jigcell.compare.objective
Class WOSSObjective

java.lang.Object
  javax.swing.TransferHandler
      jigcell.compare.impl.Transferer
          jigcell.compare.impl.DataSource
              jigcell.compare.data.DataGenerator
                  jigcell.compare.data.EditableDataGenerator
                      jigcell.compare.data.ProgrammableDataGenerator
                          jigcell.compare.objective.Objective
                              jigcell.compare.objective.WOSSObjective

All Implemented Interfaces:

java.awt.datatransfer.Transferable, java.beans.PropertyChangeListener, java.io.Serializable, java.lang.Cloneable, java.util.EventListener, IDataGenerator, IDataSource, IEditableDataGenerator, IProgrammableDataGenerator, IReadableDataSource, IWriteableDataSource, IDimensionWeightObjective, IElementWeightObjective, IInterpolationObjective, IObjective

public class WOSSObjective
extends Objective
implements IDimensionWeightObjective, IElementWeightObjective, IInterpolationObjective

A generator whose function is a weighted orthogonal sum of squares.

This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class jigcell.compare.data.EditableDataGenerator

EditableDataGenerator.EditableDataGeneratorDelegate

Nested classes/interfaces inherited from interface jigcell.compare.IDataSource

IDataSource.Option

Nested classes/interfaces inherited from interface jigcell.compare.IDataSource

IDataSource.Option

Nested classes/interfaces inherited from interface jigcell.compare.IDataSource

IDataSource.Option

Field Summary

protected static int	BUFFER_LENGTH_ELEMENT Length of element slices to work with
protected static int	BUFFER_LENGTH_VALUE Length of value slices to work with
static java.lang.String	DIMENSIONWEIGHT_RECIPROCALSQUARE Default dimension weight of the square of the reciprocal of the element
static java.lang.String	INTERPOLATION_LINEAR Linear interpolation
protected static java.lang.String	NAME_GENERATOR Display name of this generator
protected static double	SMALL_VALUE Size of the largest small double

Fields inherited from class jigcell.compare.objective.Objective

ERROR, OPTION_DATA, OPTION_FUNCTION

Fields inherited from class jigcell.compare.data.ProgrammableDataGenerator

allowDescriptionQuery, callStack, listenerList

Fields inherited from class jigcell.compare.data.DataGenerator

COMPARATOR_NAME, DESCRIPTION_READ, SEPARATOR_ESCAPE, SPECIAL_CHARS

Fields inherited from class jigcell.compare.impl.DataSource

OPTIONS_LOCK, SEPARATOR_PAIR, SEPARATOR_PART, SEPARATORS

Fields inherited from class jigcell.compare.impl.Transferer

CSV_FOOTER, CSV_LINEPOSTPEND, CSV_LINEPREPEND, CSV_LINESEPARATOR, HTML_FOOTER, HTML_HEADPOSTPEND, HTML_HEADPREPEND, HTML_HEADSEPARATOR, HTML_LINEPOSTPEND, HTML_LINEPREPEND, HTML_LINESEPARATOR

Fields inherited from class javax.swing.TransferHandler

COPY, COPY_OR_MOVE, MOVE, NONE

Fields inherited from interface jigcell.compare.objective.IDimensionWeightObjective

ATTRIBUTE_DEFAULTDIMENSIONWEIGHT, ATTRIBUTE_DIMENSIONWEIGHTS, DIMENSIONWEIGHT_0, DIMENSIONWEIGHT_1, OPTION_DEFAULTDIMENSIONWEIGHTS

Fields inherited from interface jigcell.compare.IDataGenerator

ATTRIBUTE_COMMENT, ATTRIBUTE_GUID, PROPERTY_GENERATOR_EDIT, RESOURCE_GENERATORS

Fields inherited from interface jigcell.compare.IReadableDataSource

OPTION_READDESCRIPTION, OPTION_READICON

Fields inherited from interface jigcell.compare.IDataSource

OPTION_NAME

Fields inherited from interface jigcell.compare.objective.IElementWeightObjective

