de.jstacs.classifier.scoringFunctionBased
Class ScoreClassifierParameterSet

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

public class ScoreClassifierParameterSet
extends InstanceParameterSet

The parameter set for any CL classifier.

Author:
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
ScoreClassifierParameterSet(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, boolean plugIn)
          The constructor for a simple, instantiated parameter set.
ScoreClassifierParameterSet(boolean simple, boolean variableLength)
          The default constructor.
ScoreClassifierParameterSet(StringBuffer xml)
          This is the constructor for Storable.
 
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.
protected  void loadParameters()
          Loads the parameters for this ParameterSet.
 boolean useOnlyFreeParameter()
          This method returns true if only the free parameters shall be used.
 
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

ScoreClassifierParameterSet

public ScoreClassifierParameterSet(boolean simple,
                                   boolean variableLength)
The default constructor.

Parameters:
simple - whether the AlphabetContainer shall be simple.
variableLength - whether the corresponding classifier can handle sequences of arbitrary length

ScoreClassifierParameterSet

public ScoreClassifierParameterSet(StringBuffer xml)
                            throws NonParsableException
This is the constructor for Storable.

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

ScoreClassifierParameterSet

public ScoreClassifierParameterSet(AlphabetContainer alphabet,
                                   int length,
                                   byte algo,
                                   double eps,
                                   double lineps,
                                   double startD,
                                   boolean free,
                                   boolean plugIn)
                            throws Exception
The constructor for a simple, instantiated parameter set.

Parameters:
alphabet - the alphabet
length - the length of the sequences, 0 for homogeneous
algo - the choice of algorithm
eps - the threshold for stopping the algorithm
lineps - the threshold for stopping the line search in the algorithm
startD - the start distance for the line search in the algorithm
free - indicates whether only the free parameters or all parameters should be used
plugIn - indicates whether to use plug-in parameters or not
Throws:
Exception
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

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

useOnlyFreeParameter

public boolean useOnlyFreeParameter()
This method returns true if only the free parameters shall be used.

Returns:
true if only the free parameters shall be used

getInstanceName

public String getInstanceName()
Description copied from class: ParameterSet
Returns the name of an instance of the class that can be constructed using this ParameterSet.

Specified by:
getInstanceName in class ParameterSet
Returns:
the name

getInstanceComment

public String getInstanceComment()
Description copied from class: ParameterSet
Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:
getInstanceComment in class ParameterSet
Returns:
the comment