CCopasiTask Class Reference

#include <CCopasiTask.h>

Inheritance diagram for CCopasiTask:

Collaboration 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_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 }
enum	Type {   steadyState = 0, timeCourse, scan, fluxMode,   optimization, parameterFitting, mca, lyap,   tssAnalysis, sens, moieties, crosssection,   lna, unset }
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap
Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet
typedef std::vector< Refresh * >	DataUpdateSequence
Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet
typedef std::vector < CObjectInterface * >	UpdateSequence

Public Member Functions
	CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task")
	CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task")
	CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL)
void	cleanup ()
virtual CCopasiMethod *	createMethod (const int &type) const
CProcessReport *	getCallBack () const
const CDescription &	getDescription () const
virtual const std::string &	getKey () const
CCopasiMethod *	getMethod ()
const CCopasiMethod *	getMethod () const
COutputHandler *	getOutputHandler () const
const OutputFlag &	getOutputMode () const
CCopasiProblem *	getProblem ()
const CCopasiProblem *	getProblem () const
CReport &	getReport ()
const CResult &	getResult () const
CCopasiParameterGroup *	getSliders ()
Type	getType () 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 ()
virtual void	separate (const COutputInterface::Activity &activity)
virtual bool	setCallBack (CProcessReport *pCallBack)
virtual bool	setMethodType (const int &type)
void	setScheduled (const bool &scheduled)
void	setType (const Type &type)
void	setUpdateModel (const bool &updateModel)
virtual bool	updateMatrices ()
virtual	~CCopasiTask ()
Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)
	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)
	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)
virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const
virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const
virtual const objectMap &	getObjects () const
virtual std::string	getUnits () const
virtual const CCopasiObject *	getValueObject () const
virtual bool	remove (CCopasiObject *pObject)
virtual	~CCopasiContainer ()
Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)
	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)
void	clearDirectDependencies ()
void	clearRefresh ()
bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const
void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const
virtual CCopasiObjectName	getCN () const
virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
const std::string &	getObjectName () const
CCopasiContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const
virtual Refresh *	getRefresh () const
UpdateMethod *	getUpdateMethod () const
virtual void *	getValuePointer () const
bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
bool	hasUpdateMethod () const
bool	isArray () const
bool	isContainer () const
bool	isDataModel () const
bool	isMatrix () const
bool	isNameVector () const
bool	isNonUniqueName () const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
bool	isReference () const
bool	isRoot () const
bool	isSeparator () const
bool	isStaticString () const
bool	isValueBool () const
bool	isValueDbl () const
bool	isValueInt () const
bool	isValueInt64 () const
bool	isValueString () const
bool	isVector () const
virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const
virtual void	print (std::ostream *ostream) const
void	removeDirectDependency (const CCopasiObject *pObject)
void	setDirectDependencies (const DataObjectSet &directDependencies)
bool	setObjectName (const std::string &name)
virtual bool	setObjectParent (const CCopasiContainer *pParent)
void	setObjectValue (const C_FLOAT64 &value)
void	setObjectValue (const C_INT32 &value)
void	setObjectValue (const bool &value)
template<class CType >
void	setRefresh (CType *pType, void(CType::*method)(void))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
virtual	~CCopasiObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
virtual	~CObjectInterface ()

Static Public Member Functions
static bool	isValidMethod (const unsigned int &method, const unsigned int *validMethods)
Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)

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

Static Public Attributes
static const std::string	TypeName []
static const unsigned int	ValidMethods []
static const char *	XMLType []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Attributes
CDescription	mDescription
OutputFlag	mDoOutput
std::string	mKey
unsigned C_INT32	mOutputCounter
CProcessReport *	mpCallBack
CState *	mpInitialState
CCopasiMethod *	mpMethod
COutputHandler *	mpOutputHandler
CCopasiProblem *	mpProblem
CCopasiParameterGroup *	mpSliders
CReport	mReport
CResult	mResult
bool	mScheduled
Type	mType
bool	mUpdateModel
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
void	initObjects ()

Additional Inherited Members
Protected Types inherited from CCopasiObject
enum	Flag {   Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8,   Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80,   ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800,   Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000,   Root = 0x10000, Gui = 0x20000 }
Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
void	initObjects ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 39 of file CCopasiTask.h.