ATTRIBUTE_DEFAULTELEMENTWEIGHT, ATTRIBUTE_ELEMENTWEIGHTS, ELEMENTWEIGHT_0, ELEMENTWEIGHT_1, OPTION_DEFAULTELEMENTWEIGHTS

Fields inherited from interface jigcell.compare.IDataGenerator

ATTRIBUTE_COMMENT, ATTRIBUTE_GUID, PROPERTY_GENERATOR_EDIT, RESOURCE_GENERATORS

Fields inherited from interface jigcell.compare.IReadableDataSource

OPTION_READDESCRIPTION, OPTION_READICON

Fields inherited from interface jigcell.compare.IDataSource

OPTION_NAME

Fields inherited from interface jigcell.compare.objective.IInterpolationObjective

ATTRIBUTE_INTERPOLATION, INTERPOLATION_NONE, OPTION_INTERPOLATIONS

Fields inherited from interface jigcell.compare.IDataGenerator

ATTRIBUTE_COMMENT, ATTRIBUTE_GUID, PROPERTY_GENERATOR_EDIT, RESOURCE_GENERATORS

Fields inherited from interface jigcell.compare.IReadableDataSource

OPTION_READDESCRIPTION, OPTION_READICON

Fields inherited from interface jigcell.compare.IDataSource

OPTION_NAME

Fields inherited from interface jigcell.compare.objective.IObjective

OPTION_OBJECTIVE, PROPERTY_OBJECTIVE_EDIT, RESOURCE_OBJECTIVES

Fields inherited from interface jigcell.compare.IProgrammableDataGenerator

METHOD_GENERATE, OPTION_COMPARE, OPTION_INPUTTYPECHECKER, OPTION_OUTPUTTYPECHECKER

Fields inherited from interface jigcell.compare.IWriteableDataSource

OPTION_WRITEDESCRIPTION, OPTION_WRITEICON

Constructor Summary

WOSSObjective()
Creates a new data generator based upon a least squares computation.

Method Summary

protected IDataElement	evaluate(IDataElement input) Computes the values of this generator.
protected IDataElement	evaluateLinear(IDataElement e1, IDataElement e2, IDataElement dimensionWeights, double dimensionWeightDefault, IDataElement elementWeights, double elementWeightDefault) Computes weighted orthogonal sum of squares with linear interpolation.
private double	evaluateLinear(IDataElement _e1, long l, double[] e1xBuffer, IDataElement e2, IDataElement[] e2Buffer, long l2, double[] e2xBuffer, double[] e2xBuffer2, IDataElement dimensionWeights, double dimensionWeightDefault, long dl, double[] scaleBuffer) Helper function for computing weighted orthogonal sum of squares with linear interpolation.
private double	evaluateLinear(IDataElement _e1, long l, double[] e1xBuffer, IDataElement _e2, IDataElement _e3, double[] e2xBuffer, double[] e2xBuffer2, IDataElement dimensionWeights, double dimensionWeightDefault, long dl, double[] scaleBuffer) Helper function for computing weighted orthogonal sum of squares with linear interpolation.
private double	evaluateLinear(IDataElement _e1, long l, double[] e1xBuffer, IDataElement _e2, IDataElement _e3, double[] e2xBuffer, double[] e2xBuffer2, IDataElement dimensionWeights, long dl, double[] scaleBuffer) Helper function for computing weighted orthogonal sum of squares with linear interpolation.
protected IDataElement	evaluateNone(IDataElement e1, IDataElement e2, IDataElement dimensionWeights, double dimensionWeightDefault, IDataElement elementWeights, double elementWeightDefault) Computes weighted orthogonal sum of squares without interpolation.
private double	evaluateNone(IDataElement _e1, long l, double[] e1xBuffer, IDataElement _e2, double[] e2xBuffer, IDataElement dimensionWeights, double dimensionWeightDefault, long dl, double[] scaleBuffer) Helper function for computing weighted orthogonal sum of squares without interpolation.
private double	evaluateNone(IDataElement _e1, long l, double[] e1xBuffer, IDataElement _e2, double[] e2xBuffer, IDataElement dimensionWeights, long dl, double[] scaleBuffer) Helper function for computing weighted orthogonal sum of squares without interpolation.
private double	evaluateNone(IDataElement _e1, long l, double[] e1xBuffer, IDataElement e2, IDataElement[] e2Buffer, long l2, double[] e2xBuffer, IDataElement dimensionWeights, double dimensionWeightDefault, long dl, double[] scaleBuffer) Helper function for computing weighted orthogonal sum of squares without interpolation.
static java.lang.Object	getCustomizableInstances() Generates an instance.
java.lang.String	getDefaultDimensionWeight() The dimension weight default.
java.util.List	getDefaultDimensionWeights() Valid dimension weight defaults.
java.lang.String	getDefaultElementWeight() The element weight default.
java.util.List	getDefaultElementWeights() Valid element weight defaults.
IDataElement	getDimensionWeights() The dimension weights.
IDataElement	getElementWeights() The element weights.
java.lang.String	getInterpolation() The interpolation.
java.util.List	getInterpolations() The valid interpolations
void	setDefaultDimensionWeight(java.lang.String weight) Sets the dimension weights.
void	setDefaultElementWeight(java.lang.String weight) Sets the element weights.
void	setDimensionWeights(IDataElement weights) Sets the suggested dimension weights.
void	setElementWeights(IDataElement weights) Sets the suggested element weights.
void	setInterpolation(java.lang.String interpolation) Sets the suggested interpolation.
protected void	setWeights(java.lang.String key, java.lang.String weights) Sets a weight.

