calhoun.analysis.crf
Class AbstractFeatureManager<InputType>

java.lang.Object
  calhoun.analysis.crf.AbstractFeatureManager<InputType>

All Implemented Interfaces:

FeatureManager<InputType>, java.io.Serializable

Direct Known Subclasses:

BlastInterval13, CodingStopFeature, CompositeFeatureManager, ConstraintTest.FixedEdges, EmissionMarkovFeature, EndFeatures, ESTEdge, ESTExon, ESTInterval13, ESTInterval29, ESTIntron, FelsensteinFeatures, FootprintsInterval13, FootprintsInterval29, GapConjunctionFeatures, GapFeaturesInterval13, GapFeaturesInterval29, GeneConstraints, GeneConstraintsInterval13, GeneConstraintsInterval29, GeneConstraintsToy, IndicatorEdges, IntervalPresenceFeatures, IntronLengthFeature, KmerFeatures, MaxentMotifFeatures, PfamGenic, PfamPhase, PhylogeneticLogprobInterval13, PositionWeightMatrixFeatures, PWM_evolution, PWMInterval13, PWMInterval29, ReferenceBasePredictorInterval13Base, ReferenceBasePredictorInterval29Base, StartFeatures, StateTransitionsInterval13, StateTransitionsInterval29, TestFeatures.TestFeature, WeightedEdges, WeightedStateChanges

public abstract class AbstractFeatureManager<InputType>
extends java.lang.Object
implements FeatureManager<InputType>

base class for feature implementations. Takes care of some of the details and bookkeeping involved in writing a feature.

See Also:

Serialized Form

Constructor Summary

AbstractFeatureManager()

Method Summary

CacheStrategySpec	getCacheStrategy() caching strategy that the CacheProcessor should use to cache values for this feature.
java.lang.String	getInputComponent() Specifies the particular component of the input which this feature manager uses, if the input data is a composite input which has multiple components.
void	setInputComponent(java.lang.String inputComponent) Sets which particular component of a CompositeInput this FeatureManager has access to.

Methods inherited from class java.lang.Object

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

Methods inherited from interface calhoun.analysis.crf.FeatureManager

getFeatureName, getNumFeatures, train

Constructor Detail

AbstractFeatureManager

public AbstractFeatureManager()

Method Detail

getCacheStrategy

public CacheStrategySpec getCacheStrategy()

Description copied from interface: FeatureManager

caching strategy that the CacheProcessor should use to cache values for this feature. This is only a hint, the cache processor is not required to use this (or any) caching strategy. This base class defaults to the UNSPECIFIED cache strategy.

Specified by:

getCacheStrategy in interface FeatureManager<InputType>

Returns:

cache strategy specification appropriate for this feature.

getInputComponent

public java.lang.String getInputComponent()

Description copied from interface: FeatureManager

Specifies the particular component of the input which this feature manager uses, if the input data is a composite input which has multiple components. May be null if the input is not a composite or if the feature manager has access to all of the input. See the Conrad User's Guide for how to set up input data.

Specified by:

getInputComponent in interface FeatureManager<InputType>

Returns:

string name of the input component this feature should look at, or null if the feature has access to all inputs.

setInputComponent

public void setInputComponent(java.lang.String inputComponent)

Description copied from interface: FeatureManager

Sets which particular component of a CompositeInput this FeatureManager has access to.

Specified by:

setInputComponent in interface FeatureManager<InputType>

Parameters:

inputComponent - name of the component of the CompositeInput this FeatureManager has access to. Usually set automatically during configuration.