Member Enumeration Documentation

enum CCopasiTask::eOutputFlagBase

Enumerator
INITIALIZE
STREAM
FINISH
REPORT
PLOT
TIME_SERIES

Definition at line 89 of file CCopasiTask.h.

  {
    INITIALIZE = 0x01,
    STREAM = 0x02,
    FINISH = 0x04,
    REPORT = 0x10,
    PLOT = 0x20,
    TIME_SERIES = 0x40
  };

enum CCopasiTask::OutputFlag

Enumerator
NO_OUTPUT
OUTPUT_BEFORE
OUTPUT_AFTER
OUTPUT
OUTPUT_SE
OUTPUT_UI
ONLY_TIME_SERIES

Definition at line 99 of file CCopasiTask.h.

  {
    //do no output
    NO_OUTPUT = 0,
    OUTPUT_BEFORE = INITIALIZE,
    OUTPUT_AFTER = FINISH,
    //do output except time series, but do not initialize/finish
    OUTPUT = REPORT | PLOT | STREAM,
    //do output, including initialization and closing
    OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH,
    OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH,
    // only do time series
    ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH
  };

enum CCopasiTask::Type

Enumeration of the types of tasks known to COPASI.

Enumerator
steadyState
timeCourse
scan
fluxMode
optimization
parameterFitting
mca
lyap
tssAnalysis
sens
moieties
crosssection
lna
unset

Definition at line 45 of file CCopasiTask.h.

  {
    steadyState = 0,
    timeCourse,
    scan,
    fluxMode,
    optimization,
    parameterFitting,
    mca,
    lyap,
    tssAnalysis,
    sens,
    moieties,
    crosssection,
    lna,
    unset
  };

Constructor & Destructor Documentation

CCopasiTask::CCopasiTask	(	const std::string &	name = "NoName",
		const CCopasiContainer *	pParent = NULL,
		const std::string &	type = "Task"
	)

Default constructor

Definition at line 100 of file CCopasiTask.cpp.

References initObjects().

                                                :
    CCopasiContainer(name, pParent, type),
    mType(CCopasiTask::unset),
    mKey(CCopasiRootContainer::getKeyFactory()->add("Task", this)),
    mDescription(this),
    mResult(this),
    mScheduled(false),
    mUpdateModel(false),
    mpInitialState(NULL),
    mpProblem(NULL),
    mpMethod(NULL),
    mReport(),
    mpCallBack(NULL),
    mpSliders(NULL),
    mDoOutput(OUTPUT_SE),
    mOutputCounter(0)
{initObjects();}

CCopasiTask::CCopasiTask	(	const Type &	taskType,
		const CCopasiContainer *	pParent = NULL,
		const std::string &	type = "Task"
	)

Specific constructor

Parameters

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

Definition at line 120 of file CCopasiTask.cpp.

References initObjects().

                                                :
    CCopasiContainer(CCopasiTask::TypeName[taskType], pParent, type),
    mType(taskType),
    mKey(CCopasiRootContainer::getKeyFactory()->add("Task", this)),
    mDescription(this),
    mResult(this),
    mScheduled(false),
    mUpdateModel(false),
    mpInitialState(NULL),
    mpProblem(NULL),
    mpMethod(NULL),
    mReport(),
    mpCallBack(NULL),
    mpSliders(NULL),
    mDoOutput(OUTPUT_SE),
    mpOutputHandler(NULL),
    mOutputCounter(0)
{initObjects();}

CCopasiTask::CCopasiTask	(	const CCopasiTask &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

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

Definition at line 141 of file CCopasiTask.cpp.

References initObjects().

                                                          :
    CCopasiContainer(src, pParent),
    mType(src.mType),
    mKey(CCopasiRootContainer::getKeyFactory()->add("Task", this)),
    mDescription(src.mDescription, this),
    mResult(src.mResult, this),
    mScheduled(src.mScheduled),
    mUpdateModel(src.mUpdateModel),
    mpInitialState(src.mpInitialState ? new CState(*src.mpInitialState) : NULL),
    mpProblem(NULL),
    mpMethod(NULL),
    mReport(src.mReport),
    mpCallBack(NULL),
    mpSliders(NULL),
    mDoOutput(OUTPUT_SE),
    mpOutputHandler(NULL),
    mOutputCounter(0)
{initObjects();}

CCopasiTask::~CCopasiTask ( )

virtual

Destructor

Definition at line 161 of file CCopasiTask.cpp.