Methods inherited from class jigcell.compare.objective.Objective

evaluate, getData, getFunction, getObjectiveForGenerator, setData, setFunction

Methods inherited from class jigcell.compare.data.ProgrammableDataGenerator

addEvaluationListener, clear, copy, createCustomizer, fireEvaluationError, fireEvaluationError, fireEvaluationStart, fireEvaluationStop, getAllowDescriptionQuery, getCallStack, getElement, getElement, getEvaluationLock, getInputTypeChecker, getInterface, getOutputTypeChecker, initializeSource, isCached, peekElement, peekInterface, propertyChange, removeEvaluationListener, setAllowDescriptionQuery, setInputTypeChecker, setInterfaceClass, setOutputTypeChecker, updateInterface

Methods inherited from class jigcell.compare.data.EditableDataGenerator

getPredictedCompatibility, getPredictedCompatibility, isSet, setAttribute, setComment, setElement, setElement, setOption, setState, write

Methods inherited from class jigcell.compare.data.DataGenerator

clone, compareByName, copy, generateGUID, getAttribute, getComment, getCopiedFrom, getName, getPredictedContents, getTransferData, isCopy, isCopyRelated, read, setCopyName, setName, toString

Methods inherited from class jigcell.compare.impl.DataSource

addOption, addPropertyChangeListener, addPropertyChangeListener, configure, getOption, getOptions, getOptionType, getPropertyChangeListeners, getPropertyChangeListeners, getReadDescriptionOption, getReadIconOption, getState, getWriteDescriptionOption, getWriteIconOption, persistSource, removePropertyChangeListener, removePropertyChangeListener, setOptions, setOptionType, setReadDescriptionOption, setReadIconOption, setWriteDescriptionOption, setWriteIconOption, unpersistSource

Methods inherited from class jigcell.compare.impl.Transferer

addExtension, addFlavor, createCSVTable, createFormattedTable, createHTMLTable, getExceptionRecorder, getExpectedClasses, getExpectedClasses, getExpectedClasses, getFlavors, getFlavors, getPreferredExtensions, getPreferredExtensions, getTransferClass, getTransferDataFlavors, getTransferFlavor, isDataFlavorSupported, transfer

Methods inherited from class javax.swing.TransferHandler

canImport, createTransferable, exportAsDrag, exportDone, exportToClipboard, getCopyAction, getCutAction, getPasteAction, getSourceActions, getVisualRepresentation, importData

Methods inherited from class java.lang.Object

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

Methods inherited from interface jigcell.compare.IDataGenerator

copy, getAttribute, getComment, getCopiedFrom, getElement, isCached, isCopy, isCopyRelated, setAttribute

Methods inherited from interface jigcell.compare.IReadableDataSource

getPredictedContents, getReadDescriptionOption, getReadIconOption, read, setReadDescriptionOption, setReadIconOption

