jigcell.compare.cellcycle
Class BuddingYeastPhenotypeObjective

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
                                  jigcell.compare.cellcycle.BuddingYeastPhenotypeObjective

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

public class BuddingYeastPhenotypeObjective
extends GenericPhenotypeObjective

Measures the difference between two budding yeast 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

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

Method Summary

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.

Methods inherited from class jigcell.compare.cellcycle.GenericPhenotypeObjective

checkPhenotype, evaluate, getScaleCycleCount, getScaleDivisionMass, getScaleG1Length, getScaleSubcycleCount, getWeightArrestStage, getWeightArrestType, getWeightCycleCount, getWeightDivisionMass, getWeightG1Length, getWeightSubcycleCount, getWeightViability

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

BuddingYeastPhenotypeObjective

public BuddingYeastPhenotypeObjective()

Creates a new objective function that can evaluate a phenotype.

Method Detail

getCustomizableInstances

public static java.lang.Object getCustomizableInstances()

Generates an instance.

evaluateInviable

protected double evaluateInviable(IDataElement experiment,
                                  IDataElement transform)

Computes the objective for an experiment that is inviable.

Overrides:

evaluateInviable in class GenericPhenotypeObjective

Parameters:

experiment - Experimental data

transform - Transform result

evaluateViable

protected double evaluateViable(IDataElement experiment,
                                IDataElement transform)

Computes the objective for an experiment that is viable.

Overrides:

evaluateViable in class GenericPhenotypeObjective

Parameters:

experiment - Experimental data

transform - Transform result