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

{
  CCopasiRootContainer::getKeyFactory()->remove(mKey);

  pdelete(mpInitialState);
  pdelete(mpProblem);
  pdelete(mpMethod);
  pdelete(mpSliders);
}

Member Function Documentation

void CCopasiTask::cleanup

(

)

Cleanup function

Definition at line 324 of file CCopasiTask.cpp.

{}

CCopasiMethod * CCopasiTask::createMethod ( const int &  type ) const

virtual

Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.

Parameters

const

CCopasiMethod::SubType & type

Returns

CCopasiMethod *

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

Definition at line 307 of file CCopasiTask.cpp.

Referenced by CQTaskMethodWidget::setActiveMethod().

{
  return NULL;
}

CProcessReport * CCopasiTask::getCallBack

(

)

const

Definition at line 196 of file CCopasiTask.cpp.

References mpCallBack.

{
  return mpCallBack;
}

const CCopasiTask::CDescription & CCopasiTask::getDescription

(

)

const

Retrieve the description

Definition at line 318 of file CCopasiTask.cpp.

References mDescription.

Referenced by operator<<().

{return mDescription;}

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

virtual

Retrieve the key for the task.

Returns

std::string key

Reimplemented from CCopasiObject.

Definition at line 180 of file CCopasiTask.cpp.

References mKey.

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

{return mKey;}

CCopasiMethod * CCopasiTask::getMethod

(

)

Retrieve the method

Definition at line 312 of file CCopasiTask.cpp.

References mpMethod.

Referenced by CQEFMWidget::createMethod(), CSEDMLExporter::createTimeCourseTask(), CQTSSAResultSubWidget::displayResult(), CCopasiXMLParser::TaskElement::end(), CQTSSAResultWidget::enterProtected(), TaskWidget::enterProtected(), CQTSSAResultSubWidget::init(), CNewtonMethod::initialize(), StateSubwidget::loadAll(), CLNAResultWidget::loadFromBackend(), CMCAResultWidget::loadFromBackend(), CQLNAWidget::loadParameterTable(), CQMCAWidget::loadParameterTable(), SteadyStateWidget::loadTask(), operator<<(), CQSimpleSelectionTree::populateTree(), CTSSAProblem::printResult(), TaskWidget::revertBtnClicked(), CQTSSAWidget::runTask(), CQTaskMethodWidget::saveMethod(), CQLNAWidget::saveParameterTable(), CQMCAWidget::saveParameterTable(), SensitivitiesWidget::saveTask(), SteadyStateWidget::saveTask(), CCopasiXML::saveTaskList(), CQTaskMethodWidget::setTask(), CCopasiXMLParser::MethodElement::start(), and test000087::test_simulate_reaction_flux_reference_1().

{return mpMethod;}

const CCopasiMethod * CCopasiTask::getMethod

(

)

const

Retrieve the method

Definition at line 314 of file CCopasiTask.cpp.

References mpMethod.

{return mpMethod;}

COutputHandler * CCopasiTask::getOutputHandler

(

)

const

Definition at line 201 of file CCopasiTask.cpp.

References mpOutputHandler.

{
  return mpOutputHandler;
}

const OutputFlag& CCopasiTask::getOutputMode ( ) const

inline

Definition at line 457 of file CCopasiTask.h.

References mDoOutput.

  {return mDoOutput;};

CCopasiProblem * CCopasiTask::getProblem

(

)

Retrieve the problem

Definition at line 296 of file CCopasiTask.cpp.

References mpProblem.

