de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix
Class GenDisMixClassifierParameterSet

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.parameters.InstanceParameterSet<T>
          extended by de.jstacs.parameters.SequenceScoringParameterSet
              extended by de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifierParameterSet
                  extended by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifierParameterSet
All Implemented Interfaces:
GalaxyConvertible, 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
 
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.
 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.classifiers.differentiableSequenceScoreBased.ScoreClassifierParameterSet
getInstanceComment, getInstanceName, getTerminantionCondition, useOnlyFreeParameter
 
Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet
clone, equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, reset, toXML
 
Methods inherited from class de.jstacs.parameters.InstanceParameterSet
getInstance, getInstanceClass
 
Methods inherited from class de.jstacs.parameters.ParameterSet
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy
 
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 DifferentiableSequenceScore
kind - indicates the kind of class parameter initialization
norm - the switch for using a normalization while optimization
threads - the number 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.classifiers.differentiableSequenceScoreBased.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 DifferentiableSequenceScore
kind - indicates the kind of class parameter initialization
norm - the switch for using a normalization while optimization
threads - the number 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.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter)
Method Detail

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