureOffset, getNumFeatures, setComponentFeatures, train

Methods inherited from class calhoun.analysis.crf.AbstractFeatureManager

getInputComponent, setInputComponent

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface calhoun.analysis.crf.FeatureManagerEdge

evaluateEdge

Methods inherited from interface calhoun.analysis.crf.FeatureManager

getCacheStrategy, getFeatureName, getInputComponent, getNumFeatures, setInputComponent, train

Methods inherited from interface calhoun.analysis.crf.FeatureManagerNode

evaluateNode

Methods inherited from interface calhoun.analysis.crf.FeatureManager

getCacheStrategy, getFeatureName, getInputComponent, getNumFeatures, setInputComponent, train

Methods inherited from interface calhoun.analysis.crf.FeatureManagerEdgeExplicitLength

evaluateEdgeLength

Methods inherited from interface calhoun.analysis.crf.FeatureManager

getCacheStrategy, getFeatureName, getInputComponent, getNumFeatures, setInputComponent, train

Methods inherited from interface calhoun.analysis.crf.FeatureManagerNodeExplicitLength

evaluateNodeLength

Methods inherited from interface calhoun.analysis.crf.FeatureManager

getCacheStrategy, getFeatureName, getInputComponent, getNumFeatures, setInputComponent, train

Constructor Detail

BeanModel

public BeanModel()

Method Detail

setNodes

public void setNodes(java.util.List<BeanModel.Node> nodes)

sets the list of hidden states in this model. This will usually be called by a derived class or by the Spring configuration.

Parameters:

nodes - the list of hidden states in the model

setEdges

public void setEdges(java.util.List<BeanModel.Edge> edges)

sets the list of legal state transitions in this model. This will usually be called by a derived class or by the Spring configuration.

Parameters:

edges - the list of valid state transitions in the model

getNumStates

public int getNumStates()

Description copied from interface: ModelManager

the number of hidden states.

Specified by:

getNumStates in interface ModelManager

Returns:

the number of hidden states

getStateName

public java.lang.String getStateName(int state)

Description copied from interface: ModelManager

looks up the human readable name of a hidden state given it's index.

Specified by:

getStateName in interface ModelManager

Returns:

string name of the state with this index.

getStateIndex

public int getStateIndex(java.lang.String name)

Description copied from interface: ModelManager

looks up a hidden state's index given it's human readable name.

Specified by:

getStateIndex in interface ModelManager

Returns:

index of the state with this name.

getLegalTransitions

public DenseBooleanMatrix2D getLegalTransitions()

Description copied from interface: ModelManager

returns a boolean matrix where each (row, column) entry contains true if the model has a legal transition between state row and state column. A ModelManager may safely return null if all transitions are legal.

Specified by:

getLegalTransitions in interface ModelManager

Returns:

a boolean matrix containing the legal transitions.