Referenced by CCopasiDataModel::addTask(), CFitProblem::calculate(), COptProblem::calculate(), CFitProblem::calculateCrossValidation(), CQNewMainWindow::checkForElementaryModesSlot(), COutputAssistant::createDefaultOutput(), COutputAssistant::createPlot(), CSEDMLExporter::createScanTask(), CSEDMLExporter::createSteadyStateTask(), CSEDMLExporter::createTimeCourseTask(), CQTSSAResultSubWidget::displayResult(), CNewtonMethod::doIntegration(), CQNewMainWindow::elementaryModeTriggeredSlot(), CCopasiXMLParser::TaskElement::end(), CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), CQSensResultWidget::enterProtected(), CODEExporter::exportExpression(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CEFMTask::getInternalSpecies(), CEFMTask::getNetReaction(), QFluxModeAnimation::getScales(), CCopasiDataModel::importSBML(), CCopasiDataModel::importSBMLFromString(), SEDMLImporter::importTasks(), CQTSSAResultSubWidget::init(), CSSAMethod::initialize(), CEFMMethod::initialize(), CFitProblem::initialize(), QFluxModeAnimation::initialize(), CSensMethod::initialize(), CEFMAlgorithm::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CNewtonMethod::initialize(), CScanTask::initSubtask(), StateSubwidget::loadAll(), CQLyapResultWidget::loadFromBackend(), CQSteadyStateResult::loadResult(), CQCrossSectionTaskWidget::loadTask(), CQLyapWidget::loadTask(), ScanWidget::loadTask(), CQLNAWidget::loadTask(), CQMCAWidget::loadTask(), SensitivitiesWidget::loadTask(), SteadyStateWidget::loadTask(), CQFittingWidget::loadTask(), CQTSSAWidget::loadTask(), CQOptimizationWidget::loadTask(), CQTrajectoryWidget::loadTask(), CQSensResultWidget::newResult(), operator<<(), CQSimpleSelectionTree::populateTree(), Arguments::prepareModel(), CCSPMethod::printResult(), CLNATask::process(), CScanTask::processCallback(), CFitProblem::restore(), CQTSSAResultSubWidget::saveDataToFile(), CQCrossSectionTaskWidget::saveTask(), CQLyapWidget::saveTask(), CQMCAWidget::saveTask(), CQLNAWidget::saveTask(), ScanWidget::saveTask(), SensitivitiesWidget::saveTask(), SteadyStateWidget::saveTask(), CQFittingWidget::saveTask(), CQTSSAWidget::saveTask(), CQOptimizationWidget::saveTask(), CQTrajectoryWidget::saveTask(), CCopasiXML::saveTaskList(), CQEFMReactionDM::setTask(), CQEFMSpeciesDM::setTask(), CCopasiXMLParser::TaskElement::start(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().

{return mpProblem;}

const CCopasiProblem * CCopasiTask::getProblem

(

)

const

Retrieve the problem

Definition at line 298 of file CCopasiTask.cpp.

References mpProblem.

{return mpProblem;}

CReport & CCopasiTask::getReport

(

)

Retrieve the report

Definition at line 316 of file CCopasiTask.cpp.

References mReport.

Referenced by CCopasiDataModel::addDefaultReports(), TaskWidget::commonBeforeRunTask(), CSEDMLExporter::createDataGenerators(), COptProblem::initialize(), Arguments::prepareModel(), TaskWidget::reportBtnClicked(), CCopasiXML::saveTaskList(), CCopasiXMLParser::ReportInstanceElement::start(), and test000087::test_simulate_reaction_flux_reference_1().

{return mReport;}

const CCopasiTask::CResult & CCopasiTask::getResult

(

)

const

Retrieve the result

Definition at line 321 of file CCopasiTask.cpp.

References mResult.

Referenced by CQSensResultWidget::saveToFile(), CQMoietiesTaskResult::slotSave(), CMCAResultSubwidget::slotSave(), CLNAResultSubwidget::slotSave(), and CQEFMResultWidget::slotSave().

{return mResult;}

CCopasiParameterGroup * CCopasiTask::getSliders

(

)

Retrieve a pointer to the group of sliders.

Returns

CCopasiParameterGroup * pSliders

Definition at line 326 of file CCopasiTask.cpp.

References mpSliders.

{return mpSliders;}

CCopasiTask::Type CCopasiTask::getType

(

void

)

const

Retrieve the type of the task

Returns

CCopasiTask::Type type

Definition at line 176 of file CCopasiTask.cpp.

References mType.

Referenced by COptProblem::calculate(), COutputAssistant::createPlot(), CCopasiXMLParser::ParameterGroupElement::end(), CCopasiXMLParser::TaskElement::end(), Worker::getIndexForTask(), COutputAssistant::getListOfDefaultOutputDescriptions(), COptProblem::getSubtaskType(), Worker::getWidgetForTask(), and CCopasiXML::saveTaskList().

{return mType;}

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

Definition at line 207 of file CCopasiTask.cpp.

