jigcell.compare.cellcycle
Class BuddingYeastScanTransform

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
                                  jigcell.compare.cellcycle.BuddingYeastScanTransform

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

public class BuddingYeastScanTransform
extends GenericScanTransform

Computes the phenotype of a budding yeast 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

private static class	BuddingYeastScanTransform.BuddingYeastScanEvent An event that occurs during the scan.
private static class	BuddingYeastScanTransform.BuddingYeastScanPoint A single time course point used by the scan.

Nested classes/interfaces inherited from class jigcell.compare.cellcycle.GenericScanTransform

GenericScanTransform.CellCycleReport

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_ESP1CHECKED Attribute for whether esp1 is checked
protected static java.lang.String	NAME_TRANSFORM Display name of this transform

Fields inherited from class jigcell.compare.cellcycle.GenericScanTransform

ATTRIBUTE_WILDTYPETRANSFORMNAME, OPTION_WILDTYPETRANSFORM

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

	BuddingYeastScanTransform() Creates a new transform that can perform a run evaluation.
protected	BuddingYeastScanTransform(boolean esp1Checked) Creates a new transform that can perform a run evaluation.

Method Summary

protected IDataElement	evaluate(IDataElement input) Evaluates the transform.
static java.lang.Object	getCustomizableInstances() Generates an instance.
double	getThresholdBud() The threshold for budding.
double	getThresholdEsp1() The threshold for activation.
double	getThresholdOriHigh() The threshold for origin firing.
double	getThresholdOriLow() The threshold for origin licensing.
double	getThresholdSpn() The threshold for spindle alignment.
boolean	isEsp1Checked() Whether Esp1 is checked during the cell cycle.
void	setEsp1Checked(boolean checked) Controls whether the concentration of Esp1 is a requirement for proceeding through checkpoints.

Methods inherited from class jigcell.compare.cellcycle.GenericScanTransform

clear, computeWildtypeProperties, getAnnotation, getMaximumMass, getMinimumMass, getThresholdCycB, getWildtypeMass, getWildtypeTime, getWildtypeTransformName, isSteadyState, setEvaluationContext, setWildtypeTransformName

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_ESP1CHECKED

public static final java.lang.String ATTRIBUTE_ESP1CHECKED

Attribute for whether esp1 is checked

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

Constructor Detail

BuddingYeastScanTransform

public BuddingYeastScanTransform()

Creates a new transform that can perform a run evaluation.

BuddingYeastScanTransform

protected BuddingYeastScanTransform(boolean esp1Checked)

Creates a new transform that can perform a run evaluation.

Parameters:

esp1Checked - Whether the concentration of Esp1 is monitored during cell cycle events

Method Detail

getCustomizableInstances

public static java.lang.Object getCustomizableInstances()

Generates an instance.

getThresholdBud

public double getThresholdBud()

The threshold for budding.

getThresholdEsp1

public double getThresholdEsp1()

The threshold for activation.

getThresholdOriLow

public double getThresholdOriLow()

The threshold for origin licensing.

getThresholdOriHigh

public double getThresholdOriHigh()

The threshold for origin firing.

getThresholdSpn

public double getThresholdSpn()

The threshold for spindle alignment.

isEsp1Checked

public boolean isEsp1Checked()

Whether Esp1 is checked during the cell cycle.

setEsp1Checked

public void setEsp1Checked(boolean checked)

Controls whether the concentration of Esp1 is a requirement for proceeding through checkpoints.

Parameters:

checked - Whether Esp1 is checked during the cell cycle

evaluate

protected IDataElement evaluate(IDataElement input)

Evaluates the transform.

Overrides:

evaluate in class GenericScanTransform

Parameters:

input - Transform input