CCopasiTask Class Reference

#include <CCopasiTask.h>

Inheritance diagram for CCopasiTask:

Classes
class	CDescription
class	CResult

Public Types
enum	eOutputFlagBase {   INITIALIZE = 0x01 , STREAM = 0x02 , FINISH = 0x04 , REPORT = 0x10 ,   PLOT = 0x20 , TIME_SERIES = 0x40 }
enum	OutputFlag {   NO_OUTPUT = 0 , OUTPUT_BEFORE = INITIALIZE , OUTPUT_DURING = STREAM , OUTPUT_AFTER = FINISH ,   OUTPUT = REPORT | PLOT | STREAM , OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH , OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH , ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH }
Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap
Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet
enum	Flag {   Container , Vector , Matrix , NameVector ,   Reference , ValueBool , ValueInt , ValueInt64 ,   ValueDbl , NonUniqueName , StaticString , ValueString ,   Separator , DisplayName , ModelEntity , Array ,   DataModel , Root , Gui , __SIZE }
Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList
typedef std::set< const CObjectInterface * >	ObjectSet

Public Member Functions
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CCopasiTask (const CCopasiTask &src, const CDataContainer *pParent)
	CCopasiTask (const CDataContainer *pParent, const CTaskEnum::Task &taskType, const std::string &type="Task")
void	cleanup ()
virtual void	clearCallBack ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
const CProcessReportLevel &	getCallBack () const
const CDescription &	getDescription () const
virtual const std::string &	getKey () const
CMathContainer *	getMathContainer () const
CCopasiMethod *	getMethod ()
const CCopasiMethod *	getMethod () const
COutputHandler *	getOutputHandler () const
const OutputFlag &	getOutputMode () const
CCopasiProblem *	getProblem ()
const CCopasiProblem *	getProblem () const
CReport &	getReport ()
const CReport &	getReport () const
const CResult &	getResult () const
CCopasiParameterGroup *	getSliders ()
CTaskEnum::Task	getType () const
virtual const CTaskEnum::Method *	getValidMethods () const
virtual bool	initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
const bool &	isScheduled () const
const bool &	isUpdateModel () const
virtual void	output (const COutputInterface::Activity &activity)
virtual bool	process (const bool &useInitialValues)
virtual bool	restore (const bool &updateModel=true)
virtual void	separate (const COutputInterface::Activity &activity)
virtual bool	setCallBack (CProcessReportLevel callBack)
void	setIgnoreProblemData (const bool &ignoreProblemData)
void	setMathContainer (CMathContainer *pContainer)
bool	setMethodType (const CTaskEnum::Method &type)
void	setScheduled (const bool &scheduled)
void	setType (const CTaskEnum::Task &type)
virtual void	setUpdateModel (const bool &updateModel)
virtual CData	toData () const
virtual bool	updateMatrices ()
virtual	~CCopasiTask ()
Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)
virtual bool	appendDeletedDependentData (CUndoData &undoData) const
	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)
	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
virtual std::string	getChildObjectUnits (const CDataObject *pObject) const
void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
virtual size_t	getIndex (const CDataObject *pObject) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const override
virtual objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
virtual CUndoObjectInterface *	insert (const CData &data) override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
virtual bool	remove (CDataObject *pObject)
virtual	~CDataContainer ()
Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)
void	addReference (const CDataContainer *pReference)
virtual void	calculateValue () override
	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)
virtual void	destruct () override
virtual CCommonName	getCN () const override
virtual const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName () const override
const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const
const std::string &	getObjectName () const
CDataContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override
virtual const CValidity &	getValidity () const override
virtual void *	getValuePointer () const override
bool	hasFlag (const Flag &flag) const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
bool	prerequisitsContains (const DataObjectSet &objects) const
virtual void	print (std::ostream *ostream) const override
void	removeIssue (const CIssue &issue)
void	removeReference (const CDataContainer *pReference)
bool	setObjectName (const std::string &name)
virtual bool	setObjectParent (const CDataContainer *pParent)
void	validityChanged (const CValidity &changedValidity) override
void	validityRemoved (const CValidity &changedValidity)
virtual	~CDataObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
	CObjectInterface (const CObjectInterface &src)
virtual	~CObjectInterface ()
Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()
	CUndoObjectInterface (const CUndoObjectInterface &src)
bool	generateUuid ()
const xg::Guid &	getUuid () const
bool	setUuid (const std::string &uuid)
bool	setUuid (const xg::Guid &uuid)
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CUndoObjectInterface ()

Static Public Member Functions
static CCopasiTask *	fromData (const CData &data, CUndoObjectInterface *pParent)
static bool	isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)
Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)
static void	sanitizeObjectName (std::string &name)
Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)
static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Public Attributes
std::string	Error
std::string	Warning