References COutputHandler::addInterface(), CCopasiMessage::COMMANDLINE, COutputHandler::compile(), CModel::compileIfNecessary(), CCopasiMessage::ERROR, CModel::getInitialState(), CCopasiProblem::getModel(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CReport::getTarget(), MCCopasiTask, mDoOutput, mOutputCounter, mpCallBack, mpInitialState, mpMethod, mpOutputHandler, mpProblem, mReport, NO_OUTPUT, CReport::open(), pdelete, REPORT, and CCopasiMessage::WARNING.

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

{
  bool success = true;

  if (!mpProblem)
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCCopasiTask + 1, getObjectName().c_str());
      return false;
    }

  if (!mpProblem->getModel())
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCCopasiTask + 2, getObjectName().c_str());
      return false;
    }

  if (!mpMethod)
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCCopasiTask + 3, getObjectName().c_str());
      return false;
    }

  if (!mpProblem->getModel()->compileIfNecessary(mpCallBack))
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCCopasiTask + 4, mpProblem->getModel()->getObjectName().c_str());
      return false;
    }

  pdelete(mpInitialState);

  mpInitialState = new CState(mpProblem->getModel()->getInitialState());

  mDoOutput = of;
  mpOutputHandler = pOutputHandler;

  if (mDoOutput == NO_OUTPUT ||
      mpOutputHandler == NULL) return true;

  mOutputCounter = 0;

  if (mDoOutput & REPORT)
    {
      if (mReport.open(getObjectDataModel(), pOstream) &&
          mReport.getTarget() != "")
        mpOutputHandler->addInterface(&mReport);
      else if (pOstream == NULL)
        CCopasiMessage(CCopasiMessage::COMMANDLINE, MCCopasiTask + 5, getObjectName().c_str());
    }

  std::vector< CCopasiContainer * > ListOfContainer;
  ListOfContainer.push_back(this);

  CCopasiDataModel* pDataModel = getObjectDataModel();
  assert(pDataModel != NULL);

  if (!mpOutputHandler->compile(ListOfContainer, pDataModel))
    {
      // Warning
      CCopasiMessage(CCopasiMessage::WARNING, MCCopasiTask + 7);
      success = false;
    }

  return success;
}

void CCopasiTask::initObjects ( )

private

Definition at line 390 of file CCopasiTask.cpp.

References CCopasiContainer::addObjectReference(), mOutputCounter, CCopasiTimer::PROCESS, CCopasiObject::ValueInt, and CCopasiTimer::WALL.

Referenced by CCopasiTask().

{
  addObjectReference("Output counter", mOutputCounter, CCopasiObject::ValueInt);
  new CCopasiTimer(CCopasiTimer::WALL, this);
  new CCopasiTimer(CCopasiTimer::PROCESS, this);
}

const bool & CCopasiTask::isScheduled

(

)

const

Check whether the task is scheduled

Returns

const bool & scheduled

Definition at line 184 of file CCopasiTask.cpp.

References mScheduled.

Referenced by Arguments::getFirstScheduledTask(), TaskWidget::loadCommon(), TaskWidget::saveCommon(), and CCopasiXML::saveTaskList().

{return mScheduled;}

const bool & CCopasiTask::isUpdateModel

(

)

const

Check whether the task must update the model

Returns

const bool & updateModel

Definition at line 188 of file CCopasiTask.cpp.

References mUpdateModel.

Referenced by CFitProblem::initialize(), CSensMethod::initialize(), TaskWidget::loadCommon(), CScanTask::processCallback(), TaskWidget::saveCommon(), CCopasiXML::saveTaskList(), and CQSteadyStateResult::slotUpdateModel().

{return mUpdateModel;}

bool CCopasiTask::isValidMethod ( const unsigned int &  method, const unsigned int *  validMethods  )

static

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

Parameters

const	unsigned int & method
const	unsigned int * validMethods

Returns

bool isValid

Definition at line 89 of file CCopasiTask.cpp.

References C_INT32, and CCopasiMethod::unset.

Referenced by CTrajectoryTask::setMethodType(), CTSSATask::setMethodType(), and CCrossSectionTask::setMethodType().

{
  unsigned C_INT32 i;

  for (i = 0; validMethods[i] != CCopasiMethod::unset; i++)
    if (method == validMethods[i]) return true;

  return false;
}

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

virtual

Perform an output event for the current activity

Parameters

const

Activity & activity

Definition at line 331 of file CCopasiTask.cpp.

