de.jstacs.classifier.scoringFunctionBased.sampling
Class SamplingGenDisMixClassifierParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.parameters.SequenceScoringParameterSet
              de.jstacs.classifier.scoringFunctionBased.sampling.SamplingScoreBasedClassifierParameterSet
                  de.jstacs.classifier.scoringFunctionBased.sampling.SamplingGenDisMixClassifierParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class SamplingGenDisMixClassifierParameterSet
extends SamplingScoreBasedClassifierParameterSet

ParameterSet to instantiate a SamplingGenDisMixClassifier.

Author:

Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.SequenceScoringParameterSet

alphabet, length

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent, ranged

Constructor Summary

	SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, int testSamplings, int stationarySamplings, String outfilePrefix, int threads) Create a new SamplingGenDisMixClassifierParameterSet with a grouped sampling scheme, sampling all parameters (and not only the free ones), and adaption of the variance.
	SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads) Create a new SamplingGenDisMixClassifierParameterSet.
protected	SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads) Create a new SamplingGenDisMixClassifierParameterSet.

Method Summary

String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
String	getInstanceName() Returns the name of an instance of the class that can be constructed using this ParameterSet.
int	getNumberOfThreads() Returns the number of threads for evaluating the LogGenDisMixFunction
protected void	loadParameters() Loads the parameters for this ParameterSet.

Methods inherited from class de.jstacs.classifier.scoringFunctionBased.sampling.SamplingScoreBasedClassifierParameterSet

clone, getAdaptVariance, getFreeParameters, getNumberOfStarts, getNumberOfStationarySamplings, getNumberOfTestSamplings, getOutfilePrefix, getSamplingScheme, setNumberOfStarts

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, replaceParametersWithRangedInstance, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, toGalaxy, valuesToString

Methods inherited from class java.lang.Object

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

Constructor Detail

SamplingGenDisMixClassifierParameterSet

public SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
                                               int length,
                                               int numStarts,
                                               SamplingScoreBasedClassifier.SamplingScheme scheme,
                                               int testSamplings,
                                               int stationarySamplings,
                                               boolean freeParameters,
                                               boolean adaptVariance,
                                               String outfilePrefix,
                                               int threads)
                                        throws Exception

Create a new SamplingGenDisMixClassifierParameterSet.

Parameters:

alphabet - the alphabet of the classifier

length - the length of the sequences that can be classified

numStarts - the number of independent samplings

scheme - the sampling scheme

testSamplings - the number of samplings between checks for the lenght of the burn-in phase

stationarySamplings - the number of samplings in the stationary phase

freeParameters - if only free parameters shall be used

adaptVariance - if the variance shall be adapted to the size of the event space of a random variable

outfilePrefix - the prefix of the temporary files for storing the parameters

threads - the number of threads for evaluating the LogGenDisMixFunction

Throws:

Exception - if the parameters could not be created

SamplingGenDisMixClassifierParameterSet

protected SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
                                                  AlphabetContainer alphabet,
                                                  int length,
                                                  int numStarts,
                                                  SamplingScoreBasedClassifier.SamplingScheme scheme,
                                                  int testSamplings,
                                                  int stationarySamplings,
                                                  boolean freeParameters,
                                                  boolean adaptVariance,
                                                  String outfilePrefix,
                                                  int threads)
                                           throws Exception

Create a new SamplingGenDisMixClassifierParameterSet.

Parameters:

instanceClass - the class, which must be a subclass of SamplingScoreBasedClassifier

alphabet - the alphabet of the classifier

length - the length of the sequences that can be classified

numStarts - the number of independent samplings

scheme - the sampling scheme

testSamplings - the number of samplings between checks for the lenght of the burn-in phase

stationarySamplings - the number of samplings in the stationary phase

freeParameters - if only free parameters shall be used

adaptVariance - if the variance shall be adapted to the size of the event space of a random variable

outfilePrefix - the prefix of the temporary files for storing the parameters

threads - the number of threads for evaluating the LogGenDisMixFunction

Throws:

Exception - if the parameters could not be created

SamplingGenDisMixClassifierParameterSet

public SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
                                               int length,
                                               int numStarts,
                                               int testSamplings,
                                               int stationarySamplings,
                                               String outfilePrefix,
                                               int threads)
                                        throws Exception

Create a new SamplingGenDisMixClassifierParameterSet with a grouped sampling scheme, sampling all parameters (and not only the free ones), and adaption of the variance.

Parameters:

alphabet - the alphabet of the classifier

length - the length of the sequences that can be classified

numStarts - the number of independent samplings

testSamplings - the number of samplings between checks for the lenght of the burn-in phase

stationarySamplings - the number of samplings in the stationary phase

outfilePrefix - the prefix of the temporary files for storing the parameters

threads - the number of threads for evaluating the LogGenDisMixFunction

Throws:

Exception - if the parameters could not be created

Method Detail

getInstanceComment

public String getInstanceComment()

Description copied from class: InstanceParameterSet

Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceComment in class InstanceParameterSet

Returns:

the comment of the class

getInstanceName

public String getInstanceName()

Description copied from class: InstanceParameterSet

Returns the name of an instance of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceName in class InstanceParameterSet

Returns:

the name of the class

loadParameters

protected void loadParameters()
                       throws Exception

Description copied from class: ParameterSet

Loads the parameters for this ParameterSet. This is in most cases done by calling ParameterSet.initParameterList() or ParameterSet.initParameterList(int) to initialize ParameterSet.parameters and afterwards filling ParameterSet.parameters with instances of subclasses of Parameter.

Overrides:

loadParameters in class SamplingScoreBasedClassifierParameterSet

Throws:

Exception - if the parameters could not be loaded

See Also:

Parameter, ParameterSet.parameters, ParameterSet.initParameterList(), ParameterSet.initParameterList(int)

getNumberOfThreads

public int getNumberOfThreads()

Returns the number of threads for evaluating the LogGenDisMixFunction

Returns:

the number of threads