Protected Member Functions
bool	isTaskValid () const
virtual void	signalMathContainerChanged ()
virtual void	signalMethodChanged ()
Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
	CDataContainer (const CDataContainer &src)
void	initObjects ()
Protected Member Functions inherited from CDataObject
	CDataObject ()
	CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes
CDescription	mDescription
OutputFlag	mDoOutput
bool	mIgnoreProblemData
CVector< C_FLOAT64 >	mInitialState
std::string	mKey
unsigned C_INT32	mOutputCounter
CMathContainer *	mpContainer
CCopasiMethod *	mpMethod
COutputHandler *	mpOutputHandler
CCopasiProblem *	mpProblem
CProcessReportLevel	mProcessReport
CCopasiParameterGroup *	mpSliders
CReport	mReport
CResult	mResult
bool	mScheduled
CTaskEnum::Task	mType
bool	mUpdateModel
Protected Attributes inherited from CDataContainer
objectMap	mObjects
Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits
std::set< CDataContainer * >	mReferences
Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Private Member Functions
	CCopasiTask ()
void	initObjects ()

Additional Inherited Members
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Member Enumeration Documentation

eOutputFlagBase

enum CCopasiTask::eOutputFlagBase

Enumerator
INITIALIZE
STREAM
FINISH
REPORT
PLOT
TIME_SERIES

OutputFlag

enum CCopasiTask::OutputFlag

Enumerator
NO_OUTPUT
OUTPUT_BEFORE
OUTPUT_DURING
OUTPUT_AFTER
OUTPUT
OUTPUT_SE
OUTPUT_UI
ONLY_TIME_SERIES

Constructor & Destructor Documentation

CCopasiTask() [1/3]

CCopasiTask::CCopasiTask ( )

private

Default constructor

References initObjects().

CCopasiTask() [2/3]

CCopasiTask::CCopasiTask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	taskType,
		const std::string &	type = "Task"
	)

Specific constructor

Parameters

const	Type & taskType
const	CDataContainer * pParent
const	std::string & type (default: "Task")

References CProblemFactory::create(), initObjects(), and mpProblem.

CCopasiTask() [3/3]

CCopasiTask::CCopasiTask	(	const CCopasiTask &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const	CCopasiTask & src
const	CDataContainer * pParent (default: NULL)

References CMethodFactory::copy(), CProblemFactory::copy(), initObjects(), mpMethod, and mpProblem.

~CCopasiTask()

CCopasiTask::~CCopasiTask ( )

virtual

Destructor

References CRootContainer::getKeyFactory(), mKey, mpMethod, mpProblem, mpSliders, pdelete, and CKeyFactory::remove().

Member Function Documentation

applyData()

bool CCopasiTask::applyData ( const CData &  data, CUndoData::CChangeSet &  changes  )

virtual

Apply the provided data to the object

Parameters

const

CData & data

Returns

bool success

Reimplemented from CDataContainer.

References CCopasiParameterGroup::applyData(), CDataContainer::applyData(), fatalError, CDataObject::getObjectFromCN(), CData::getProperty(), CCopasiMethod::getSubType(), CData::isSetProperty(), CData::METHOD, CData::METHOD_TYPE, CTaskEnum::MethodName, mpMethod, mpProblem, mReport, mScheduled, mType, mUpdateModel, CData::PROBLEM, CReport::setAppend(), CReport::setConfirmOverwrite(), setMethodType(), CReport::setReportDefinition(), CReport::setTarget(), CData::TASK_REPORT, CData::TASK_REPORT_APPEND, CData::TASK_REPORT_CONFIRM_OVERWRITE, CData::TASK_REPORT_TARGET, CData::TASK_SCHEDULED, CData::TASK_TYPE, CData::TASK_UPDATE_MODEL, CTaskEnum::TaskName, CDataValue::toBool(), CDataValue::toData(), toEnum(), and CDataValue::toString().

cleanup()

void CCopasiTask::cleanup

(

)

Cleanup function

clearCallBack()

void CCopasiTask::clearCallBack ( )

virtual

resets the currently set callback by calling setCallBack(NULL)

References setCallBack().

createUndoData()

void CCopasiTask::createUndoData ( CUndoData &  undoData, const CUndoData::Type &  type, const CData &  oldData = CData(), const CCore::Framework &  framework = CCore::Framework::ParticleNumbers  ) const

virtual

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

CUndoData	& undoData
const	CUndoData::Type & type
const	CData & oldData (default: empty data)
const	CCore::Framework & framework (default: CCore::Framework::ParticleNumbers)

Returns

CUndoData undoData

Reimplemented from CDataContainer.