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

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

{
  if (mpOutputHandler != NULL)
    switch (activity)
      {
        case COutputInterface::DURING:

          if (mDoOutput != NO_OUTPUT)
            {
              mpOutputHandler->output(activity);
              ++mOutputCounter;
            }

          break;

        case COutputInterface::BEFORE:

          if (mDoOutput & OUTPUT_BEFORE)
            mpOutputHandler->output(activity);

          break;

        case COutputInterface::AFTER:

          if (mDoOutput & OUTPUT_AFTER)
            mpOutputHandler->output(activity);

          break;
      }
}

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

Definition at line 274 of file CCopasiTask.cpp.

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

{return false;}

bool CCopasiTask::restore ( )

virtual

Perform necessary cleanup procedures

Reimplemented in CCrossSectionTask, CSteadyStateTask, CTrajectoryTask, CTSSATask, CMCATask, CLyapTask, CScanTask, CLNATask, CSensTask, and CMoietiesTask.

Definition at line 277 of file CCopasiTask.cpp.

References CCopasiProblem::getModel(), mpInitialState, mpProblem, mUpdateModel, CCopasiProblem::restore(), setCallBack(), CModel::setInitialState(), and CModel::updateInitialValues().

Referenced by TaskWidget::finishTask(), CLNATask::restore(), CSensMethod::restore(), CScanTask::restore(), CLyapTask::restore(), CMCATask::restore(), COptProblem::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), and CCrossSectionTask::restore().

{
  setCallBack(NULL);

  if (!mUpdateModel)
    {
      if (mpInitialState)
        {
          mpProblem->getModel()->setInitialState(*mpInitialState);
        }

      mpProblem->getModel()->updateInitialValues();
    }

  mpProblem->restore(mUpdateModel);

  return true;
}

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

virtual

Introduce an additional separator into the output

Parameters

const

Activity & activity

Definition at line 362 of file CCopasiTask.cpp.

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

Referenced by CScanTask::outputSeparatorCallback().

{
  if (mpOutputHandler != NULL)
    switch (activity)
      {
        case COutputInterface::DURING:

          if (mDoOutput)
            mpOutputHandler->separate(activity);

          break;

        case COutputInterface::BEFORE:

          if (mDoOutput & OUTPUT_BEFORE)
            mpOutputHandler->separate(activity);

          break;

        case COutputInterface::AFTER:

          if (mDoOutput & OUTPUT_AFTER)
            mpOutputHandler->separate(activity);

          break;
      }
}

bool CCopasiTask::setCallBack ( CProcessReport *  pCallBack )

virtual

Set the call back of the task

Parameters

CProcessReport

* pCallBack

Returns

bool success

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

Definition at line 190 of file CCopasiTask.cpp.

References mpCallBack.

Referenced by TaskWidget::commonAfterRunTask(), TaskWidget::commonBeforeRunTask(), CNewtonMethod::doIntegration(), CSensMethod::initialize(), CScanTask::initSubtask(), CSensMethod::process(), CLNATask::process(), CScanTask::process(), CMCATask::process(), restore(), CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), CEFMTask::setCallBack(), and COptTask::setCallBack().

{
  mpCallBack = pCallBack;
  return true;
}

bool CCopasiTask::setMethodType ( const int &  type )

virtual

Set the method type applied to solve the task

Parameters

const

CCopasiMethod::SubType & type

Returns

bool success

Reimplemented in CCrossSectionTask, CLyapTask, CTrajectoryTask, CTSSATask, CEFMTask, COptTask, COscillationTask, CMoietiesTask, and CFitTask.

Definition at line 301 of file CCopasiTask.cpp.

Referenced by CQEFMWidget::createMethod(), CQTaskMethodWidget::saveMethod(), and CCopasiXMLParser::MethodElement::start().

{
  return false;
}

void CCopasiTask::setScheduled

(

const bool &

scheduled

)

Set whether the task is scheduled

Parameters

const

bool & scheduled

Definition at line 182 of file CCopasiTask.cpp.

References mScheduled.

Referenced by SEDMLImporter::importTasks(), TaskWidget::saveCommon(), CCopasiXMLParser::TaskElement::start(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().

{mScheduled = scheduled;}

void CCopasiTask::setType

(

const Type &

type

)

Set the type of the task

Parameters

CCopasiTask::Type

& type

Definition at line 178 of file CCopasiTask.cpp.

References mType.

