jigcell.compare.cellcycle
Class GenericPhenotypeObjective

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.cellcycle.GenericPhenotypeObjective

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, IObjective

Direct Known Subclasses:

BuddingYeastPhenotypeObjective

public class GenericPhenotypeObjective
extends Objective

Measures the difference between two generic phenotypes.

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

Field Summary

protected static java.lang.String

NAME_OBJECTIVE Display name of this objective function

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.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.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.IWriteableDataSource

OPTION_WRITEDESCRIPTION, OPTION_WRITEICON

Constructor Summary

GenericPhenotypeObjective()
Creates a new objective function that can evaluate a phenotype.

Method Summary

protected static boolean	checkPhenotype(IDataElement element, long index, IDataElement.Type type, boolean optional, java.lang.String field) Validates that the data in a given element matches the phenotype pattern.
protected IDataElement	evaluate(IDataElement input) Computes the values of this generator.
protected double	evaluateInviable(IDataElement experiment, IDataElement transform) Computes the objective for an experiment that is inviable.
protected double	evaluateViable(IDataElement experiment, IDataElement transform) Computes the objective for an experiment that is viable.
static java.lang.Object	getCustomizableInstances() Generates an instance.
double	getScaleCycleCount() Scale factor for cycle counts.
double	getScaleDivisionMass() Scale factor for division mass.
double	getScaleG1Length() Scale factor for time in G1.
double	getScaleSubcycleCount() Scale factor for subcycle counts.
double	getWeightArrestStage() Penalty weight for arrest stage.
double	getWeightArrestType() Penalty weight for arrest type.
double	getWeightCycleCount() Penalty weight for cycle count.
double	getWeightDivisionMass() Penalty weight for division mass.
double	getWeightG1Length() Penalty weight for time in G1.
double	getWeightSubcycleCount() Penalty weight for subcycle count.
double	getWeightViability() Penalty weight for viability.

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.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.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 java.awt.datatransfer.Transferable

getTransferData, getTransferDataFlavors, isDataFlavorSupported

Methods inherited from interface jigcell.compare.IWriteableDataSource

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

Field Detail

NAME_OBJECTIVE

protected static final java.lang.String NAME_OBJECTIVE

Display name of this objective function

See Also:

Constant Field Values

Constructor Detail

GenericPhenotypeObjective

public GenericPhenotypeObjective()

Creates a new objective function that can evaluate a phenotype.

Method Detail

getCustomizableInstances

public static java.lang.Object getCustomizableInstances()

Generates an instance.

checkPhenotype

protected static boolean checkPhenotype(IDataElement element,
                                        long index,
                                        IDataElement.Type type,
                                        boolean optional,
                                        java.lang.String field)

Validates that the data in a given element matches the phenotype pattern. Returns whether data is present.

Parameters:

element - Data element

index - Index into element

type - Type expected at index

optional - Whether an empty value is acceptable

field - Name of the field being matched

getScaleCycleCount

public double getScaleCycleCount()

Scale factor for cycle counts.

getScaleDivisionMass

public double getScaleDivisionMass()

Scale factor for division mass.

getScaleG1Length

public double getScaleG1Length()

Scale factor for time in G1.

getScaleSubcycleCount

public double getScaleSubcycleCount()

Scale factor for subcycle counts.

getWeightArrestStage

public double getWeightArrestStage()

Penalty weight for arrest stage.

getWeightArrestType

public double getWeightArrestType()

Penalty weight for arrest type.

getWeightCycleCount

public double getWeightCycleCount()

Penalty weight for cycle count.

getWeightDivisionMass

public double getWeightDivisionMass()

Penalty weight for division mass.

getWeightG1Length

public double getWeightG1Length()

Penalty weight for time in G1.

getWeightSubcycleCount

public double getWeightSubcycleCount()

Penalty weight for subcycle count.

getWeightViability

public double getWeightViability()

Penalty weight for viability.

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

evaluateInviable

protected double evaluateInviable(IDataElement experiment,
                                  IDataElement transform)

Computes the objective for an experiment that is inviable.

Parameters:

experiment - Experimental data

transform - Transform result

evaluateViable

protected double evaluateViable(IDataElement experiment,
                                IDataElement transform)

Computes the objective for an experiment that is viable.

Parameters:

experiment - Experimental data

transform - Transform result