org.cipres.kepler

Class GUIRunCIPRes

java.lang.Object

ptolemy.kernel.util.NamedObj

ptolemy.kernel.InstantiableNamedObj

ptolemy.kernel.Entity<T>

ptolemy.kernel.ComponentEntity<T>

ptolemy.actor.AtomicActor<TypedIOPort>

ptolemy.actor.TypedAtomicActor

org.cipres.kepler.GUIRunCIPRes

All Implemented Interfaces:

java.lang.Cloneable, java.util.Observer, Actor, Executable, FiringsRecordable, Initializable, TypedActor, Changeable, Debuggable, DebugListener, Derivable, Instantiable, ModelErrorHandler, MoMLExportable, Moveable, Nameable

Direct Known Subclasses:

ClustalWSeqAlign, PAUPConsensusTrees, PAUPInfer

public class GUIRunCIPRes
extends TypedAtomicActor
implements java.util.Observer

This actor calls external Cipres applications with GUIGen interfaces. The GUIRunCIPRes actor provides a template to invoke external Cipres applications. A set of parameters is configured in the actor to collect application related information. The value of these parameters will be fed to the GUIRun object when the actor fires. Thus the GUIRun object will invoke the corresponding application with those values, like the input/output file names and the working directory. After the execution, if the external program returns correctly, the standard output of the execution will be sent to the standard output file, the standard error will be sent to the standard error file, and the program output file name will be sent to the outputParameterValue port. The user can also set some words to be monitored in the standard output stream. The observer/observable design pattern is used here. The GUIRunCIPRes object is an observer. The GUIRun object is an observable. Whenever the GUIRun object find any of these monitored words in the standard output steam of the program execution, it will notify the GUIRunCIPRes objects to promote the user handling the issue. Usually the GUIRunCIPRes actor will stop the execution of the program.

Author:

Zhijie Guan

Nested Class Summary

Nested classes/interfaces inherited from class ptolemy.kernel.Entity

Entity.ContainedObjectsIterator

Field Summary

Fields

Modifier and Type	Field and Description
protected org.cipres.helpers.GUIRun	_grun GUIRun object to invoke external programs.
FileParameter	command The command path and name are defined in this parameter.
FileParameter	errorFile The standard error file's path and name are defined in this parameter.
TypedIOPort	exitCode The exit code of the execution is sent out through this port.
TypedIOPort	inputParameterName The input parameter name (usually "infile") is sent through this port.
TypedIOPort	inputParameterValue The input parameter value (usually the name of the input file of the execution) is sent through this port.
Parameter	monitoredErrorWords The monitored words are defined in this parameter.
FileParameter	outputFile The standard output file's path and name are defined in this parameter.
TypedIOPort	outputParameterValue The output parameter value, usually the name of the output file of the execution, is sent out throught this port.
Parameter	parameterForOutput The GUIRun parameter to be send out is defined in this parameter.
TypedIOPort	standardError The standard error stream of the execution is sent out through this port.
TypedIOPort	standardOutput The standard output stream of the execution is sent out through this port.
FileParameter	uiXMLFile The GUIGen xml file's path and name are defined in this parameter.
Parameter	workingDirectory The workfing directory of the external program is defined in this parameter.

Fields inherited from class ptolemy.actor.TypedAtomicActor

_typesValid

Fields inherited from class ptolemy.actor.AtomicActor

_actorFiringListeners, _initializables, _notifyingActorFiring, _stopRequested

Fields inherited from class ptolemy.kernel.util.NamedObj

_changeListeners, _changeLock, _changeRequests, _debugging, _debugListeners, _deferChangeRequests, _elementName, _isPersistent, _verbose, _workspace, ATTRIBUTES, CLASSNAME, COMPLETE, CONTENTS, DEEP, FULLNAME, LINKS

Fields inherited from interface ptolemy.actor.Executable

COMPLETED, NOT_READY, STOP_ITERATING

Constructor Summary

Constructors

Constructor and Description
GUIRunCIPRes(CompositeEntity container, java.lang.String name) Construct GUIRunCIPRes source with the given container and name.

Method Summary

Modifier and Type	Method and Description
void	fire() Invoke the external program by setting the parameters of the execution using GUIGen.
void	postExecutionProcess(java.lang.String outputFileName) This function processes the output data after the execution.
boolean	postfire() Post fire the actor.
void	update(java.util.Observable guiRunObj, java.lang.Object obj) Observer function update guiRunObj is the GUIRun object that runs the program obj is the String message that GUIRun object send back.

Methods inherited from class ptolemy.actor.TypedAtomicActor

_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints

Methods inherited from class ptolemy.actor.AtomicActor

_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, getCausalityInterface, getDirector, getExecutiveDirector, getManager, initialize, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, prefire, preinitialize, pruneDependencies, recordFiring, removeActorFiringListener, removeDependency, removeInitializable, setContainer, stop, stopFire, terminate, wrapup

Methods inherited from class ptolemy.kernel.ComponentEntity

_adjustDeferrals, _checkContainer, _getContainedObject, _propagateExistence, getContainer, instantiate, isAtomic, isOpaque, moveDown, moveToFirst, moveToIndex, moveToLast, moveUp, propagateExistence, setName

Methods inherited from class ptolemy.kernel.Entity

_addPort, _description, _exportMoMLContents, _removePort, _validateSettables, connectedPortList, connectedPorts, containedObjectsIterator, getAttribute, getPort, getPorts, linkedRelationList, linkedRelations, portList, removeAllPorts, setClassDefinition, uniqueName