{mType = type;}

void CCopasiTask::setUpdateModel

(

const bool &

updateModel

)

Set whether the task must update the model

Parameters

const

bool & updateModel

Definition at line 186 of file CCopasiTask.cpp.

References mUpdateModel.

Referenced by CFitProblem::initialize(), CSensMethod::initialize(), CFitProblem::restore(), CSensMethod::restore(), TaskWidget::saveCommon(), CQSteadyStateResult::slotUpdateModel(), and CCopasiXMLParser::TaskElement::start().

{mUpdateModel = updateModel;}

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, CTSSATask, CMCATask, CLNATask, and CSensTask.

Definition at line 347 of file CCopasiTask.h.

Referenced by CQSimpleSelectionTree::populateTree().

{return true;};

Member Data Documentation

std::string CCopasiTask::Error

Definition at line 372 of file CCopasiTask.h.

CDescription CCopasiTask::mDescription

protected

The description of the task.

Definition at line 207 of file CCopasiTask.h.

Referenced by getDescription().

OutputFlag CCopasiTask::mDoOutput

protected

Definition at line 463 of file CCopasiTask.h.

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

std::string CCopasiTask::mKey

protected

The key of the task

Definition at line 202 of file CCopasiTask.h.

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

unsigned C_INT32 CCopasiTask::mOutputCounter

protected

Definition at line 465 of file CCopasiTask.h.

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

CProcessReport* CCopasiTask::mpCallBack

protected

progress bar handler

Definition at line 249 of file CCopasiTask.h.

Referenced by CCrossSectionTask::eventCallBack(), CCrossSectionTask::finish(), getCallBack(), CLNATask::initialize(), CMCATask::initialize(), initialize(), CLyapTask::methodCallback(), CSensTask::process(), CLNATask::process(), CScanTask::process(), CLyapTask::process(), CMCATask::process(), CTrajectoryTask::process(), CTSSATask::process(), CSteadyStateTask::process(), CCrossSectionTask::process(), CScanTask::processCallback(), CTrajectoryTask::processStep(), CCrossSectionTask::processStep(), setCallBack(), and CSensTask::updateMatrices().

CState* CCopasiTask::mpInitialState

protected

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

Definition at line 229 of file CCopasiTask.h.

Referenced by initialize(), restore(), and ~CCopasiTask().

CCopasiMethod* CCopasiTask::mpMethod

protected

The method used to solve the problem.

Definition at line 239 of file CCopasiTask.h.

Referenced by CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CLyapTask::CLyapTask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), CScanTask::CScanTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CEFMTask::getFluxModeDescription(), getMethod(), CEFMTask::getReactionEquation(), CMoietiesTask::initialize(), COscillationTask::initialize(), CLNATask::initialize(), CEFMTask::initialize(), COptTask::initialize(), CScanTask::initialize(), CLyapTask::initialize(), CMCATask::initialize(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), initialize(), CLNATask::load(), CMCATask::load(), CTrajectoryTask::load(), CSteadyStateTask::load(), CLNATask::printResult(), CMCATask::printResult(), CMoietiesTask::process(), CFitTask::process(), CSensTask::process(), COscillationTask::process(), CLNATask::process(), COptTask::process(), CEFMTask::process(), CScanTask::process(), CMCATask::process(), CSteadyStateTask::process(), CSensTask::restore(), CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), COptTask::setCallBack(), CEFMTask::setCallBack(), CFitTask::setMethodType(), CMoietiesTask::setMethodType(), COscillationTask::setMethodType(), COptTask::setMethodType(), CEFMTask::setMethodType(), CTSSATask::setMethodType(), CTrajectoryTask::setMethodType(), CLyapTask::setMethodType(), CCrossSectionTask::setMethodType(), CSensTask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), CTSSATask::updateMatrices(), and ~CCopasiTask().

COutputHandler* CCopasiTask::mpOutputHandler

protected

Definition at line 464 of file CCopasiTask.h.

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

CCopasiProblem* CCopasiTask::mpProblem

protected

The problem of the task

Definition at line 234 of file CCopasiTask.h.

