#include <CTSSATask.h>

Inheritance diagram for CTSSATask:

Collaboration diagram for CTSSATask:

Public Member Functions
virtual CCopasiMethod *	createMethod (const int &type) const

	CTSSATask (const CCopasiContainer *pParent=NULL)

	CTSSATask (const CTSSATask &src, const CCopasiContainer *pParent=NULL)

CState *	getState ()

const CTimeSeries &	getTimeSeries () const

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

virtual bool	process (const bool &useInitialValues)

void	processStart (const bool &useInitialValues)

bool	processStep (const C_FLOAT64 &nextTime)

virtual bool	restore ()

virtual bool	setMethodType (const int &type)

virtual bool	updateMatrices ()

	~CTSSATask ()

Public Member Functions inherited from CCopasiTask
	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 ()

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

const bool &	isScheduled () const

const bool &	isUpdateModel () const

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

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

virtual bool	setCallBack (CProcessReport *pCallBack)

void	setScheduled (const bool &scheduled)

void	setType (const Type &type)

void	setUpdateModel (const bool &updateModel)

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 Attributes
static const unsigned int	ValidMethods []

Static Public Attributes inherited from CCopasiTask
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

Private Member Functions
void	cleanup ()

Private Attributes
CState *	mpCurrentState

const C_FLOAT64 *	mpCurrentTime

CTSSAMethod *	mpTSSAMethod

CTSSAProblem *	mpTSSAProblem

CTimeSeries	mTimeSeries

bool	mTimeSeriesRequested

bool	mUpdateMoieties

Additional Inherited Members
Public Types inherited from CCopasiTask
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

Static Public Member Functions inherited from CCopasiTask
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 inherited from CCopasiTask
std::string	Error

std::string	Warning

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)

Protected Attributes inherited from CCopasiTask
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

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 43 of file CTSSATask.h.

Constructor & Destructor Documentation

CTSSATask::CTSSATask ( const CCopasiContainer * pParent = NULL )

Default constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 61 of file CTSSATask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, CCopasiParameter::Value::pBOOL, and CCopasiMethod::tssILDM.

                                                     :
   CCopasiTask(CCopasiTask::tssAnalysis, pParent),
   mTimeSeriesRequested(true),
   mTimeSeries(),
   mpTSSAProblem(NULL),
   mpTSSAMethod(NULL),
   mpCurrentState(NULL),
   mpCurrentTime(NULL)
 {
   mpProblem = new CTSSAProblem(this);
   mpMethod = createMethod(CCopasiMethod::tssILDM);
   this->add(mpMethod, true);
 
   CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");
 
   if (pParameter != NULL)
     mUpdateMoieties = *pParameter->getValue().pBOOL;
   else
     mUpdateMoieties = false;
 }

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

Copy constructor

Parameters

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

Definition at line 82 of file CTSSATask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::elevateChildren(), CCopasiMethod::getSubType(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, and CCopasiParameter::Value::pBOOL.

                                                       :
   CCopasiTask(src, pParent),
   mTimeSeriesRequested(src.mTimeSeriesRequested),
   mTimeSeries(),
   mpTSSAProblem(NULL),
   mpTSSAMethod(NULL),
   mpCurrentState(NULL),
   mpCurrentTime(NULL)
 {
   mpProblem =
     new CTSSAProblem(*static_cast< CTSSAProblem * >(src.mpProblem), this);
 
   mpMethod = createMethod(src.mpMethod->getSubType());
   * mpMethod = * src.mpMethod;
   mpMethod->elevateChildren();
 
   this->add(mpMethod, true);
 
   CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");
 
   if (pParameter != NULL)
     mUpdateMoieties = *pParameter->getValue().pBOOL;
   else
     mUpdateMoieties = false;
 }

CTSSATask::~CTSSATask ( )

Destructor

Definition at line 109 of file CTSSATask.cpp.

References cleanup().

