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 (CLL) 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 that creates a new CLLClassifier from a given parameter set, a prior and ScoringFunctions for the classes.

CLLClassifier(CLLClassifierParameterSet params, ScoringFunction... score)
The default constructor that creates a new CLLClassifier from a given parameter set and ScoringFunctions for the classes.

CLLClassifier(StringBuffer xml)
The standard constructor for the interface Storable.

Method Summary

CLLClassifier	clone()
static CLLClassifier[]	create(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction[]... functions) This method creates an array of CLLClassifiers 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 that 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 String	getXMLTag() Returns the String that is used as tag for the XML representation of the classifier.
void	setPrior(LogPrior prior) This method sets a new prior that should be used for optimization.

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

createStructure, doOptimization, getClassifierAnnotation, getLastScore, getNumericalCharacteristics, getScore, 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 that creates a new CLLClassifier from a given parameter set and ScoringFunctions for the classes.

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

See Also:

CLLClassifier(CLLClassifierParameterSet, LogPrior, ScoringFunction...)

CLLClassifier

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

The default constructor that creates a new CLLClassifier from a given parameter set, a prior and ScoringFunctions for the classes.

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

See Also:

ScoreClassifier.ScoreClassifier(de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet, ScoringFunction...), setPrior(LogPrior)

CLLClassifier

public CLLClassifier(StringBuffer xml)
              throws NonParsableException

The standard constructor for the interface Storable. Constructs a CLLClassifier out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the CLLClassifier could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

ScoreClassifier.ScoreClassifier(StringBuffer), Storable

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 that 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 that should be optimized

Throws:

Exception - if something went wrong

setPrior

public void setPrior(LogPrior prior)

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

Parameters:

prior - the new prior

See Also:

ScoreClassifier.hasBeenOptimized()

getXMLTag

protected String getXMLTag()

Description copied from class: AbstractClassifier

Returns the String that is used as tag for the XML representation of the classifier. This method is used by the methods AbstractClassifier.fromXML(StringBuffer) and AbstractClassifier.toXML().

Specified by:

getXMLTag in class ScoreClassifier

Returns:

the String that is used as tag for the XML representation of the classifier

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 AbstractClassifier.toXML() and should not be made public.

Overrides:

getFurtherClassifierInfos in class ScoreClassifier

Returns:

further information of a classifier as a StringBuffer

See Also:

AbstractClassifier.toXML()

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 AbstractClassifier.fromXML(StringBuffer) and should not be made public.

Overrides:

extractFurtherClassifierInfosFromXML in class ScoreClassifier

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the information could not be parsed out of the XML representation (the StringBuffer could not be parsed)

See Also:

AbstractClassifier.fromXML(StringBuffer)

create

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

This method creates an array of CLLClassifiers 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 CLLClassifiers

Throws:

CloneNotSupportedException - if 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