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.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.InstanceParameterSet
alphabet, length
 
Fields inherited from class de.jstacs.parameters.ParameterSet
alternativeInstanceClass, errorMessage, parameters, parent, ranged
 
Constructor Summary
CLLClassifierParameterSet(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, boolean plugIn, boolean norm)
          The default constructor.
CLLClassifierParameterSet(StringBuffer xml)
          This is the constructor for Storable.
 
Method Summary
protected  void loadParameters()
          Loads the parameters for this ParameterSet.
 boolean shouldBeNormalized()
          This method true 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.InstanceParameterSet
clone, equals, fromXML, getAlphabet, getIndex, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, replaceParametersWithRangedInstance, reset, toXML
 
Methods inherited from class de.jstacs.parameters.ParameterSet
getErrorMessage, getId, getInstance, getInstanceClass, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setAlternativeInstanceClass, 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
This is the constructor for Storable.

Parameters:
xml - the xml representation
Throws:
NonParsableException - if the representation could not be parsed.

CLLClassifierParameterSet

public CLLClassifierParameterSet(AlphabetContainer alphabet,
                                 int length,
                                 byte algo,
                                 double eps,
                                 double lineps,
                                 double startD,
                                 boolean free,
                                 boolean plugIn,
                                 boolean norm)
                          throws Exception
The default constructor.

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 the free or all parameters in a ScoringFunction
plugIn - the switch for using plug-in parameters in a ScoringFuncton
norm - the switch for using a normalization while optimization
Throws:
Exception - if something went wrong
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 simply creating a new ArrayList<Parameter> for the field parameters/code> and filling it with instances of subclasses of Parameter

Overrides:
loadParameters in class ScoreClassifierParameterSet
Throws:
Exception - an Exception is thrown if the parameters could not be loaded
See Also:
ParameterSet.parameters, Parameter

shouldBeNormalized

public boolean shouldBeNormalized()
This method true if a normalization shall be used while optimization. The normalization is done by division with the number of sequences.

Returns:
true if a normalization shall be used while optimization