Methods inherited from interface jigcell.compare.IDataSource

addOption, clone, configure, getName, getOption, getState, setOption, setState

Methods inherited from interface jigcell.compare.IDataGenerator

copy, getAttribute, getComment, getCopiedFrom, getElement, isCached, isCopy, isCopyRelated, setAttribute

Methods inherited from interface jigcell.compare.IReadableDataSource

getPredictedContents, getReadDescriptionOption, getReadIconOption, read, setReadDescriptionOption, setReadIconOption

Methods inherited from interface jigcell.compare.IDataSource

addOption, clone, configure, getName, getOption, getState, setOption, setState

Methods inherited from interface jigcell.compare.IDataGenerator

copy, getAttribute, getComment, getCopiedFrom, getElement, isCached, isCopy, isCopyRelated, setAttribute

Methods inherited from interface jigcell.compare.IReadableDataSource

getPredictedContents, getReadDescriptionOption, getReadIconOption, read, setReadDescriptionOption, setReadIconOption

Methods inherited from interface jigcell.compare.IDataSource

addOption, clone, configure, getName, getOption, getState, setOption, setState

Methods inherited from interface jigcell.compare.objective.IObjective

clear

Methods inherited from interface jigcell.compare.IProgrammableDataGenerator

addEvaluationListener, getCallStack, getElement, getEvaluationLock, getInputTypeChecker, getInterface, getOutputTypeChecker, peekElement, removeEvaluationListener

Methods inherited from interface jigcell.compare.IEditableDataGenerator

setComment, setCopyName, setElement, setName

Methods inherited from interface jigcell.compare.IWriteableDataSource

getPredictedCompatibility, getPredictedCompatibility, getWriteDescriptionOption, getWriteIconOption, setWriteDescriptionOption, setWriteIconOption, write

Field Detail

INTERPOLATION_LINEAR

public static final java.lang.String INTERPOLATION_LINEAR

Linear interpolation

See Also:

Constant Field Values

DIMENSIONWEIGHT_RECIPROCALSQUARE

public static final java.lang.String DIMENSIONWEIGHT_RECIPROCALSQUARE

Default dimension weight of the square of the reciprocal of the element

See Also:

Constant Field Values

SMALL_VALUE

protected static final double SMALL_VALUE

Size of the largest small double

See Also:

Constant Field Values

BUFFER_LENGTH_ELEMENT

protected static final int BUFFER_LENGTH_ELEMENT

Length of element slices to work with

See Also:

Constant Field Values

BUFFER_LENGTH_VALUE

protected static final int BUFFER_LENGTH_VALUE

Length of value slices to work with

See Also:

Constant Field Values

NAME_GENERATOR

protected static final java.lang.String NAME_GENERATOR

Display name of this generator

See Also:

Constant Field Values

Constructor Detail

WOSSObjective

public WOSSObjective()

Creates a new data generator based upon a least squares computation.

Method Detail

getCustomizableInstances

public static java.lang.Object getCustomizableInstances()

Generates an instance.

getDefaultDimensionWeight

public java.lang.String getDefaultDimensionWeight()

The dimension weight default.

Specified by:

getDefaultDimensionWeight in interface IDimensionWeightObjective

getDefaultDimensionWeights

public java.util.List getDefaultDimensionWeights()

Valid dimension weight defaults.

Specified by:

getDefaultDimensionWeights in interface IDimensionWeightObjective

getDefaultElementWeight

public java.lang.String getDefaultElementWeight()

The element weight default.

Specified by:

getDefaultElementWeight in interface IElementWeightObjective

getDefaultElementWeights

public java.util.List getDefaultElementWeights()

Valid element weight defaults.

Specified by:

getDefaultElementWeights in interface IElementWeightObjective

getDimensionWeights

public IDataElement getDimensionWeights()

The dimension weights.

Specified by:

getDimensionWeights in interface IDimensionWeightObjective

getElementWeights

public IDataElement getElementWeights()

The element weights.

Specified by:

getElementWeights in interface IElementWeightObjective

getInterpolation

public java.lang.String getInterpolation()

The interpolation.