Referenced by CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CLyapTask::CLyapTask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), CScanTask::CScanTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CCrossSectionTask::eventCallBack(), CFitTask::fixBuild55(), CScanTask::fixBuild81(), CEFMTask::getFluxModeDescription(), CEFMTask::getFluxModes(), CEFMTask::getNetReactionData(), getProblem(), CEFMTask::getReactionEquation(), CEFMTask::getSpeciesChanges(), CMoietiesTask::initialize(), COscillationTask::initialize(), CLNATask::initialize(), CEFMTask::initialize(), COptTask::initialize(), CScanTask::initialize(), CLyapTask::initialize(), CMCATask::initialize(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), initialize(), CScanTask::initSubtask(), CLNATask::load(), CMCATask::load(), CTrajectoryTask::load(), CSteadyStateTask::load(), operator<<(), CLNATask::printResult(), CMCATask::printResult(), CFitTask::process(), CSensTask::process(), COscillationTask::process(), CLNATask::process(), COptTask::process(), CScanTask::process(), CMCATask::process(), CSteadyStateTask::process(), CMoietiesTask::restore(), CLNATask::restore(), CLyapTask::restore(), CMCATask::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), CCrossSectionTask::restore(), restore(), CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), COptTask::setCallBack(), CEFMTask::setCallBack(), CSteadyStateTask::setInitialState(), CSensTask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), CTSSATask::updateMatrices(), CSteadyStateTask::updateMatrices(), and ~CCopasiTask().

CCopasiParameterGroup* CCopasiTask::mpSliders

protected

Pointer to group of sliders associated with the task.

Definition at line 254 of file CCopasiTask.h.

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

CReport CCopasiTask::mReport

protected

The report that belongs to this specific task

Definition at line 244 of file CCopasiTask.h.

Referenced by getReport(), CLNATask::initialize(), CScanTask::initialize(), CMCATask::initialize(), initialize(), and CSensTask::process().

CResult CCopasiTask::mResult

protected

The result of the task.

Definition at line 212 of file CCopasiTask.h.

Referenced by getResult().

bool CCopasiTask::mScheduled

protected

Tells whether the task is scheduled for execution

Definition at line 217 of file CCopasiTask.h.

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

Type CCopasiTask::mType

protected

The type of the task

Definition at line 197 of file CCopasiTask.h.

Referenced by getType(), and setType().

bool CCopasiTask::mUpdateModel

protected

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

Definition at line 223 of file CCopasiTask.h.

Referenced by isUpdateModel(), CSensTask::restore(), CLyapTask::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), CCrossSectionTask::restore(), restore(), and setUpdateModel().

const std::string CCopasiTask::TypeName

static

Initial value:

=
{
  "Steady-State",
  "Time-Course",
  "Scan",
  "Elementary Flux Modes",
  "Optimization",
  "Parameter Estimation",
  "Metabolic Control Analysis",
  "Lyapunov Exponents",
  "Time Scale Separation Analysis",
  "Sensitivities",
  "Moieties",
  "Cross Section",
  "Linear Noise Approximation",
  "not specified",
  ""
}

String literals for the GUI to display type names of tasks known to COPASI.

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

Definition at line 67 of file CCopasiTask.h.

Referenced by CCopasiDataModel::addDefaultReports(), CCopasiDataModel::addDefaultTasks(), CCopasiDataModel::addReport(), CQReportDefinition::CQReportDefinition(), CQOptimizationWidget::init(), CScanTask::initSubtask(), CQOptimizationWidget::loadTask(), and CQOptimizationWidget::saveTask().

const unsigned int CCopasiTask::ValidMethods

static

Initial value:

=
{
  CCopasiMethod::unset
}

The methods which can be selected for performing this task.

Definition at line 77 of file CCopasiTask.h.

std::string CCopasiTask::Warning

Definition at line 373 of file CCopasiTask.h.

const char * CCopasiTask::XMLType

static

Initial value:

=
{
  "steadyState",
  "timeCourse",
  "scan",
  "fluxMode",
  "optimization",
  "parameterFitting",
  "metabolicControlAnalysis",
  "lyapunovExponents",
  "timeScaleSeparationAnalysis",
  "sensitivities",
  "moieties",
  "crosssection",
  "linearNoiseApproximation",
  "unset",
  NULL
}

XML type names of tasks known to COPASI.

Definition at line 72 of file CCopasiTask.h.

Referenced by CCopasiXML::saveReportList(), CCopasiXML::saveTaskList(), CCopasiXMLParser::TaskElement::start(), and CCopasiXMLParser::ReportElement::start().

---

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

• CCopasiTask.h
• CCopasiTask.cpp