References CUndoData::addPostProcessData(), CUndoData::addPreProcessData(), CUndoData::addProperty(), CReport::append(), CUndoData::CHANGE, CUndoData::clear(), CReport::confirmOverwrite(), CMethodFactory::create(), CCopasiParameterGroup::createUndoData(), CDataContainer::createUndoData(), CDataObject::getCN(), CUndoData::getNewData(), CUndoData::getOldData(), CData::getProperty(), CReport::getReportDefinition(), CCopasiMethod::getSubType(), CReport::getTarget(), getType(), CUndoData::isChangedProperty(), CData::METHOD, CData::METHOD_TYPE, CTaskEnum::MethodName, mIgnoreProblemData, mpMethod, mpProblem, mReport, mScheduled, mType, mUpdateModel, CCore::ParticleNumbers, CData::PROBLEM, CData::TASK_REPORT, CData::TASK_REPORT_APPEND, CData::TASK_REPORT_CONFIRM_OVERWRITE, CData::TASK_REPORT_TARGET, CData::TASK_SCHEDULED, CData::TASK_TYPE, CData::TASK_UPDATE_MODEL, CTaskEnum::TaskName, CDataValue::toData(), CCopasiParameterGroup::toData(), toEnum(), CDataValue::toString(), and CTaskEnum::UnsetMethod.

fromData()

CCopasiTask * CCopasiTask::fromData ( const CData &  data, CUndoObjectInterface *  pParent  )

static

Static method to create a CDataObject based on the provided data

Parameters

const

CData & data

Returns

CCopasiTask * pDataObject

CCopasiTask class. This class is used to describe a task in COPASI. This class is intended to be used as the parent class for all tasks within COPASI.

Created for COPASI by Stefan Hoops 2003

References CTaskFactory::create(), CData::getProperty(), NO_PARENT, CData::OBJECT_NAME, CDataObject::setObjectName(), CData::TASK_TYPE, CTaskEnum::TaskName, toEnum(), and CDataValue::toString().

getCallBack()

const CProcessReportLevel & CCopasiTask::getCallBack

(

)

const

Returns

the currently set callback

References mProcessReport.

getDescription()

const CCopasiTask::CDescription & CCopasiTask::getDescription

(

)

const

Retrieve the description

References mDescription.

getKey()

const std::string & CCopasiTask::getKey ( ) const

virtual

Retrieve the key for the task.

Returns

std::string key

Reimplemented from CDataObject.

References mKey.

Referenced by CCopasiXML::saveTaskList(), CLNAProblem::setSteadyStateRequested(), and CMCAProblem::setSteadyStateRequested().

getMathContainer()

CMathContainer * CCopasiTask::getMathContainer

(

)

const

Retrieve the pointer to the container used for calculations

Returns

CMathContainer * pContainer

References mpContainer.

Referenced by CCopasiProblem::CCopasiProblem(), CMethodFactory::copy(), CProblemFactory::copy(), CMethodFactory::create(), CProblemFactory::create(), and COutputAssistant::createDefaultOutput().

getMethod() [1/2]

CCopasiMethod * CCopasiTask::getMethod

(

)

Retrieve the method

References mpMethod.

Referenced by SEDMLImporter::applyAlgorithm(), CFitProblem::calculate(), CSEDMLExporter::createTimeCourseTask(), COptProblem::initialize(), CNewtonMethod::initialize(), CTSSAProblem::printResult(), TaskHandler::processEnd(), MethodHandler::processStart(), and CCopasiXML::saveTaskList().

getMethod() [2/2]

const CCopasiMethod * CCopasiTask::getMethod

(

)

const

Retrieve the method

References mpMethod.

getOutputHandler()

COutputHandler * CCopasiTask::getOutputHandler

(

)

const

References mpOutputHandler.

getOutputMode()

const OutputFlag& CCopasiTask::getOutputMode ( ) const

inline

References mDoOutput.

getProblem() [1/2]

CCopasiProblem * CCopasiTask::getProblem

(

)

Retrieve the problem

References mpProblem.

Referenced by ResultData::appliesTo(), ResultData::applyToModelStateFromOptTask(), COptProblem::calculate(), CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CModel::createEventsForTimeseries(), COutputAssistant::createPlot(), CSEDMLExporter::createScanTask(), CSEDMLExporter::createSteadyStateTask(), CSEDMLExporter::createTimeCourseTask(), CNewtonMethod::doIntegration(), CODEExporter::exportExpression(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), SEDMLImporter::importTask(), CEFMMethod::initialize(), CSSAMethod::initialize(), CFitProblem::initialize(), CNewtonMethod::initialize(), isTaskValid(), CLNATask::process(), CMCATask::process(), CScanTask::processCallback(), TaskHandler::processEnd(), TaskHandler::processStart(), CCopasiXML::saveTaskList(), ResultData::setOptItemStartValues(), SEDMLImporter::updateCopasiTaskForSimulation(), and ResultData::updateFitItemsFromOptItems().

getProblem() [2/2]

const CCopasiProblem * CCopasiTask::getProblem

(

)

const

Retrieve the problem

References mpProblem.

getReport() [1/2]

CReport & CCopasiTask::getReport

(

)

Retrieve the report

References mReport.

