de.jstacs.classifier.scoringFunctionBased.cll
Class CLLClassifier

java.lang.Object
  de.jstacs.classifier.AbstractClassifier
      de.jstacs.classifier.AbstractScoreBasedClassifier
          de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
              de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier

All Implemented Interfaces:

Storable, Cloneable

public class CLLClassifier
extends ScoreClassifier

This class implements the conditional log likelihood classifier.

Author:

Jens Keilwagen, Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.classifier.AbstractScoreBasedClassifier

AbstractScoreBasedClassifier.DoubleTableResult

Field Summary

protected LogPrior

prior The prior that is used in this instance.

Fields inherited from class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier

hasBeenOptimized, params, score, sostream

Constructor Summary

CLLClassifier(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction... score)
The default constructor.

CLLClassifier(CLLClassifierParameterSet params, ScoringFunction... score)
The default constructor.

CLLClassifier(StringBuffer xml)
This is the constructor for Storable.

Method Summary

CLLClassifier	clone()
static CLLClassifier[]	create(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction[]... functions) This method creates an array of CLLClassifier by using the cross-product of the given ScoringFunctions.
protected void	extractFurtherClassifierInfosFromXML(StringBuffer xml) Extracts further information of a classifier from an xml-representation.
protected NormConditionalLogLikelihood	getFunction(Sample[] data, double[][] weights) Returns the function the should be optimized
protected StringBuffer	getFurtherClassifierInfos() This method returns further information of a classifier as a StringBuffer.
String	getInstanceName() Returns a short description of the classifier.
protected double	getScore(Sequence seq, int i, boolean check) This method returns the score for a given sequence and a given class.
protected String	getXMLTag() Returns the String that is used as tag for the xml-representation.
void	setPrior(LogPrior prior) This method set a new prior that should be used for optimization.

Methods inherited from class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier

createStructure, doOptimization, getClassifierAnnotation, getLastScore, getNumericalCharacteristics, getScoringFunction, getScoringFunctions, hasBeenOptimized, isTrained, setOutputStream, train

Methods inherited from class de.jstacs.classifier.AbstractScoreBasedClassifier

check, check, classify, classify, createDefaultClassWeights, getClassWeight, getClassWeights, getNumberOfClasses, getPValue, getPValue, getResults, getScore, getScores, setClassWeights, setThresholdClassWeights, test

Methods inherited from class de.jstacs.classifier.AbstractClassifier

classify, evaluate, evaluateAll, getAlphabetContainer, getCharacteristics, getClassificationRate, getLength, getMeasuresForEvaluate, getMeasuresForEvaluateAll, setNewAlphabetContainerInstance, toXML, train

Methods inherited from class java.lang.Object

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

Field Detail

prior

protected LogPrior prior

The prior that is used in this instance.

Constructor Detail

CLLClassifier

public CLLClassifier(CLLClassifierParameterSet params,
                     ScoringFunction... score)
              throws CloneNotSupportedException

The default constructor.

Parameters:

params - the parameter set for the classifier

score - the ScoringFunctions for the classes

Throws:

CloneNotSupportedException - if at least one ScoringFunction could not be cloned

CLLClassifier

public CLLClassifier(CLLClassifierParameterSet params,
                     LogPrior prior,
                     ScoringFunction... score)
              throws CloneNotSupportedException

The default constructor.

Parameters:

params - the parameter set for the classifier

prior - the prior that shall be used

score - the ScoringFunctions for the classes

Throws:

CloneNotSupportedException - if at least one ScoringFunction could not be cloned

CLLClassifier

public CLLClassifier(StringBuffer xml)
              throws NonParsableException

This is the constructor for Storable.

Parameters:

xml - the xml representation

Throws:

NonParsableException - if the representation could not be parsed.

Method Detail

clone

public CLLClassifier clone()
                    throws CloneNotSupportedException

Overrides:

clone in class ScoreClassifier

Throws:

CloneNotSupportedException

getFunction

protected NormConditionalLogLikelihood getFunction(Sample[] data,
                                                   double[][] weights)
                                            throws Exception

Description copied from class: ScoreClassifier

Returns the function the should be optimized

Specified by:

getFunction in class ScoreClassifier

Parameters:

data - the samples

weights - the weights of the sequences of the samples

Returns:

the function the should be optimized

Throws:

Exception - if something went wrong

setPrior

public void setPrior(LogPrior prior)

This method set a new prior that should be used for optimization. Since it could not be ensured that the classifier is optimal now hasBeenOptimized will return false after invokating this method.

Parameters:

prior - the new prior

getXMLTag

protected String getXMLTag()

Description copied from class: AbstractClassifier

Returns the String that is used as tag for the xml-representation. This method is used by the methods fromXML( StringBuffer ) and toXML().

Specified by:

getXMLTag in class ScoreClassifier

Returns:

the String that is used as tag for the xml-representation

getFurtherClassifierInfos

protected StringBuffer getFurtherClassifierInfos()

Description copied from class: AbstractClassifier

This method returns further information of a classifier as a StringBuffer. This method is used by the method toXML() and should not be made public.

Overrides:

getFurtherClassifierInfos in class ScoreClassifier

Returns:

further information of a classifier as a StringBuffer

extractFurtherClassifierInfosFromXML

protected void extractFurtherClassifierInfosFromXML(StringBuffer xml)
                                             throws NonParsableException

Description copied from class: AbstractClassifier

Extracts further information of a classifier from an xml-representation. This method is used by the method fromXML( StringBuffer ) and should not be made public.

Overrides:

extractFurtherClassifierInfosFromXML in class ScoreClassifier

Parameters:

xml - the xml-representation

Throws:

NonParsableException

getScore

protected double getScore(Sequence seq,
                          int i,
                          boolean check)
                   throws IllegalArgumentException,
                          NotTrainedException,
                          Exception

Description copied from class: AbstractScoreBasedClassifier

This method returns the score for a given sequence and a given class.

Overrides:

getScore in class ScoreClassifier

Parameters:

seq - the sequence

i - the index of the class

check - the switch to decide whether to check AlphabetContainer and length of the sequence or not

Returns:

the score

Throws:

IllegalArgumentException

NotTrainedException

Exception

create

public static CLLClassifier[] create(CLLClassifierParameterSet params,
                                     LogPrior prior,
                                     ScoringFunction[]... functions)
                              throws CloneNotSupportedException

This method creates an array of CLLClassifier by using the cross-product of the given ScoringFunctions.

Parameters:

params - the parameters that will be used in all classifiers

prior - the prior that will be used in all classifiers

functions - the ScoringFunctions

1. functions[i] are the ScoringFunctions that can be used for class i
2. functions.length has to be at least 2

Returns:

an array of CLLClassifier

Throws:

CloneNotSupportedException - if the some item could not be cloned

getInstanceName

public String getInstanceName()

Description copied from class: AbstractClassifier

Returns a short description of the classifier.

Overrides:

getInstanceName in class ScoreClassifier

Returns:

a short description of the classifier