de.jstacs.classifier.assessment
Class RepeatedHoldOutAssessParameterSet

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

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class RepeatedHoldOutAssessParameterSet
extends ClassifierAssessmentAssessParameterSet

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

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

RepeatedHoldOutAssessParameterSet()
Constructs a new RepeatedHoldOutAssessParameterSet with empty parameter values.

RepeatedHoldOutAssessParameterSet(Sample.PartitionMethod dataSplitMethod, int elementLength, boolean exceptionIfMPNotComputable, int repeats, double[] percents)
Constructs a new RepeatedHoldOutAssessParameterSet with given parameter values.

RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Method Summary

Collection<Result>	getAnnotation() Returns a Collection of parameters containing informations about this ClassifierAssessmentAssessParameterSet.
Sample.PartitionMethod	getDataSplitMethod() Returns the Sample.PartitionMethod defining how the mutually exclusive random-splits of user supplied data are generated.
double[]	getPercents() Returns an array containing for each class the percentage of user supplied data that is used in each iteration as test dataset.
int	getRepeats() Returns the repeats defined by this RepeatedHoldOutAssessParameterSet (repeats define how many iterations (train and test classifiers) of that RepeatedHoldOutExperiment this RepeatedHoldOutAssessParameterSet is used with are performed).
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

RepeatedHoldOutAssessParameterSet

public RepeatedHoldOutAssessParameterSet()
                                  throws UnsupportedOperationException

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

Throws:

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

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet()

RepeatedHoldOutAssessParameterSet

public RepeatedHoldOutAssessParameterSet(StringBuffer representation)
                                  throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet(StringBuffer), Storable

RepeatedHoldOutAssessParameterSet

public RepeatedHoldOutAssessParameterSet(Sample.PartitionMethod dataSplitMethod,
                                         int elementLength,
                                         boolean exceptionIfMPNotComputable,
                                         int repeats,
                                         double[] percents)
                                  throws SimpleParameter.IllegalValueException

Constructs a new RepeatedHoldOutAssessParameterSet with given parameter values.

Parameters:

dataSplitMethod - defines the method used to split user supplied data into k mutually exclusive random-splits (available options are: Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_ELEMENTS and Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_SYMBOLS)

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

exceptionIfMPNotComputable - a RepeatedHoldOutAssessParameterSet is used in combination with a MeasureParameters-object to call assess( ... )-methods of RepeatedHoldOutExperiments. 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 (mutually exclusive, randomly split data to obtain test and train datasets, train classifiers using train datasets and test them using test datasets) of that RepeatedHoldOutExperiment this RepeatedHoldOutAssessParameterSet is used with

percents - this array contains class-wise the percentage of the user supplied data that should be used as test data in each iteration of that RepeatedHoldOutExperiment this RepeatedHoldOutAssessParameterSet is used with

Throws:

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

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet(int, boolean), Sample.PartitionMethod

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 RepeatedHoldOutAssessParameterSet (repeats define how many iterations (train and test classifiers) of that RepeatedHoldOutExperiment this RepeatedHoldOutAssessParameterSet is used with are performed).

Returns:

the repeats defined by this RepeatedHoldOutAssessParameterSet (repeats define how many iterations (train and test classifiers) of that RepeatedHoldOutExperiment this RepeatedHoldOutAssessParameterSet is used with are performed)

getPercents

public double[] getPercents()

Returns an array containing for each class the percentage of user supplied data that is used in each iteration as test dataset.

Returns:

an array containing for each class the percentage of user supplied data that is used in each iteration as test dataset

getDataSplitMethod

public Sample.PartitionMethod getDataSplitMethod()

Returns the Sample.PartitionMethod defining how the mutually exclusive random-splits of user supplied data are generated.

Returns:

the Sample.PartitionMethod defining how the mutually exclusive random-splits of user supplied data are generated

See Also:

Sample.PartitionMethod

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