Referenced by CDataModel::addDefaultReports(), CSEDMLExporter::createDataGenerators(), COptProblem::initialize(), ReportTargetHandler::processStart(), and CCopasiXML::saveTaskList().

getReport() [2/2]

const CReport & CCopasiTask::getReport

(

)

const

Retrieve the report

References mReport.

getResult()

const CCopasiTask::CResult & CCopasiTask::getResult

(

)

const

Retrieve the result

References mResult.

getSliders()

CCopasiParameterGroup * CCopasiTask::getSliders

(

)

Retrieve a pointer to the group of sliders.

Returns

CCopasiParameterGroup * pSliders

References mpSliders.

getType()

CTaskEnum::Task CCopasiTask::getType

(

void

)

const

Retrieve the type of the task

Returns

CTaskEnum::Task type

References mType.

Referenced by CPlotSpecification::appliesTo(), COptProblem::calculate(), CAnalyticsTask::CAnalyticsTask(), CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), CTaskFactory::copy(), COscillationTask::COscillationTask(), CMethodFactory::create(), COutputAssistant::createPlot(), createUndoData(), CScanTask::CScanTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTimeSensTask::CTimeSensTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), COutputAssistant::getListOfDefaultOutputDescriptions(), COptProblem::getSubtaskType(), CTrajectoryTask::load(), ParameterGroupHandler::processEnd(), TaskHandler::processEnd(), CCopasiXML::saveTaskList(), and setMethodType().

getValidMethods()

const CTaskEnum::Method * CCopasiTask::getValidMethods ( ) const

virtual

Retrieve the list of valid methods

Returns

const CTaskEnum::Method * pValidMethods

Reimplemented in CSteadyStateTask, CMCATask, CFitTask, COptTask, CMoietiesTask, CLNATask, CCrossSectionTask, CAnalyticsTask, CTSSATask, CTrajectoryTask, CTimeSensTask, CSensTask, CScanTask, CLyapTask, and CEFMTask.

References CTaskEnum::UnsetMethod.

Referenced by CMethodFactory::create(), and setMethodType().

initialize()

bool CCopasiTask::initialize ( const OutputFlag &  of, COutputHandler *  pOutputHandler, std::ostream *  pOstream  )

virtual

Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler
std::ostream	* pOstream (default: NULL)

Returns

bool success

Reimplemented in CSteadyStateTask, CMCATask, CFitTask, COptTask, CMoietiesTask, CLNATask, CCrossSectionTask, CAnalyticsTask, CTSSATask, CTrajectoryTask, CTimeSensTask, CSensTask, CScanTask, COscillationTask, CLyapTask, and CEFMTask.

References COutputHandler::addInterface(), CCopasiMessage::COMMANDLINE, COutputHandler::compile(), CMathContainer::getInitialState(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CReport::getTarget(), isTaskValid(), MCCopasiTask, mDoOutput, mInitialState, mOutputCounter, mpContainer, mpOutputHandler, mReport, NO_OUTPUT, CReport::open(), REPORT, CVector< CType >::resize(), and CCopasiMessage::WARNING.

Referenced by COptProblem::calculate(), CEFMTask::initialize(), CLyapTask::initialize(), COscillationTask::initialize(), CScanTask::initialize(), CSensTask::initialize(), CTimeSensTask::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CLNATask::initialize(), CMoietiesTask::initialize(), COptTask::initialize(), CMCATask::initialize(), CSteadyStateTask::initialize(), CSensMethod::initialize(), COptProblem::initializeSubtaskBeforeOutput(), and CScanTask::initSubtask().

initObjects()

void CCopasiTask::initObjects ( )

private

References CDataContainer::addObjectReference(), CModel::getMathContainer(), CDataModel::getModel(), CDataObject::getObjectDataModel(), mOutputCounter, CCopasiTimer::PROCESS, setMathContainer(), CDataObject::ValueInt, and CCopasiTimer::WALL.

Referenced by CCopasiTask().

isScheduled()

const bool & CCopasiTask::isScheduled

(

)

const

Check whether the task is scheduled

Returns

const bool & scheduled

References mScheduled.

Referenced by CSEDMLExporter::createTasks(), and CCopasiXML::saveTaskList().

isTaskValid()

bool CCopasiTask::isTaskValid ( ) const

protected

Check whether the task definition is valid

Returns

bool isValid

References CCopasiMessage::ERROR, CDataObject::getObjectName(), getProblem(), CCopasiProblem::getSubTask(), CDataContainer::insert(), MCCopasiTask, mpContainer, mpMethod, and mpProblem.

