de.jstacs.classifiers.assessment

Class RepeatedSubSamplingAssessParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.classifiers.assessment.ClassifierAssessmentAssessParameterSet

de.jstacs.classifiers.assessment.RepeatedSubSamplingAssessParameterSet

All Implemented Interfaces:

GalaxyConvertible, 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

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
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).
double[]	getTrain_TestNumbers(boolean train_case) Returns an array containing the number of elements the subsampled (train | test) data sets should consist of.

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

getElementLength, getExceptionIfMPNotComputable, getStoreAll, setStoreAll

Methods inherited from class de.jstacs.parameters.ParameterSet

clone, fromGalaxy, fromXML, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

RepeatedSubSamplingAssessParameterSet

public RepeatedSubSamplingAssessParameterSet()
                                      throws UnsupportedOperationException,
                                             CloneNotSupportedException,
                                             SimpleParameter.IllegalValueException

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

CloneNotSupportedException - if the parameter for the subsampled sequences could not be created

SimpleParameter.IllegalValueException - if the parameters could not be filled with the default values

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet()

RepeatedSubSamplingAssessParameterSet

public 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,
                                     double[] trainNumbers,
                                     double[] testNumbers)
                                      throws SimpleParameter.IllegalValueException,
                                             CloneNotSupportedException

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 an AbstractPerformanceMeasure-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 data sets from user supplied data, train classifiers using train data sets and test them using test data sets) 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 data sets 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 data sets should contain

Throws:

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

CloneNotSupportedException - if the parameter for the subsampled sequences could not be created

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet(int, boolean)

Method Detail

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 double[] getTrain_TestNumbers(boolean train_case)

Returns an array containing the number of elements the subsampled (train | test) data sets 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) data sets 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