de.jstacs.classifier.scoringFunctionBased.gendismix
Class GenDisMixClassifierParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.parameters.SequenceScoringParameterSet
              de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet
                  de.jstacs.classifier.scoringFunctionBased.gendismix.GenDisMixClassifierParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class GenDisMixClassifierParameterSet
extends ScoreClassifierParameterSet

This class contains the parameters for the GenDisMixClassifier.

Author:

Jan Grau, Jens Keilwagen

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

	GenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm, int threads) The default constructor that constructs a new GenDisMixClassifierParameterSet.
protected	GenDisMixClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm, int threads) The default constructor that constructs a new GenDisMixClassifierParameterSet.
	GenDisMixClassifierParameterSet(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

int	getNumberOfThreads() This method returns the number of threads that should be used during optimization.
protected void	loadParameters() Loads the parameters for this ParameterSet.
void	setNumberOfThreads(int threads) This method set the number of threads used during optimization.
boolean	shouldBeNormalized() This method indicates if a normalization shall be used while optimization.

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

getInstanceComment, getInstanceName, useOnlyFreeParameter

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

clone, 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

GenDisMixClassifierParameterSet

public GenDisMixClassifierParameterSet(StringBuffer xml)
                                throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

See Also:

ScoreClassifierParameterSet.ScoreClassifierParameterSet(StringBuffer), Storable

GenDisMixClassifierParameterSet

public GenDisMixClassifierParameterSet(AlphabetContainer alphabet,
                                       int length,
                                       byte algo,
                                       double eps,
                                       double lineps,
                                       double startD,
                                       boolean free,
                                       OptimizableFunction.KindOfParameter kind,
                                       boolean norm,
                                       int threads)
                                throws Exception

The default constructor that constructs a new GenDisMixClassifierParameterSet.

Parameters:

alphabet - the AlphabetContainer

length - the length of the sequences

algo - the algorithm that shall be used for optimization

eps - the epsilon for stopping the optimization

lineps - the epsilon for stopping the line search

startD - the start distance for the line search

free - the switch for using only the free or all parameters in a ScoringFunction

kind - indicates the kind of class parameter initialization

norm - the switch for using a normalization while optimization

threads - the NumberFormatException of threads used during an optimization

Throws:

Exception - if something went wrong

See Also:

OptimizableFunction.KindOfParameter, GenDisMixClassifierParameterSet(Class, de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean, de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter, boolean,int)

GenDisMixClassifierParameterSet

protected GenDisMixClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
                                          AlphabetContainer alphabet,
                                          int length,
                                          byte algo,
                                          double eps,
                                          double lineps,
                                          double startD,
                                          boolean free,
                                          OptimizableFunction.KindOfParameter kind,
                                          boolean norm,
                                          int threads)
                                   throws Exception

The default constructor that constructs a new GenDisMixClassifierParameterSet.

Parameters:

instanceClass - the class of the instance

alphabet - the AlphabetContainer

length - the length of the sequences

algo - the algorithm that shall be used for optimization

eps - the epsilon for stopping the optimization

lineps - the epsilon for stopping the line search

startD - the start distance for the line search

free - the switch for using only the free or all parameters in a ScoringFunction

kind - indicates the kind of class parameter initialization

norm - the switch for using a normalization while optimization

threads - the NumberFormatException of threads used during an optimization

Throws:

Exception - if something went wrong

See Also:

OptimizableFunction.KindOfParameter, ScoreClassifierParameterSet.ScoreClassifierParameterSet(Class, de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean, de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter)

Method Detail

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 ScoreClassifierParameterSet

Throws:

Exception - if the parameters could not be loaded

See Also:

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

shouldBeNormalized

public boolean shouldBeNormalized()

This method indicates if a normalization shall be used while optimization. The normalization is done through division by the number of sequences.

Returns:

true if a normalization shall be used while optimization, false otherwise

getNumberOfThreads

public int getNumberOfThreads()

This method returns the number of threads that should be used during optimization.

Returns:

the number of threads that should be used during optimization

setNumberOfThreads

public void setNumberOfThreads(int threads)
                        throws SimpleParameter.IllegalValueException

This method set the number of threads used during optimization.

Parameters:

threads - the number of threads used during optimization

Throws:

SimpleParameter.IllegalValueException - if the value could not be set