Referenced by CScanTask::initialize(), CSensTask::initialize(), initialize(), COptTask::initialize(), and setCallBack().

isUpdateModel()

const bool & CCopasiTask::isUpdateModel

(

)

const

Check whether the task must update the model

Returns

const bool & updateModel

References mUpdateModel.

Referenced by CSensMethod::initialize(), CScanTask::processCallback(), and CCopasiXML::saveTaskList().

isValidMethod()

bool CCopasiTask::isValidMethod ( const CTaskEnum::Method &  method, const CTaskEnum::Method *  validMethods  )

static

Check whether the given method is in the list of valid methods This list must end with CCopasiMethod::unset

Parameters

const	CTaskEnum::Method & method
const	CTaskEnum::Method * validMethods

Returns

bool isValid

References C_INT32, and CTaskEnum::UnsetMethod.

Referenced by CMethodFactory::create(), and setMethodType().

output()

void CCopasiTask::output ( const COutputInterface::Activity &  activity )

virtual

Perform an output event for the current activity

Parameters

const

Activity & activity

Reimplemented in CTimeSensTask.

References COutputInterface::AFTER, COutputInterface::BEFORE, COutputInterface::DURING, mDoOutput, mOutputCounter, mpOutputHandler, NO_OUTPUT, COutputHandler::output(), OUTPUT_AFTER, and OUTPUT_BEFORE.

Referenced by COptMethodNL2SOL::calcr(), CExperimentSet::calculateStatistics(), COptMethodPS::create(), COptMethodPraxis::evaluateFunction(), CCrossSectionTask::eventCallBack(), CAnalyticsTask::finish(), CCrossSectionTask::finish(), CLyapTask::methodCallback(), COptMethodPS::move(), COptMethodCoranaWalk::optimise(), COptMethodDE::optimise(), COptMethodEP::optimise(), COptMethodGA::optimise(), COptMethodGASR::optimise(), COptMethodHookeJeeves::optimise(), COptMethodLevenbergMarquardt::optimise(), COptMethodNelderMead::optimise(), COptMethodNL2SOL::optimise(), COptMethodPraxis::optimise(), COptMethodPS::optimise(), COptMethodSA::optimise(), COptMethodSRES::optimise(), COptMethodSS::optimise(), COptMethodStatistics::optimise(), COptMethodSteepestDescent::optimise(), COptMethodTruncatedNewton::optimise(), CRandomSearch::optimise(), CTrajectoryMethod::output(), CTimeSensTask::output(), CEFMTask::process(), CLyapTask::process(), COscillationTask::process(), CScanTask::process(), CSensTask::process(), CTSSATask::process(), CCrossSectionTask::process(), CLNATask::process(), CMoietiesTask::process(), COptTask::process(), CFitTask::process(), CMCATask::process(), CSteadyStateTask::process(), CScanTask::processCallback(), CTrajectoryTask::processStep(), CTrajectoryTask::processTrajectory(), CTrajectoryTask::processValues(), and COptMethodTruncatedNewton::sFun().

process()

bool CCopasiTask::process ( const bool &  useInitialValues )

virtual

Process the task with or without initializing to the initial state.

Parameters

const

bool & useInitialValues

Returns

bool success

Reimplemented in CSteadyStateTask, CMCATask, CFitTask, COptTask, CMoietiesTask, CLNATask, CCrossSectionTask, CAnalyticsTask, CTSSATask, CTrajectoryTask, CTimeSensTask, CSensTask, CScanTask, COscillationTask, CLyapTask, and CEFMTask.

Referenced by COptProblem::calculate(), CSensMethod::do_target_calculation(), and CScanTask::processCallback().

restore()

bool CCopasiTask::restore ( const bool &  updateModel = true )

virtual

Perform necessary cleanup procedures

Parameters

const

bool & updateModel (default: true)

Reimplemented in CSteadyStateTask, CCrossSectionTask, and CAnalyticsTask.

References CMathContainer::getCountFixed(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getInitialState(), CMathContainer::getState(), CMathContainer::isAutonomous(), CMathContainer::isStateValid(), mInitialState, mpContainer, mpProblem, mUpdateModel, CCore::ParticleNumbers, CMathContainer::pushAllTransientValues(), CMathContainer::pushInitialState(), CCopasiProblem::restore(), setCallBack(), CMathContainer::setInitialState(), CMathContainer::updateInitialValues(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().

Referenced by CSensMethod::restore(), COptProblem::restore(), CScanProblem::restore(), CFitProblem::restore(), CAnalyticsTask::restore(), and CCrossSectionTask::restore().

separate()

void CCopasiTask::separate ( const COutputInterface::Activity &  activity )

virtual

Introduce an additional separator into the output

Parameters

const

Activity & activity

References COutputInterface::AFTER, COutputInterface::BEFORE, COutputInterface::DURING, mDoOutput, mpOutputHandler, OUTPUT_AFTER, OUTPUT_BEFORE, and COutputHandler::separate().