Methods inherited from class ptolemy.kernel.InstantiableNamedObj

_setParent, exportMoML, getChildren, getElementName, getParent, getPrototypeList, isClassDefinition, isWithinClassDefinition

Methods inherited from class ptolemy.kernel.util.NamedObj

_addAttribute, _adjustOverride, _attachText, _cloneFixAttributeFields, _containedDecorators, _copyChangeRequestList, _debug, _debug, _debug, _debug, _debug, _executeChangeRequests, _getIndentPrefix, _isMoMLSuppressed, _markContentsDerived, _notifyHierarchyListenersAfterChange, _notifyHierarchyListenersBeforeChange, _propagateValue, _removeAttribute, _splitName, _stripNumericSuffix, addChangeListener, addDebugListener, addHierarchyListener, attributeChanged, attributeDeleted, attributeList, attributeList, decorators, deepContains, depthInHierarchy, description, description, event, executeChangeRequests, exportMoML, exportMoML, exportMoML, exportMoML, exportMoMLPlain, getAttribute, getAttributes, getChangeListeners, getClassName, getDecoratorAttribute, getDecoratorAttributes, getDerivedLevel, getDerivedList, getDisplayName, getFullName, getModelErrorHandler, getName, getName, getSource, handleModelError, isDeferringChangeRequests, isOverridden, isPersistent, lazyContainedObjectsIterator, message, notifyOfNameChange, propagateValue, propagateValues, removeAttribute, removeChangeListener, removeDebugListener, removeHierarchyListener, requestChange, setClassName, setDeferringChangeRequests, setDerivedLevel, setDisplayName, setModelErrorHandler, setPersistent, setSource, sortContainedObjects, toplevel, toString, validateSettables, workspace

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ptolemy.actor.Actor

createReceivers, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, newReceiver, outputPortList

Methods inherited from interface ptolemy.actor.Executable

isFireFunctional, isStrict, iterate, prefire, stop, stopFire, terminate

Methods inherited from interface ptolemy.actor.Initializable

addInitializable, initialize, preinitialize, removeInitializable, wrapup

Methods inherited from interface ptolemy.kernel.util.Nameable

description, getContainer, getDisplayName, getFullName, getName, getName, setName

Methods inherited from interface ptolemy.kernel.util.Derivable

getDerivedLevel, getDerivedList, propagateValue

Field Detail

command

public FileParameter command

The command path and name are defined in this parameter.

uiXMLFile

public FileParameter uiXMLFile

The GUIGen xml file's path and name are defined in this parameter.

outputFile

public FileParameter outputFile

The standard output file's path and name are defined in this parameter.

errorFile

public FileParameter errorFile

The standard error file's path and name are defined in this parameter.

workingDirectory

public Parameter workingDirectory

The workfing directory of the external program is defined in this parameter.

parameterForOutput

public Parameter parameterForOutput

The GUIRun parameter to be send out is defined in this parameter. Usually this GUIRun parameter is "outfile".

monitoredErrorWords

public Parameter monitoredErrorWords

The monitored words are defined in this parameter.

standardOutput

public TypedIOPort standardOutput

The standard output stream of the execution is sent out through this port.

standardError

public TypedIOPort standardError

The standard error stream of the execution is sent out through this port.

exitCode

public TypedIOPort exitCode

The exit code of the execution is sent out through this port.

outputParameterValue

public TypedIOPort outputParameterValue

The output parameter value, usually the name of the output file of the execution, is sent out throught this port.

inputParameterName

public TypedIOPort inputParameterName

The input parameter name (usually "infile") is sent through this port.

inputParameterValue

public TypedIOPort inputParameterValue

The input parameter value (usually the name of the input file of the execution) is sent through this port.

_grun

protected org.cipres.helpers.GUIRun _grun

GUIRun object to invoke external programs.

Constructor Detail

GUIRunCIPRes

public GUIRunCIPRes(CompositeEntity container,
                    java.lang.String name)
             throws NameDuplicationException,
                    IllegalActionException

Construct GUIRunCIPRes source with the given container and name.

Parameters:

container - The container.

name - The name of this actor.

Throws:

IllegalActionException - If the entity cannot be contained by the proposed container.

NameDuplicationException - If the container already has an actor with this name.

Method Detail

fire

public void fire()
          throws IllegalActionException

Invoke the external program by setting the parameters of the execution using GUIGen. The monitored words are being monitored during the execution.

Specified by:

fire in interface Executable

Overrides:

fire in class AtomicActor<TypedIOPort>

Throws:

IllegalActionException - If it is thrown by the send() method sending out the token.

postExecutionProcess

public void postExecutionProcess(java.lang.String outputFileName)

This function processes the output data after the execution. Usually subclasses of the GUIRunCIPRes class will implement this function.

Parameters:

outputFileName - is the output file name of the execution

update

public void update(java.util.Observable guiRunObj,
                   java.lang.Object obj)

Observer function update guiRunObj is the GUIRun object that runs the program obj is the String message that GUIRun object send back. This string message is the standard output/error line that contains the monitored words

Specified by:

update in interface java.util.Observer

postfire

public boolean postfire()
                 throws IllegalActionException

Post fire the actor. Return false to indicated that the process has finished. If it returns true, the process will continue indefinitely.

Specified by:

postfire in interface Executable

Overrides:

postfire in class AtomicActor<TypedIOPort>

Returns:

True if execution can continue into the next iteration.

Throws:

IllegalActionException - Not thrown in this base class.