jigcell.compare.cellcycle
Class GenericScanTransform

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.transform.Transform
                              jigcell.compare.cellcycle.GenericScanTransform

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, ITransform

Direct Known Subclasses:

BuddingYeastScanTransform

public class GenericScanTransform
extends Transform

Computes the phenotype of a generic mutant from a time course of concentrations.

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

protected static class	GenericScanTransform.CellCycleReport The statistics collected from a cycle.
private static class	GenericScanTransform.GenericScanEvent An event that occurs during the scan.
private static class	GenericScanTransform.GenericScanPoint A single time course point used by the scan.

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

static java.lang.String	ATTRIBUTE_WILDTYPETRANSFORMNAME Attribute for the name of the transform that computes the wildtype properties
protected static java.lang.String	NAME_TRANSFORM Display name of this transform
protected static java.lang.String	OPTION_WILDTYPETRANSFORM Option for the transform that computes the wildtype properties

Fields inherited from class jigcell.compare.transform.Transform

allowContextInsertion, allowContextRemoval, container, context

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.transform.ITransform

OPTION_ANNOTATION, OPTION_COMPATIBLE, OPTION_NEXTSTATEMENT, OPTION_PREVIOUSSTATEMENT, OPTION_TRANSFORM, PROPERTY_TRANSFORM_EDIT, RESOURCE_TRANSFORMS

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

GenericScanTransform()
Creates a new transform that can perform a run evaluation.

Method Summary

void	clear() Nulls out the stored element.
protected IDataElement	computeWildtypeProperties() Computes the wildtype properties for the growth medium of this mutant.
protected IDataElement	evaluate(IDataElement input) Evaluates the transform.
ITransformAnnotation	getAnnotation() An annotation object for this generator.
static java.lang.Object	getCustomizableInstances() Generates an instance.
double	getMaximumMass() The maximum mass before the mutant is declared inviable.
double	getMinimumMass() The minimum mass before the mutant is declared inviable.
double	getThresholdCycB() The threshold for cyclin-B.
protected double	getWildtypeMass() The mass at division for the wildtype cell.
protected double	getWildtypeTime() The cycle time for the wildtype cell.
java.lang.String	getWildtypeTransformName() The name of the transform to evaluate for the wildtype properties.
protected boolean	isSteadyState(GenericScanTransform.CellCycleReport oldCycle, GenericScanTransform.CellCycleReport cycle) Whether the system is in steady state.
void	setEvaluationContext(ITransformContext context) Sets the runtime context for performing an evaluation.
void	setWildtypeTransformName(java.lang.String transformName) Sets the name of the transform to evaluate for the wildtype properties.

Methods inherited from class jigcell.compare.transform.Transform

copy, evaluate, flush, getAllowContextInsertion, getAllowContextRemoval, getCompatibleTransforms, getContainer, getDependencies, getEvaluationContext, getNextStatement, getPreviousElement, getPreviousStatement, getSource, getTransformForGenerator, hasNextStatement, hasPreviousStatement, initializeSource, isReorderable, isRunnable, setAllowContextInsertion, setAllowContextRemoval, setAnnotation, setCompatibleTransforms, setContainer, setNextStatement, setPreviousStatement

Methods inherited from class jigcell.compare.data.ProgrammableDataGenerator

addEvaluationListener, createCustomizer, fireEvaluationError, fireEvaluationError, fireEvaluationStart, fireEvaluationStop, getAllowDescriptionQuery, getCallStack, getElement, getElement, getEvaluationLock, getInputTypeChecker, getInterface, getOutputTypeChecker, 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.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

ATTRIBUTE_WILDTYPETRANSFORMNAME

public static final java.lang.String ATTRIBUTE_WILDTYPETRANSFORMNAME

Attribute for the name of the transform that computes the wildtype properties

See Also:

Constant Field Values

NAME_TRANSFORM

protected static final java.lang.String NAME_TRANSFORM

Display name of this transform

See Also:

Constant Field Values

OPTION_WILDTYPETRANSFORM

protected static final java.lang.String OPTION_WILDTYPETRANSFORM

Option for the transform that computes the wildtype properties

See Also:

Constant Field Values

Constructor Detail

GenericScanTransform

public GenericScanTransform()

Creates a new transform that can perform a run evaluation.

Method Detail

getCustomizableInstances

public static java.lang.Object getCustomizableInstances()

Generates an instance.

clear

public void clear()

Nulls out the stored element.

Specified by:

clear in interface IEditableDataGenerator

Specified by:

clear in interface ITransform

Overrides:

clear in class Transform

getAnnotation

public ITransformAnnotation getAnnotation()

An annotation object for this generator.

Specified by:

getAnnotation in interface ITransform

Overrides:

getAnnotation in class Transform

getMaximumMass

public double getMaximumMass()

The maximum mass before the mutant is declared inviable.

getMinimumMass

public double getMinimumMass()

The minimum mass before the mutant is declared inviable.

getThresholdCycB

public double getThresholdCycB()

The threshold for cyclin-B.

getWildtypeTransformName

public java.lang.String getWildtypeTransformName()

The name of the transform to evaluate for the wildtype properties.

setEvaluationContext

public void setEvaluationContext(ITransformContext context)

Sets the runtime context for performing an evaluation.

Specified by:

setEvaluationContext in interface ITransform

Overrides:

setEvaluationContext in class Transform

Parameters:

context - Evaluation context

setWildtypeTransformName

public void setWildtypeTransformName(java.lang.String transformName)

Sets the name of the transform to evaluate for the wildtype properties.

Parameters:

transformName - Name of transform

computeWildtypeProperties

protected IDataElement computeWildtypeProperties()

Computes the wildtype properties for the growth medium of this mutant.

evaluate

protected IDataElement evaluate(IDataElement input)

Evaluates the transform.

Overrides:

evaluate in class Transform

Parameters:

input - Transform input

getWildtypeMass

protected double getWildtypeMass()

The mass at division for the wildtype cell.

getWildtypeTime

protected double getWildtypeTime()

The cycle time for the wildtype cell.

isSteadyState

protected boolean isSteadyState(GenericScanTransform.CellCycleReport oldCycle,
                                GenericScanTransform.CellCycleReport cycle)

Whether the system is in steady state.

Parameters:

oldCycle - Previous cycle statistics

cycle - Current cycle statistics