calhoun.analysis.crf.features.tricycle13
Class GeneConstraints

java.lang.Object
  calhoun.analysis.crf.AbstractFeatureManager<java.lang.Character>
      calhoun.analysis.crf.features.tricycle13.GeneConstraints

All Implemented Interfaces:

FeatureManager<java.lang.Character>, FeatureManagerEdge<java.lang.Character>, java.io.Serializable

public class GeneConstraints
extends AbstractFeatureManager<java.lang.Character>
implements FeatureManagerEdge<java.lang.Character>

lmplements basic constraints on gene calls.

1. Transition from intergenic to start must occur at ATG
2. Splice sites must be canonical GT/AG or GC/AG
3. Transition from exon to stop must be followed by a stop codon

See Also:

Serialized Form

Constructor Summary

GeneConstraints()

Method Summary

void	evaluateEdge(InputSequence<? extends java.lang.Character> seq, int pos, int prevState, int state, FeatureList result) Evaluates the set of features managed by this object for the given arguments.
java.lang.String	getFeatureName(int featureIndex) Returns a human identifiable name for the feature referenced by a given index.
int	getNumFeatures() This is a constraint class, so we don't return features
void	train(int startingIndex, ModelManager modelInfo, java.util.List<? extends TrainingSequence<? extends java.lang.Character>> data) Set up the matrix Depends on states starting with the words 'intergenic, intron, and exon'.

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

GeneConstraints

public GeneConstraints()

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<java.lang.Character>

Parameters:

featureIndex - the index of this feature

Returns:

the human readable name of this feature

getNumFeatures

public int getNumFeatures()

This is a constraint class, so we don't return features

Specified by:

getNumFeatures in interface FeatureManager<java.lang.Character>

Returns:

number of features managed by this FeatureManager

train

public void train(int startingIndex,
                  ModelManager modelInfo,
                  java.util.List<? extends TrainingSequence<? extends java.lang.Character>> data)

Set up the matrix Depends on states starting with the words 'intergenic, intron, and exon'. Also depends on the negative strand states ending in m.

Specified by:

train in interface FeatureManager<java.lang.Character>

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

evaluateEdge

public void evaluateEdge(InputSequence<? extends java.lang.Character> seq,
                         int pos,
                         int prevState,
                         int state,
                         FeatureList result)

Description copied from interface: FeatureManagerEdge

Evaluates the set of features managed by this object for the given arguments.

Specified by:

evaluateEdge in interface FeatureManagerEdge<java.lang.Character>