de.jstacs.classifier.assessment
Class RepeatedSubSamplingAssessParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
          de.jstacs.classifier.assessment.RepeatedSubSamplingAssessParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class RepeatedSubSamplingAssessParameterSet
extends ClassifierAssessmentAssessParameterSet

This class implements a ClassifierAssessmentAssessParameterSet that must be used to call method assess( ... ) of a RepeatedSubSamplingExperiment. It contains user specific parameters necessary for a run of a RepeatedSubSamplingExperiment.

Author:

Andre Gohr (bioinf (nospam:.) ag (nospam:@) googlemail (nospam:.) com)

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent, ranged

Constructor Summary

	RepeatedSubSamplingAssessParameterSet() Constructs a new RepeatedSubSamplingAssessParameterSet with empty parameter values.
	RepeatedSubSamplingAssessParameterSet(int elementLength, boolean exceptionIfMPNotComputable, int repeats, int[] trainNumbers, int[] testNumbers) Constructs a new RepeatedSubSamplingAssessParameterSet with given parameter values.
protected	RepeatedSubSamplingAssessParameterSet(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Collection<Result>	getAnnotation() Returns a Collection of parameters containing informations about this ClassifierAssessmentAssessParameterSet.
int	getRepeats() Returns the repeats defined by this RepeatedSubSamplingAssessParameterSet (repeats defines how many iterations (train and test classifiers) of that RepeatedSubSamplingExperiment this RepeatedSubSamplingAssessParameterSet is used with are performed).
int[]	getTrain_TestNumbers(boolean train_case) Returns an array containing the number of elements the subsampled (train | test) datasets should consist of.
protected void	initializeMyParametersArrayList() Initializes the list of Parameters in this ClassifierAssessmentAssessParameterSet.
protected void	loadParameters() Loads the parameters for this ParameterSet.

Methods inherited from class de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet

getElementLength, getExceptionIfMPNotComputable

Methods inherited from class de.jstacs.parameters.ParameterSet

clone, fromGalaxy, fromXML, getErrorMessage, getId, getIndex, getNumberOfParameters, getNumberOfValues, getParameterAt, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, replaceParametersWithRangedInstance, reset, resetToFirst, setParent, simplify, toGalaxy, toXML, valuesToString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RepeatedSubSamplingAssessParameterSet

public RepeatedSubSamplingAssessParameterSet()
                                      throws UnsupportedOperationException

Constructs a new RepeatedSubSamplingAssessParameterSet with empty parameter values. This constructor should only be used to create "filled" RepeatedSubSamplingAssessParameterSets, i.e. to create RepeatedSubSamplingAssessParameterSets from a set of values and not to fill it from the platform user interface.

Throws:

UnsupportedOperationException - if the RepeatedSubSamplingAssessParameterSet could not be constructed or the parameters could not be loaded

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet()

RepeatedSubSamplingAssessParameterSet

protected RepeatedSubSamplingAssessParameterSet(StringBuffer representation)
                                         throws NonParsableException

The standard constructor for the interface Storable. Constructs a RepeatedSubSamplingAssessParameterSet out of its XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet(StringBuffer)

RepeatedSubSamplingAssessParameterSet

public RepeatedSubSamplingAssessParameterSet(int elementLength,
                                             boolean exceptionIfMPNotComputable,
                                             int repeats,
                                             int[] trainNumbers,
                                             int[] testNumbers)
                                      throws SimpleParameter.IllegalValueException

Constructs a new RepeatedSubSamplingAssessParameterSet with given parameter values.

Parameters:

elementLength - defines the length of elements (sequences) the classifiers to be assessed are able to classify

exceptionIfMPNotComputable - a RepeatedSubSamplingAssessParameterSet is used in combination with a MeasureParameters-object to call assess( ... )-methods of RepeatedSubSamplingExperiments. If exceptionIfMPNotComputable==true an Exception is thrown in case of a user selected measure parameters that could not be computed.

repeats - the number of repeats of each iteration (subsample test and train datasets from user supplied data, train classifiers using train datasets and test them using test datasets) of that RepeatedHoldOutExperiment this RepeatedSubSamplingAssessParameterSet is used with

trainNumbers - an array containing for each class (the classifiers to be assessed are capable to distinguish) the number of elements the subsampled train datasets should contain

testNumbers - an array containing for each class (the classifiers to be assessed are capable to distinguish) the number of elements the subsampled test datasets should contain

Throws:

SimpleParameter.IllegalValueException - in case of out-of-range or invalid given parameters

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet(int, boolean)

Method Detail

initializeMyParametersArrayList

protected void initializeMyParametersArrayList()

Description copied from class: ClassifierAssessmentAssessParameterSet

Initializes the list of Parameters in this ClassifierAssessmentAssessParameterSet.

Overrides:

initializeMyParametersArrayList in class ClassifierAssessmentAssessParameterSet

See Also:

ParameterSet.initParameterList(int initCapacity)

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 ClassifierAssessmentAssessParameterSet

Throws:

Exception - if the parameters could not be loaded

See Also:

Parameter, ParameterSet.parameters, ParameterSet.initParameterList(), ParameterSet.initParameterList(int)

getRepeats

public int getRepeats()

Returns the repeats defined by this RepeatedSubSamplingAssessParameterSet (repeats defines how many iterations (train and test classifiers) of that RepeatedSubSamplingExperiment this RepeatedSubSamplingAssessParameterSet is used with are performed).

Returns:

the repeats defined by this RepeatedSubSamplingAssessParameterSet (repeats defines how many iterations (train and test classifiers) of that RepeatedSubSamplingExperiment this RepeatedSubSamplingAssessParameterSet is used with are performed)

getTrain_TestNumbers

public int[] getTrain_TestNumbers(boolean train_case)

Returns an array containing the number of elements the subsampled (train | test) datasets should consist of.

Parameters:

train_case - if true then (train | test)=train else (train | test)=test

Returns:

an array class-wise containing the number of elements the subsampled (train | test) datasets should consist of

getAnnotation

public Collection<Result> getAnnotation()

Description copied from class: ClassifierAssessmentAssessParameterSet

Returns a Collection of parameters containing informations about this ClassifierAssessmentAssessParameterSet.

Overrides:

getAnnotation in class ClassifierAssessmentAssessParameterSet

Returns:

a Collection of parameters containing informations about this ClassifierAssessmentAssessParameterSet