calhoun.analysis.crf.features.tricycle13
Class IntronLengthFeature

java.lang.Object
  calhoun.analysis.crf.AbstractFeatureManager
      calhoun.analysis.crf.features.tricycle13.IntronLengthFeature

All Implemented Interfaces:

FeatureManager, FeatureManagerNodeExplicitLength, java.io.Serializable

public class IntronLengthFeature
extends AbstractFeatureManager
implements FeatureManagerNodeExplicitLength

Learns from data an explicit length distribution for introns, and also subtracts out what it would have gotten from just the exponential distribution given by DenseWeightedEdgeFeatures.

See Also:

Serialized Form

Constructor Summary

IntronLengthFeature()

Method Summary

void	evaluateNodeLength(InputSequence seq, int pos, int length, int state, FeatureList result)
java.lang.String	getFeatureName(int featureIndex) Returns a human identifiable name for the feature referenced by a given index.
int	getNumFeatures() Returns the number of features maintained by this FeatureManager.
void	train(int startingIndex, ModelManager modelInfo, java.util.List data) Provides access to the entire training set so that FeatureManager can compute global properties and assign feature indices.

Methods inherited from class calhoun.analysis.crf.AbstractFeatureManager

getCacheStrategy, 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.FeatureManager

getCacheStrategy, getInputComponent, setInputComponent

Constructor Detail

IntronLengthFeature

public IntronLengthFeature()

Method Detail

getFeatureName

public java.lang.String getFeatureName(int featureIndex)

Description copied from interface: FeatureManager

Returns a human identifiable name for the feature referenced by a given index. Used for display purposes only.

Specified by:

getFeatureName in interface FeatureManager

Parameters:

featureIndex - the index of this feature

Returns:

the human readable name of this feature

getNumFeatures

public int getNumFeatures()

Description copied from interface: FeatureManager

Returns the number of features maintained by this FeatureManager. This number must be fixed after the call to trainFeatures is complete.

Specified by:

getNumFeatures in interface FeatureManager

Returns:

number of features managed by this FeatureManager

evaluateNodeLength

public void evaluateNodeLength(InputSequence seq,
                               int pos,
                               int length,
                               int state,
                               FeatureList result)

Specified by:

evaluateNodeLength in interface FeatureManagerNodeExplicitLength

train

public void train(int startingIndex,
                  ModelManager modelInfo,
                  java.util.List data)

Description copied from interface: FeatureManager

Provides access to the entire training set so that FeatureManager can compute global properties and assign feature indices. This will be called before any evaluations are requested. If the FeatureManager can have a variable number of features, this must be fixed within this method.

Specified by:

train in interface FeatureManager

Parameters:

startingIndex - the feature index of the first feature owned by this FeatureManager. Each FeatureManager must use up consecutive indexes, so the last index used will be startingIndex + numFeatures - 1.

modelInfo - the model that contains this feature

data - the full list of training sequences to use to train the feature