de.jstacs.classifiers.differentiableSequenceScoreBased

Class ScoreClassifierParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.parameters.SequenceScoringParameterSet

de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifierParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

GenDisMixClassifierParameterSet

public abstract class ScoreClassifierParameterSet
extends SequenceScoringParameterSet

A set of Parameters for any ScoreClassifier.

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.SequenceScoringParameterSet

alphabet, length

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Constructor and Description
ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, AbstractTerminationCondition tc, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind) The constructor for a simple, instantiated parameter set.
ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind) The constructor for a simple, instantiated parameter set.
ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, boolean simple, AlphabetContainer.AlphabetContainerType type, boolean variableLength) Creates a new ScoreClassifierParameterSet with empty parameter values.
ScoreClassifierParameterSet(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
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.
AbstractTerminationCondition	getTerminantionCondition() This method returns the AbstractTerminationCondition for stopping the training, e.g., if the difference of the scores between two iterations is smaller than a given threshold the training is stopped.
boolean	useOnlyFreeParameter() This method indicates if only the free parameters shall be used.

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

ScoreClassifierParameterSet

public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
                                   boolean simple,
                                   AlphabetContainer.AlphabetContainerType type,
                                   boolean variableLength)
                            throws Exception

Creates a new ScoreClassifierParameterSet with empty parameter values.

Parameters:

instanceClass - the class of the instance

simple - indicates whether the AlphabetContainer shall be simple

type - the type of the AlphabetContainer

variableLength - indicates whether the corresponding classifier can handle sequences of arbitrary length

Throws:

Exception - if the parameters could not be loaded

See Also:

SequenceScoringParameterSet.SequenceScoringParameterSet(Class, de.jstacs.data.AlphabetContainer.AlphabetContainerType, boolean, boolean)

ScoreClassifierParameterSet

public ScoreClassifierParameterSet(StringBuffer xml)
                            throws NonParsableException

The standard constructor for the interface Storable. Creates a new ScoreClassifierParameterSet out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

See Also:

SequenceScoringParameterSet.SequenceScoringParameterSet(StringBuffer), Storable

ScoreClassifierParameterSet

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

The constructor for a simple, instantiated parameter set.

Parameters:

instanceClass - the class of the instance

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

kind - indicates the kind of class parameter initialization

Throws:

Exception - if something went wrong

See Also:

SequenceScoringParameterSet.SequenceScoringParameterSet(Class, AlphabetContainer, int, boolean), ScoreClassifierParameterSet(Class, AlphabetContainer, int, byte, AbstractTerminationCondition, double, double, boolean, de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter), SmallDifferenceOfFunctionEvaluationsCondition

ScoreClassifierParameterSet

public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
                                   AlphabetContainer alphabet,
                                   int length,
                                   byte algo,
                                   AbstractTerminationCondition tc,
                                   double lineps,
                                   double startD,
                                   boolean free,
                                   OptimizableFunction.KindOfParameter kind)
                            throws Exception

The constructor for a simple, instantiated parameter set.

Parameters:

instanceClass - the class of the instance

alphabet - the alphabet

length - the length of the sequences, 0 for homogeneous

algo - the choice of algorithm

tc - the termination condition 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

kind - indicates the kind of class parameter initialization

Throws:

Exception - if something went wrong

See Also:

SequenceScoringParameterSet.SequenceScoringParameterSet(Class, AlphabetContainer, int, boolean)

Method Detail

useOnlyFreeParameter

public boolean useOnlyFreeParameter()

This method indicates if only the free parameters shall be used.

Returns:

true if only the free parameters shall be used, false otherwise

getInstanceName

public String getInstanceName()

Description copied from class: InstanceParameterSet

Returns the name of an instance of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceName in class InstanceParameterSet

Returns:

the name of the class

getInstanceComment

public String getInstanceComment()

Description copied from class: InstanceParameterSet

Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceComment in class InstanceParameterSet

Returns:

the comment of the class

getTerminantionCondition

public AbstractTerminationCondition getTerminantionCondition()
                                                      throws ParameterSetParser.NotInstantiableException

This method returns the AbstractTerminationCondition for stopping the training, e.g., if the difference of the scores between two iterations is smaller than a given threshold the training is stopped.

Returns:

the AbstractTerminationCondition for stopping the training

Throws:

ParameterSetParser.NotInstantiableException - if the AbstractTerminationCondition could not be created from its ParameterSet