Referenced by CScanTask::outputSeparatorCallback().

setCallBack()

bool CCopasiTask::setCallBack ( CProcessReportLevel  callBack )

virtual

Set the call back of the task

Parameters

CProcessReport

& callBack

Returns

bool success

Reimplemented in CMCATask, CFitTask, COscillationTask, COptTask, CMoietiesTask, CLNATask, and CEFMTask.

References isTaskValid(), mpMethod, mProcessReport, and CCopasiMethod::setCallBack().

Referenced by clearCallBack(), CNewtonMethod::doIntegration(), CFitProblem::initialize(), CSensMethod::initialize(), COptProblem::initializeSubtaskBeforeOutput(), CScanTask::initSubtask(), CSensMethod::process(), CScanTask::process(), CLNATask::process(), CMCATask::process(), restore(), CSteadyStateTask::restore(), CEFMTask::setCallBack(), CLNATask::setCallBack(), CMoietiesTask::setCallBack(), COptProblem::setCallBack(), COptTask::setCallBack(), COscillationTask::setCallBack(), CFitProblem::setCallBack(), CFitTask::setCallBack(), CSensMethod::setCallBack(), and CMCATask::setCallBack().

setIgnoreProblemData()

void CCopasiTask::setIgnoreProblemData

(

const bool &

ignoreProblemData

)

Set whether the task shall ignoew problem data

Parameters

const

bool & ignoreProblemData

References mIgnoreProblemData.

setMathContainer()

void CCopasiTask::setMathContainer

(

CMathContainer *

pContainer

)

Set the pointer to container used for calculations

Parameters

CMathContainer

* pContainer

References mpContainer, mpMethod, mpProblem, CCopasiMethod::setMathContainer(), CCopasiProblem::setMathContainer(), and signalMathContainerChanged().

Referenced by SEDMLImporter::importTask(), CFitProblem::initialize(), CSensMethod::initialize(), COptProblem::initializeSubtaskBeforeOutput(), initObjects(), CScanTask::initSubtask(), TaskHandler::processStart(), and SEDMLImporter::updateCopasiTaskForSimulation().

setMethodType()

bool CCopasiTask::setMethodType

(

const CTaskEnum::Method &

type

)

Set the method type applied to solve the task

Parameters

const

CTaskEnum::Method & type

Returns

bool success

References CMethodFactory::create(), CCopasiMethod::getSubType(), getType(), getValidMethods(), isValidMethod(), mpMethod, pdelete, and signalMethodChanged().

Referenced by SEDMLImporter::applyAlgorithm(), applyData(), CNewtonMethod::initialize(), and MethodHandler::processStart().

setScheduled()

void CCopasiTask::setScheduled

(

const bool &

scheduled

)

Set whether the task is scheduled

Parameters

const

bool & scheduled

References mScheduled.

Referenced by SEDMLImporter::importTask(), TaskHandler::processStart(), and SEDMLImporter::updateCopasiTaskForSimulation().

setType()

void CCopasiTask::setType

(

const CTaskEnum::Task &

type

)

Set the type of the task

Parameters

CTaskEnum::Task

& type

References mType.

setUpdateModel()

void CCopasiTask::setUpdateModel ( const bool &  updateModel )

virtual

Set whether the task must update the model

Parameters

const

bool & updateModel

References mUpdateModel.

Referenced by CFitProblem::initialize(), CSensMethod::process(), and TaskHandler::processStart().

signalMathContainerChanged()

void CCopasiTask::signalMathContainerChanged ( )

protectedvirtual

Signal that the math container has changed

Reimplemented in CTrajectoryTask, and CTimeSensTask.

Referenced by setMathContainer().

signalMethodChanged()

void CCopasiTask::signalMethodChanged ( )

protectedvirtual

Signal that the method has changed

Reimplemented in CTrajectoryTask, and CTimeSensTask.

Referenced by setMethodType().

toData()

CData CCopasiTask::toData ( ) const

virtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CDataContainer.