 {
   cleanup();
 }

Member Function Documentation

void CTSSATask::cleanup ( )

private

cleanup()

Definition at line 114 of file CTSSATask.cpp.

References mpCurrentState, and pdelete.

Referenced by ~CTSSATask().

 {
   pdelete(mpCurrentState);
 }

CCopasiMethod * CTSSATask::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 from CCopasiTask.

Definition at line 418 of file CTSSATask.cpp.

References CTSSAMethod::createMethod().

Referenced by CTSSATask(), and setMethodType().

 {
   CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;
 
   return CTSSAMethod::createMethod(Type);
 }

CState * CTSSATask::getState ( )

Retrieves a pointer to current state of the integration.

Returns: CState * pState

Definition at line 425 of file CTSSATask.cpp.

References mpCurrentState.

426 {return mpCurrentState;}

CTSSATask::mpCurrentState

CState * mpCurrentState

Definition: CTSSATask.h:82

const CTimeSeries & CTSSATask::getTimeSeries ( ) const

gets a reference to the time series

Returns: time series

Definition at line 428 of file CTSSATask.cpp.

References mTimeSeries.

429 {return mTimeSeries;}

CTSSATask::mTimeSeries

CTimeSeries mTimeSeries

Definition: CTSSATask.h:62

bool CTSSATask::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 from CCopasiTask.

Definition at line 138 of file CTSSATask.cpp.

References COutputHandler::addInterface(), CTimeSeries::allocate(), CTimeSeries::clear(), CCopasiProblem::getModel(), CCopasiParameterGroup::getParameter(), CModel::getState(), CTSSAProblem::getStepNumber(), CState::getTime(), CCopasiParameter::getValue(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), mpCurrentState, mpCurrentTime, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpTSSAMethod, mpTSSAProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CCopasiParameter::Value::pBOOL, pdelete, CTSSAMethod::predifineAnnotation(), CTSSAMethod::setModel(), CTSSAMethod::setProblem(), and CTSSAProblem::timeSeriesRequested().

 {
   assert(mpProblem && mpMethod);
 
   mpTSSAProblem = dynamic_cast<CTSSAProblem *>(mpProblem);
   assert(mpTSSAProblem);
 
   mpTSSAMethod = dynamic_cast<CTSSAMethod *>(mpMethod);
   assert(mpTSSAMethod);
 
   mpTSSAMethod->setProblem(mpTSSAProblem);
 
   bool success = mpMethod->isValidProblem(mpProblem);
 
   CCopasiParameter * pParameter = mpMethod->getParameter("Integrate Reduced Model");
 
   if (pParameter != NULL)
     mUpdateMoieties = *pParameter->getValue().pBOOL;
   else
     mUpdateMoieties = false;
 
   pdelete(mpCurrentState);
   mpCurrentState = new CState(mpTSSAProblem->getModel()->getState());
   mpCurrentTime = &mpCurrentState->getTime();
 
   // Handle the time series as a regular output.
   mTimeSeriesRequested = mpTSSAProblem->timeSeriesRequested();
 
   if (pOutputHandler != NULL)
     {
       if (mTimeSeriesRequested)
         {
           mTimeSeries.allocate(mpTSSAProblem->getStepNumber());
           pOutputHandler->addInterface(&mTimeSeries);
         }
       else
         {
           mTimeSeries.clear();
         }
     }
 
 //NEW
 
   mpTSSAMethod->setModel(mpTSSAProblem->getModel());
 
   mpTSSAMethod->predifineAnnotation();
 
 //
 
   if (!CCopasiTask::initialize(of, pOutputHandler, pOstream)) success = false;
 
   return success;
 }

bool CTSSATask::process ( const bool & useInitialValues )

virtual

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

Parameters

const bool & useInitialValues

Returns: bool success

Reimplemented from CCopasiTask.

Definition at line 194 of file CTSSATask.cpp.

