jigcell.compare.cellcycle
Class JigCellRunManagerTransform

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.JigCellRunManagerTransform

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 JigCellRunManagerTransform
extends Transform

Uses the JigCell Run Manager to execute a simulation.

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

static java.lang.String	ATTRIBUTE_RUNFILE Attribute for the name of the run file
static java.lang.String	ATTRIBUTE_RUNNUMBER Attribute for the number of the run within the run file
static java.lang.String	CONFIG_SIMULATORS Property key for the list of simulators to register
protected static java.lang.String	NAME_TRANSFORM Display name of this transform
protected static java.lang.String	OPTION_COLUMNHEADERS Option for the column headers
protected static java.lang.String	OPTION_DEFAULTRUN Option for the run number to use if the default run has been selected
protected static java.lang.String	OPTION_RUNDATA Option for the run data
static int	RUN_DEFAULT Run number when a run should be picked automatically
static int	RUN_UNKNOWN Run number when no run has been selected
protected static java.lang.String	SEPARATOR_ANNOTATION Separator between files and numbers
protected static java.lang.String	TYPE_ANNOTATION The type of objects this transform produces

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

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

Method Summary

protected IDataElement	evaluate() Evaluates the associated element.
ITransformAnnotation	getAnnotation() An annotation object for this generator.
protected java.util.List	getColumnHeaders(int runNumber) Retrieves the names of the columns that will come back when a run is executed.
static java.lang.Object	getCustomizableInstances() Generates an instance.
protected int	getDefaultRunNumber() The run number to use if the default run is selected.
protected jigcell.runsupport.RunFile	getRunData() Loads the run file if one is specified and not already cached.
java.lang.String	getRunFile() The run file to read from.
java.util.List	getRunNames() A List[String] containing the names of the runs in the current run file.
int	getRunNumber() The run number to use.
static void	initializeSimulators(Config config) Registers any simulators identified by the configuration.
boolean	isReorderable() Whether the evaluation of this transform has no indirect dependencies.
boolean	isRunnable() Whether this transform can be executed.
protected IDataElement	run(int runNumber) Executes one of the runs from the run file.
protected void	setDefaultRunNumber(int runNumber) Sets the run number to use if the default run is selected.
void	setRunFile(java.lang.String runFile) Sets the currently used run file.
void	setRunNumber(int runNumber) Sets the currently used run number.

Methods inherited from class jigcell.compare.transform.Transform

clear, copy, evaluate, flush, getAllowContextInsertion, getAllowContextRemoval, getCompatibleTransforms, getContainer, getDependencies, getEvaluationContext, getNextStatement, getPreviousElement, getPreviousStatement, getSource, getTransformForGenerator, hasNextStatement, hasPreviousStatement, initializeSource, setAllowContextInsertion, setAllowContextRemoval, setAnnotation, setCompatibleTransforms, setContainer, setEvaluationContext, 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

RUN_UNKNOWN

public static final int RUN_UNKNOWN

Run number when no run has been selected

See Also:

Constant Field Values

RUN_DEFAULT

public static final int RUN_DEFAULT

Run number when a run should be picked automatically

See Also:

Constant Field Values

ATTRIBUTE_RUNFILE

public static final java.lang.String ATTRIBUTE_RUNFILE

Attribute for the name of the run file

See Also:

Constant Field Values

ATTRIBUTE_RUNNUMBER

public static final java.lang.String ATTRIBUTE_RUNNUMBER

Attribute for the number of the run within the run file

See Also:

Constant Field Values

CONFIG_SIMULATORS

public static final java.lang.String CONFIG_SIMULATORS

Property key for the list of simulators to register

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_COLUMNHEADERS

protected static final java.lang.String OPTION_COLUMNHEADERS

Option for the column headers

See Also:

Constant Field Values

OPTION_DEFAULTRUN

protected static final java.lang.String OPTION_DEFAULTRUN

Option for the run number to use if the default run has been selected

See Also:

Constant Field Values

OPTION_RUNDATA

protected static final java.lang.String OPTION_RUNDATA

Option for the run data

See Also:

Constant Field Values

SEPARATOR_ANNOTATION

protected static final java.lang.String SEPARATOR_ANNOTATION

Separator between files and numbers

See Also:

Constant Field Values

TYPE_ANNOTATION

protected static final java.lang.String TYPE_ANNOTATION

The type of objects this transform produces

See Also:

Constant Field Values

Constructor Detail

JigCellRunManagerTransform

public JigCellRunManagerTransform()

Creates a new transform that can perform a run evaluation.

Method Detail

getCustomizableInstances

public static java.lang.Object getCustomizableInstances()

Generates an instance.

initializeSimulators

public static void initializeSimulators(Config config)

Registers any simulators identified by the configuration.

Parameters:

config - Comparator configuration

getAnnotation

public ITransformAnnotation getAnnotation()

An annotation object for this generator.

Specified by:

getAnnotation in interface ITransform

Overrides:

getAnnotation in class Transform

getRunFile

public java.lang.String getRunFile()

The run file to read from.

getRunNames

public java.util.List getRunNames()

A List[String] containing the names of the runs in the current run file.

getRunNumber

public int getRunNumber()

The run number to use.

isReorderable

public boolean isReorderable()

Whether the evaluation of this transform has no indirect dependencies.

Specified by:

isReorderable in interface ITransform

Overrides:

isReorderable in class Transform

isRunnable

public boolean isRunnable()

Whether this transform can be executed.

Specified by:

isRunnable in interface ITransform

Overrides:

isRunnable in class Transform

setRunFile

public void setRunFile(java.lang.String runFile)

Sets the currently used run file.

Parameters:

runFile - Run file

setRunNumber

public void setRunNumber(int runNumber)

Sets the currently used run number.

Parameters:

runNumber - Run number

evaluate

protected IDataElement evaluate()

Evaluates the associated element.

Overrides:

evaluate in class Transform

getColumnHeaders

protected java.util.List getColumnHeaders(int runNumber)
                                   throws java.io.IOException

Retrieves the names of the columns that will come back when a run is executed.

Parameters:

runNumber - Run number

Throws:

java.io.IOException

getDefaultRunNumber

protected int getDefaultRunNumber()

The run number to use if the default run is selected.

getRunData

protected jigcell.runsupport.RunFile getRunData()

Loads the run file if one is specified and not already cached.

run

protected IDataElement run(int runNumber)
                    throws java.io.IOException

Executes one of the runs from the run file.

Parameters:

runNumber - Run number

Throws:

java.io.IOException

setDefaultRunNumber

protected void setDefaultRunNumber(int runNumber)

Sets the run number to use if the default run is selected.

Parameters:

runNumber - Run number