de.jstacs.classifier.scoringFunctionBased.cll
Class CLLClassifierParameterSet

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.parameters.InstanceParameterSet
          extended by de.jstacs.parameters.SequenceScoringParameterSet
              extended by de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet
                  extended by de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
All Implemented Interfaces:
RangeIterator, Storable, Cloneable

public class CLLClassifierParameterSet
extends ScoreClassifierParameterSet

This class contains the parameters for the CLLClassifier.

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
  CLLClassifierParameterSet(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm)
          The default constructor that constructs a new CLLClassifierParameterSet.
protected CLLClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm)
          The default constructor that constructs a new CLLClassifierParameterSet.
  CLLClassifierParameterSet(StringBuffer xml)
          The standard constructor for the interface Storable.
 
Method Summary
protected  void loadParameters()
          Loads the parameters for this ParameterSet.
 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, getAlphabet, getIndex, 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
getErrorMessage, getId, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, valuesToString
 
Methods inherited from class java.lang.Object
finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

CLLClassifierParameterSet

public CLLClassifierParameterSet(StringBuffer xml)
                          throws NonParsableException
The standard constructor for the interface Storable. Constructs a CLLClassifierParameterSet out of its XML representation.

Parameters:
xml - the XML representation as StringBuffer
Throws:
NonParsableException - if the CLLClassifierParameterSet could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)
See Also:
ScoreClassifierParameterSet.ScoreClassifierParameterSet(StringBuffer), Storable

CLLClassifierParameterSet

public CLLClassifierParameterSet(AlphabetContainer alphabet,
                                 int length,
                                 byte algo,
                                 double eps,
                                 double lineps,
                                 double startD,
                                 boolean free,
                                 OptimizableFunction.KindOfParameter kind,
                                 boolean norm)
                          throws Exception
The default constructor that constructs a new CLLClassifierParameterSet.

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
Throws:
Exception - if something went wrong
See Also:
OptimizableFunction.KindOfParameter, CLLClassifierParameterSet(Class, de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean, de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter, boolean)

CLLClassifierParameterSet

protected CLLClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
                                    AlphabetContainer alphabet,
                                    int length,
                                    byte algo,
                                    double eps,
                                    double lineps,
                                    double startD,
                                    boolean free,
                                    OptimizableFunction.KindOfParameter kind,
                                    boolean norm)
                             throws Exception
The default constructor that constructs a new CLLClassifierParameterSet.

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
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