de.jstacs.classifier.assessment
Class KFoldCVAssessParameterSet

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

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class KFoldCVAssessParameterSet
extends ClassifierAssessmentAssessParameterSet

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

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

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

KFoldCVAssessParameterSet(Sample.PartitionMethod dataSplitMethod, int elementLength, boolean exceptionIfMPNotComputable, int k)
Constructs a new KFoldCVAssessParameterSet with given parameter values.

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

Method Summary

ArrayList<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.
int	getK() Returns the number of mutually exclusive random-splits of user supplied data defined by this KFoldCVAssessParameterSet.
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

KFoldCVAssessParameterSet

public KFoldCVAssessParameterSet()
                          throws UnsupportedOperationException

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

Throws:

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

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet()

KFoldCVAssessParameterSet

public KFoldCVAssessParameterSet(StringBuffer representation)
                          throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

ClassifierAssessmentAssessParameterSet.ClassifierAssessmentAssessParameterSet(StringBuffer), Storable

KFoldCVAssessParameterSet

public KFoldCVAssessParameterSet(Sample.PartitionMethod dataSplitMethod,
                                 int elementLength,
                                 boolean exceptionIfMPNotComputable,
                                 int k)
                          throws SimpleParameter.IllegalValueException

Constructs a new KFoldCVAssessParameterSet 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 KFoldCVAssessParameterSet is used in combination with a MeasureParameters-object to call assess( ... )-methods of KFoldCrossValidations, if exceptionIfMPNotComputable==true an Exception is thrown in case of a user selected measure parameters that could not be computed.

k - defines the number of mutually exclusive random-splits of user supplied data. Each part is used once as a test dataset and the union of the remaining k-1 parts is once used as train dataset. Thus k also defines how many ( k) repeated classifier trainings and classifier evaluations (tests) are performed.

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)

getK

public int getK()

Returns the number of mutually exclusive random-splits of user supplied data defined by this KFoldCVAssessParameterSet.

Returns:

the number of mutually exclusive random-splits of user-supplied data defined by this KFoldCVAssessParameterSet

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 ArrayList<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