References CData::addProperty(), CReport::append(), CReport::confirmOverwrite(), CDataObject::getCN(), CReport::getReportDefinition(), CCopasiMethod::getSubType(), CReport::getTarget(), CData::METHOD, CData::METHOD_TYPE, CTaskEnum::MethodName, mIgnoreProblemData, mpMethod, mpProblem, mReport, mScheduled, mType, mUpdateModel, CData::PROBLEM, CData::TASK_REPORT, CData::TASK_REPORT_APPEND, CData::TASK_REPORT_CONFIRM_OVERWRITE, CData::TASK_REPORT_TARGET, CData::TASK_SCHEDULED, CData::TASK_TYPE, CData::TASK_UPDATE_MODEL, CTaskEnum::TaskName, CCopasiParameterGroup::toData(), CDataContainer::toData(), and CTaskEnum::UnsetMethod.

updateMatrices()

virtual bool CCopasiTask::updateMatrices ( )

inlinevirtual

Resizes result matrices and updates array annotations for a specific task. For now this will be hard coded in the respective derived classes. We may introduce a more generic mechanism for this in the future. This is used when we need to know about the data structures of a task result without actually performing the task, e.g. when selecting objects for output. For now we assume that this functionality is also performed when initialize() is called.

Reimplemented in CSteadyStateTask, CMCATask, CLNATask, CTSSATask, CTimeSensTask, and CSensTask.

Member Data Documentation

Error

std::string CCopasiTask::Error

mDescription

CDescription CCopasiTask::mDescription

protected

The description of the task.

Referenced by getDescription().

mDoOutput

OutputFlag CCopasiTask::mDoOutput

protected

Referenced by getOutputMode(), initialize(), output(), and separate().

mIgnoreProblemData

bool CCopasiTask::mIgnoreProblemData

protected

Referenced by createUndoData(), setIgnoreProblemData(), and toData().

mInitialState

CVector< C_FLOAT64 > CCopasiTask::mInitialState

protected

The state of the model before execution of the task. If mUpdateModel is false this state is restored.

Referenced by initialize(), restore(), and CSteadyStateTask::restore().

mKey

std::string CCopasiTask::mKey

protected

The key of the task

Referenced by getKey(), and ~CCopasiTask().

mOutputCounter

unsigned C_INT32 CCopasiTask::mOutputCounter

protected

Referenced by initialize(), initObjects(), and output().

mpContainer

CMathContainer* CCopasiTask::mpContainer

protected

A pointer to the math container used for calculation

Referenced by CAnalyticsTask::computeSelectedStatistics(), CAnalyticsTask::createEvent(), CCrossSectionTask::createEvent(), CAnalyticsTask::eventCallBack(), CCrossSectionTask::eventCallBack(), CAnalyticsTask::finish(), CEFMTask::getInternalSpecies(), getMathContainer(), CEFMTask::getNetReaction(), CTSSATask::initialize(), initialize(), CFitTask::initialize(), CSteadyStateTask::initialize(), CScanTask::initSubtask(), isTaskValid(), CLyapTask::process(), CScanTask::process(), CSensTask::process(), CTimeSensTask::process(), CTSSATask::process(), CAnalyticsTask::process(), CCrossSectionTask::process(), CLNATask::process(), CMoietiesTask::process(), CMCATask::process(), CSteadyStateTask::process(), CTimeSensTask::processStart(), CTrajectoryTask::processStart(), CTSSATask::processStart(), CTSSATask::processStep(), CTimeSensTask::processStep(), CTrajectoryTask::processStep(), CTrajectoryTask::processTrajectory(), CTrajectoryTask::processValues(), CAnalyticsTask::relativeDifferenceOfStates(), CCrossSectionTask::relativeDifferenceOfStates(), CAnalyticsTask::removeEvent(), CCrossSectionTask::removeEvent(), restore(), CSteadyStateTask::restore(), setMathContainer(), CTimeSensTask::signalMathContainerChanged(), CTrajectoryTask::signalMathContainerChanged(), CTSSATask::updateMatrices(), and CSteadyStateTask::updateMatrices().

mpMethod

CCopasiMethod* CCopasiTask::mpMethod

protected

The method used to solve the problem.

Referenced by applyData(), CAnalyticsTask::CAnalyticsTask(), CCopasiTask(), CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CLyapTask::CLyapTask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), createUndoData(), CScanTask::CScanTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTimeSensTask::CTimeSensTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CEFMTask::getFluxModeDescription(), getMethod(), CEFMTask::getReactionEquation(), CEFMTask::initialize(), CLyapTask::initialize(), COscillationTask::initialize(), CScanTask::initialize(), CTimeSensTask::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CAnalyticsTask::initialize(), CCrossSectionTask::initialize(), CLNATask::initialize(), CMoietiesTask::initialize(), COptTask::initialize(), CMCATask::initialize(), CSteadyStateTask::initialize(), isTaskValid(), CLNATask::load(), CMCATask::load(), CSteadyStateTask::load(), CTrajectoryTask::load(), CLNATask::printResult(), CMCATask::printResult(), CEFMTask::process(), COscillationTask::process(), CScanTask::process(), CSensTask::process(), CTSSATask::process(), CLNATask::process(), CMoietiesTask::process(), COptTask::process(), CFitTask::process(), CMCATask::process(), CSteadyStateTask::process(), CEFMTask::setCallBack(), setCallBack(), CMoietiesTask::setCallBack(), COscillationTask::setCallBack(), CFitTask::setCallBack(), setMathContainer(), setMethodType(), CTimeSensTask::signalMethodChanged(), CTrajectoryTask::signalMethodChanged(), toData(), CSensTask::updateMatrices(), CTimeSensTask::updateMatrices(), CTSSATask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), and ~CCopasiTask().

