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java.lang.Objectde.jstacs.classifier.AbstractClassifier
de.jstacs.classifier.AbstractScoreBasedClassifier
de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
public class CLLClassifier
This class implements the conditional log likelihood classifier.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.classifier.AbstractScoreBasedClassifier |
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AbstractScoreBasedClassifier.DoubleTableResult |
Field Summary | |
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protected LogPrior |
prior
The prior that is used in this instance. |
Fields inherited from class de.jstacs.classifier.scoringFunctionBased.ScoreClassifier |
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hasBeenOptimized, params, score, sostream |
Constructor Summary | |
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CLLClassifier(CLLClassifierParameterSet params,
LogPrior prior,
ScoringFunction... score)
The default constructor. |
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CLLClassifier(CLLClassifierParameterSet params,
ScoringFunction... score)
The default constructor. |
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CLLClassifier(StringBuffer xml)
This is the constructor for Storable . |
Method Summary | |
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CLLClassifier |
clone()
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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 |
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createStructure, doOptimization, getClassifierAnnotation, getLastScore, getNumericalCharacteristics, getScoringFunction, getScoringFunctions, hasBeenOptimized, isTrained, setOutputStream, train |
Methods inherited from class de.jstacs.classifier.AbstractScoreBasedClassifier |
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check, check, classify, classify, createDefaultClassWeights, getClassWeight, getClassWeights, getNumberOfClasses, getPValue, getPValue, getResults, getScore, getScores, setClassWeights, setThresholdClassWeights, test |
Methods inherited from class de.jstacs.classifier.AbstractClassifier |
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classify, evaluate, evaluateAll, getAlphabetContainer, getCharacteristics, getClassificationRate, getLength, getMeasuresForEvaluate, getMeasuresForEvaluateAll, setNewAlphabetContainerInstance, toXML, train |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected LogPrior prior
Constructor Detail |
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public CLLClassifier(CLLClassifierParameterSet params, ScoringFunction... score) throws CloneNotSupportedException
params
- the parameter set for the classifierscore
- the ScoringFunctions for the classes
CloneNotSupportedException
- if at least one ScoringFunction could not be clonedpublic CLLClassifier(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction... score) throws CloneNotSupportedException
params
- the parameter set for the classifierprior
- the prior that shall be usedscore
- the ScoringFunctions for the classes
CloneNotSupportedException
- if at least one ScoringFunction could not be clonedpublic CLLClassifier(StringBuffer xml) throws NonParsableException
Storable
.
xml
- the xml representation
NonParsableException
- if the representation could not be parsed.Method Detail |
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public CLLClassifier clone() throws CloneNotSupportedException
clone
in class ScoreClassifier
CloneNotSupportedException
protected NormConditionalLogLikelihood getFunction(Sample[] data, double[][] weights) throws Exception
ScoreClassifier
getFunction
in class ScoreClassifier
data
- the samplesweights
- the weights of the sequences of the samples
Exception
- if something went wrongpublic void setPrior(LogPrior prior)
hasBeenOptimized
will return false
after invokating this method.
prior
- the new priorprotected String getXMLTag()
AbstractClassifier
fromXML( StringBuffer )
and toXML()
.
getXMLTag
in class ScoreClassifier
protected StringBuffer getFurtherClassifierInfos()
AbstractClassifier
toXML()
and should not be made public.
getFurtherClassifierInfos
in class ScoreClassifier
protected void extractFurtherClassifierInfosFromXML(StringBuffer xml) throws NonParsableException
AbstractClassifier
fromXML( StringBuffer )
and should not be made public.
extractFurtherClassifierInfosFromXML
in class ScoreClassifier
xml
- the xml-representation
NonParsableException
protected double getScore(Sequence seq, int i, boolean check) throws IllegalArgumentException, NotTrainedException, Exception
AbstractScoreBasedClassifier
getScore
in class ScoreClassifier
seq
- the sequencei
- the index of the classcheck
- the switch to decide whether to check AlphabetContainer and length of the sequence or not
IllegalArgumentException
NotTrainedException
Exception
public static CLLClassifier[] create(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction[]... functions) throws CloneNotSupportedException
params
- the parameters that will be used in all classifiersprior
- the prior that will be used in all classifiersfunctions
- the ScoringFunctions
CloneNotSupportedException
- if the some item could not be clonedpublic String getInstanceName()
AbstractClassifier
getInstanceName
in class ScoreClassifier
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