Specified by:

getInterpolation in interface IInterpolationObjective

getInterpolations

public java.util.List getInterpolations()

The valid interpolations

Specified by:

getInterpolations in interface IInterpolationObjective

setDefaultDimensionWeight

public void setDefaultDimensionWeight(java.lang.String weight)

Sets the dimension weights. Implementations should act on this reasonably.

Specified by:

setDefaultDimensionWeight in interface IDimensionWeightObjective

Parameters:

weight - Dimension weight default

setDefaultElementWeight

public void setDefaultElementWeight(java.lang.String weight)

Sets the element weights. Implementations should act on this reasonably.

Specified by:

setDefaultElementWeight in interface IElementWeightObjective

Parameters:

weight - Element weight default

setDimensionWeights

public void setDimensionWeights(IDataElement weights)

Sets the suggested dimension weights. Implementations should act on this reasonably.

Specified by:

setDimensionWeights in interface IDimensionWeightObjective

Parameters:

weights - Dimension weights

setElementWeights

public void setElementWeights(IDataElement weights)

Sets the suggested element weights. Implementations should act on this reasonably.

Specified by:

setElementWeights in interface IElementWeightObjective

Parameters:

weights - Element weights

setInterpolation

public void setInterpolation(java.lang.String interpolation)

Sets the suggested interpolation. Implementations should act on this reasonably.

Specified by:

setInterpolation in interface IInterpolationObjective

Parameters:

interpolation - Interpolation

evaluate

protected IDataElement evaluate(IDataElement input)

Computes the values of this generator.

Overrides:

evaluate in class Objective

Parameters:

input - List of the inputs provided to this generator

evaluateLinear

protected IDataElement evaluateLinear(IDataElement e1,
                                      IDataElement e2,
                                      IDataElement dimensionWeights,
                                      double dimensionWeightDefault,
                                      IDataElement elementWeights,
                                      double elementWeightDefault)

Computes weighted orthogonal sum of squares with linear interpolation.

Parameters:

e1 - Experimental point set

e2 - Model point set

dimensionWeights - Linear transformation of point vectors

dimensionWeightDefault - Default dimension weight

elementWeights - Scale of point results

elementWeightDefault - Default element weight

evaluateNone

protected IDataElement evaluateNone(IDataElement e1,
                                    IDataElement e2,
                                    IDataElement dimensionWeights,
                                    double dimensionWeightDefault,
                                    IDataElement elementWeights,
                                    double elementWeightDefault)

Computes weighted orthogonal sum of squares without interpolation.

Parameters:

e1 - Experimental point set

e2 - Model point set

dimensionWeights - Linear transformation of point vectors

dimensionWeightDefault - Default dimension weight

elementWeights - Scale of point results

elementWeightDefault - Default element weight

setWeights

protected void setWeights(java.lang.String key,
                          java.lang.String weights)

Sets a weight.

Parameters:

key - Weight name

weights - Weights

evaluateLinear

private double evaluateLinear(IDataElement _e1,
                              long l,
                              double[] e1xBuffer,
                              IDataElement e2,
                              IDataElement[] e2Buffer,
                              long l2,
                              double[] e2xBuffer,
                              double[] e2xBuffer2,
                              IDataElement dimensionWeights,
                              double dimensionWeightDefault,
                              long dl,
                              double[] scaleBuffer)

Helper function for computing weighted orthogonal sum of squares with linear interpolation.

Parameters:

_e1 - One row from experimental point set

l - Length of row from experimental point set

e1xBuffer - Temporary storage for values from experimental point set

e2 - Model point set

e2Buffer - Temporary storage for rows from model point set

l2 - Number of model point set rows

e2xBuffer - Temporary storage for values from model point set

e2xBuffer2 - Temporary storage for values from model point set

dimensionWeights - Linear transformation of point vectors

dimensionWeightDefault - Default value for dimension weight

dl - Number of dimension weights available

scaleBuffer - Temporary storage for dimension weight values

evaluateLinear

private double evaluateLinear(IDataElement _e1,
                              long l,
                              double[] e1xBuffer,
                              IDataElement _e2,
                              IDataElement _e3,
                              double[] e2xBuffer,
                              double[] e2xBuffer2,
                              IDataElement dimensionWeights,
                              double dimensionWeightDefault,
                              long dl,
                              double[] scaleBuffer)

Helper function for computing weighted orthogonal sum of squares with linear interpolation.

