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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 (CLL) 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, lastScore, params, score, sostream |
Constructor Summary | |
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CLLClassifier(CLLClassifierParameterSet params,
LogPrior prior,
ScoringFunction... score)
The default constructor that creates a new CLLClassifier from a
given parameter set, a prior and ScoringFunction s for the
classes. |
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CLLClassifier(CLLClassifierParameterSet params,
ScoringFunction... score)
The default constructor that creates a new CLLClassifier from a
given parameter set and ScoringFunction s for the classes. |
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CLLClassifier(StringBuffer xml)
The standard constructor for the interface 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 s by using the
cross-product of the given ScoringFunction s. |
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 |
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createStructure, doOptimization, getClassifierAnnotation, getLastScore, getNumericalCharacteristics, getScore, 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
CLLClassifier
from a
given parameter set and ScoringFunction
s for the classes.
params
- the parameter set for the classifierscore
- the ScoringFunction
s for the classes
CloneNotSupportedException
- if at least one ScoringFunction
could not be clonedCLLClassifier(CLLClassifierParameterSet, LogPrior,
ScoringFunction...)
public CLLClassifier(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction... score) throws CloneNotSupportedException
CLLClassifier
from a
given parameter set, a prior and ScoringFunction
s for the
classes.
params
- the parameter set for the classifierprior
- the prior that shall be usedscore
- the ScoringFunction
s for the classes
CloneNotSupportedException
- if at least one ScoringFunction
could not be clonedScoreClassifier.ScoreClassifier(de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet,
ScoringFunction...)
,
setPrior(LogPrior)
public CLLClassifier(StringBuffer xml) throws NonParsableException
Storable
.
Constructs a CLLClassifier
out of its XML representation.
xml
- the XML representation as StringBuffer
NonParsableException
- if the CLLClassifier
could not be reconstructed out
of the XML representation (the StringBuffer
could not
be parsed)ScoreClassifier.ScoreClassifier(StringBuffer)
,
Storable
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)
ScoreClassifier.hasBeenOptimized()
will return false
after invoking this method.
prior
- the new priorScoreClassifier.hasBeenOptimized()
protected String getXMLTag()
AbstractClassifier
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()
.
getXMLTag
in class ScoreClassifier
String
that is used as tag for the XML representation
of the classifierprotected StringBuffer getFurtherClassifierInfos()
AbstractClassifier
StringBuffer
. This method is used by the method AbstractClassifier.toXML()
and should not be made public.
getFurtherClassifierInfos
in class ScoreClassifier
StringBuffer
AbstractClassifier.toXML()
protected void extractFurtherClassifierInfosFromXML(StringBuffer xml) throws NonParsableException
AbstractClassifier
AbstractClassifier.fromXML(StringBuffer)
and
should not be made public.
extractFurtherClassifierInfosFromXML
in class ScoreClassifier
xml
- the XML representation as StringBuffer
NonParsableException
- if the information could not be parsed out of the XML
representation (the StringBuffer
could not be parsed)AbstractClassifier.fromXML(StringBuffer)
public static CLLClassifier[] create(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction[]... functions) throws CloneNotSupportedException
CLLClassifier
s by using the
cross-product of the given ScoringFunction
s.
params
- the parameters that will be used in all classifiersprior
- the prior that will be used in all classifiersfunctions
- the ScoringFunction
s
functions[i]
are the ScoringFunction
s
that can be used for class i
functions.length
has to be at least 2
CLLClassifier
s
CloneNotSupportedException
- if some item could not be clonedpublic String getInstanceName()
AbstractClassifier
getInstanceName
in class ScoreClassifier
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