mpOutputHandler

COutputHandler* CCopasiTask::mpOutputHandler

protected

Referenced by getOutputHandler(), initialize(), output(), CMoietiesTask::process(), and separate().

mpProblem

CCopasiProblem* CCopasiTask::mpProblem

protected

The problem of the task

Referenced by applyData(), CCopasiTask(), CFitTask::CFitTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), createUndoData(), CScanTask::CScanTask(), CFitTask::fixBuild55(), CScanTask::fixBuild81(), CEFMTask::getFluxModeDescription(), CEFMTask::getFluxModes(), CEFMTask::getNetReactionData(), getProblem(), CEFMTask::getReactionEquation(), CEFMTask::getSpeciesChanges(), CEFMTask::initialize(), CLyapTask::initialize(), COscillationTask::initialize(), CScanTask::initialize(), CTimeSensTask::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CAnalyticsTask::initialize(), CCrossSectionTask::initialize(), CLNATask::initialize(), CMoietiesTask::initialize(), COptTask::initialize(), CFitTask::initialize(), CMCATask::initialize(), CSteadyStateTask::initialize(), CScanTask::initSubtask(), isTaskValid(), CLNATask::load(), CMCATask::load(), CSteadyStateTask::load(), CTrajectoryTask::load(), CLNATask::printResult(), CMCATask::printResult(), COscillationTask::process(), CScanTask::process(), CSensTask::process(), CTSSATask::process(), CCrossSectionTask::process(), CLNATask::process(), COptTask::process(), CFitTask::process(), CMCATask::process(), CSteadyStateTask::process(), restore(), CEFMTask::setCallBack(), CLNATask::setCallBack(), CMoietiesTask::setCallBack(), COptTask::setCallBack(), COscillationTask::setCallBack(), CFitTask::setCallBack(), CMCATask::setCallBack(), setMathContainer(), toData(), CSensTask::updateMatrices(), CTSSATask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), and ~CCopasiTask().

mProcessReport

CProcessReportLevel CCopasiTask::mProcessReport

protected

progress bar handler

Referenced by CAnalyticsTask::eventCallBack(), CCrossSectionTask::eventCallBack(), CAnalyticsTask::finish(), CCrossSectionTask::finish(), getCallBack(), CLyapTask::methodCallback(), CLyapTask::process(), CScanTask::process(), CTimeSensTask::process(), CTSSATask::process(), CAnalyticsTask::process(), CCrossSectionTask::process(), CLNATask::process(), COptTask::process(), CFitTask::process(), CMCATask::process(), CSteadyStateTask::process(), CScanTask::processCallback(), CTimeSensTask::processStep(), CTrajectoryTask::processStep(), CTrajectoryTask::processTrajectory(), CTrajectoryTask::processValues(), CEFMTask::setCallBack(), setCallBack(), CLNATask::setCallBack(), CMoietiesTask::setCallBack(), COptTask::setCallBack(), CFitTask::setCallBack(), and CMCATask::setCallBack().

mpSliders

CCopasiParameterGroup* CCopasiTask::mpSliders

protected

Pointer to group of sliders associated with the task.

Referenced by getSliders(), and ~CCopasiTask().

mReport

CReport CCopasiTask::mReport

protected

The report that belongs to this specific task

Referenced by applyData(), createUndoData(), getReport(), CScanTask::initialize(), initialize(), CLNATask::initialize(), CMCATask::initialize(), and toData().

mResult

CResult CCopasiTask::mResult

protected

The result of the task.

Referenced by getResult().

mScheduled

bool CCopasiTask::mScheduled

protected

Tells whether the task is scheduled for execution

Referenced by applyData(), createUndoData(), isScheduled(), CLNATask::load(), CMCATask::load(), CSteadyStateTask::load(), CTrajectoryTask::load(), setScheduled(), and toData().

mType

CTaskEnum::Task CCopasiTask::mType

protected

The type of the task

Referenced by applyData(), createUndoData(), getType(), setType(), and toData().

mUpdateModel

bool CCopasiTask::mUpdateModel

protected

Tells whether the task shall update the model with the result. The restore method must act accordingly.

Referenced by applyData(), createUndoData(), isUpdateModel(), restore(), CSteadyStateTask::restore(), setUpdateModel(), and toData().

Warning

std::string CCopasiTask::Warning

---

The documentation for this class was generated from the following files:

• CCopasiTask.h
• CCopasiTask.cpp