Parameters:

_e1 - One row from experimental point set

l - Length of row from experimental point set

e1xBuffer - Temporary storage for values from experimental point set

_e2 - One row from model point set

_e3 - Next row from model point set

e2xBuffer - Temporary storage for values from model point set

e2xBuffer2 - Temporary storage for values from model point set

dimensionWeights - Linear transformation of point vectors

dimensionWeightDefault - Default value for dimension weight

dl - Number of dimension weights available

scaleBuffer - Temporary storage for dimension weight values

evaluateLinear

private double evaluateLinear(IDataElement _e1,
                              long l,
                              double[] e1xBuffer,
                              IDataElement _e2,
                              IDataElement _e3,
                              double[] e2xBuffer,
                              double[] e2xBuffer2,
                              IDataElement dimensionWeights,
                              long dl,
                              double[] scaleBuffer)

Helper function for computing weighted orthogonal sum of squares with linear interpolation.

Parameters:

_e1 - One row from experimental point set

l - Length of row from experimental point set

e1xBuffer - Temporary storage for values from experimental point set

_e2 - One row from model point set

_e3 - Next row from model point set

e2xBuffer - Temporary storage for values from model point set

e2xBuffer2 - Temporary storage for values from model point set

dimensionWeights - Linear transformation of point vectors

dl - Number of dimension weights available

scaleBuffer - Temporary storage for dimension weight values

evaluateNone

private double evaluateNone(IDataElement _e1,
                            long l,
                            double[] e1xBuffer,
                            IDataElement e2,
                            IDataElement[] e2Buffer,
                            long l2,
                            double[] e2xBuffer,
                            IDataElement dimensionWeights,
                            double dimensionWeightDefault,
                            long dl,
                            double[] scaleBuffer)

Helper function for computing weighted orthogonal sum of squares without interpolation.

Parameters:

_e1 - One row from experimental point set

l - Length of row from experimental point set

e1xBuffer - Temporary storage for values from experimental point set

e2 - Model point set

e2Buffer - Temporary storage for rows from model point set

l2 - Number of model point set rows

e2xBuffer - Temporary storage for values from model point set

dimensionWeights - Linear transformation of point vectors

dimensionWeightDefault - Default value for dimension weight

dl - Number of dimension weights available

scaleBuffer - Temporary storage for dimension weight values

evaluateNone

private double evaluateNone(IDataElement _e1,
                            long l,
                            double[] e1xBuffer,
                            IDataElement _e2,
                            double[] e2xBuffer,
                            IDataElement dimensionWeights,
                            double dimensionWeightDefault,
                            long dl,
                            double[] scaleBuffer)

Helper function for computing weighted orthogonal sum of squares without interpolation.

Parameters:

_e1 - One row from experimental point set

l - Length of row from experimental point set

e1xBuffer - Temporary storage for values from experimental point set

_e2 - One row from model point set

e2xBuffer - Temporary storage for values from model point set

dimensionWeights - Linear transformation of point vectors

dimensionWeightDefault - Default value for dimension weight

dl - Number of dimension weights available

scaleBuffer - Temporary storage for dimension weight values

evaluateNone

private double evaluateNone(IDataElement _e1,
                            long l,
                            double[] e1xBuffer,
                            IDataElement _e2,
                            double[] e2xBuffer,
                            IDataElement dimensionWeights,
                            long dl,
                            double[] scaleBuffer)

Helper function for computing weighted orthogonal sum of squares without interpolation.

Parameters:

_e1 - One row from experimental point set

l - Length of row from experimental point set

e1xBuffer - Temporary storage for values from experimental point set

_e2 - One row from model point set

e2xBuffer - Temporary storage for values from model point set

dimensionWeights - Linear transformation of point vectors

dl - Number of dimension weights available

scaleBuffer - Temporary storage for dimension weight values