References CProcessReport::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, C_FLOAT64, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReport::finishItem(), CTSSAProblem::getDuration(), CCopasiException::getMessage(), CCopasiProblem::getModel(), CTSSAProblem::getOutputStartTime(), CTSSAProblem::getStepSize(), MCTSSAMethod, MCTSSAProblem, CCopasiTask::mpCallBack, mpCurrentState, mpCurrentTime, mpTSSAProblem, mUpdateMoieties, CCopasiTask::output(), processStart(), processStep(), CProcessReport::progressItem(), CProcessReport::setName(), CModel::setState(), tbl(), tble(), tfl(), tfle(), and CModel::updateSimulatedValues().

 {
   //*****
 
   processStart(useInitialValues);
 
   //*****
 
   C_FLOAT64 StepSize = mpTSSAProblem->getStepSize();
   C_FLOAT64 NextTimeToReport;
 
   const C_FLOAT64 EndTime = *mpCurrentTime + mpTSSAProblem->getDuration();
   const C_FLOAT64 StartTime = *mpCurrentTime;
 
   C_FLOAT64 StepNumber = (mpTSSAProblem->getDuration()) / StepSize;
 
   bool (*LE)(const C_FLOAT64 &, const C_FLOAT64 &);
   bool (*L)(const C_FLOAT64 &, const C_FLOAT64 &);
 
   if (StepSize < 0.0)
     {
       LE = &tble;
       L = &tbl;
     }
   else
     {
       LE = &tfle;
       L = &tfl;
     }
 
   size_t StepCounter = 1;
 
   C_FLOAT64 outputStartTime = mpTSSAProblem->getOutputStartTime();
 
   if (StepSize == 0.0 && mpTSSAProblem->getDuration() != 0.0)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCTSSAProblem + 1, StepSize);
       return false;
     }
 
   output(COutputInterface::BEFORE);
 
   bool flagProceed = true;
   C_FLOAT64 handlerFactor = 100.0 / mpTSSAProblem->getDuration();
 
   C_FLOAT64 Percentage = 0;
   size_t hProcess;
 
   if (mpCallBack)
     {
       mpCallBack->setName("performing simulation...");
       C_FLOAT64 hundred = 100;
       hProcess = mpCallBack->addItem("Completion",
                                      Percentage,
                                      &hundred);
     }
 
   //if ((*LE)(outputStartTime, *mpCurrentTime)) output(COutputInterface::DURING);
 
   try
     {
       do
         {
           // This is numerically more stable then adding
           // mpTSSAProblem->getStepSize().
           NextTimeToReport =
             StartTime + (EndTime - StartTime) * StepCounter++ / StepNumber;
 
           flagProceed &= processStep(NextTimeToReport);
 
           if (mpCallBack)
             {
               Percentage = (*mpCurrentTime - StartTime) * handlerFactor;
               flagProceed &= mpCallBack->progressItem(hProcess);
             }
 
           if ((*LE)(outputStartTime, *mpCurrentTime))
             {
               output(COutputInterface::DURING);
             }
         }
       while ((*L)(*mpCurrentTime, EndTime) && flagProceed);
     }
 
   catch (int)
     {
       mpTSSAProblem->getModel()->setState(*mpCurrentState);
       mpTSSAProblem->getModel()->updateSimulatedValues(mUpdateMoieties);
 
       if ((*LE)(outputStartTime, *mpCurrentTime))
         {
           output(COutputInterface::DURING);
         }
 
       if (mpCallBack) mpCallBack->finishItem(hProcess);
 
       output(COutputInterface::AFTER);
 
       CCopasiMessage(CCopasiMessage::EXCEPTION, MCTSSAMethod + 4);
     }
 
   catch (CCopasiException & Exception)
     {
       mpTSSAProblem->getModel()->setState(*mpCurrentState);
       mpTSSAProblem->getModel()->updateSimulatedValues(mUpdateMoieties);
 
       if ((*LE)(outputStartTime, *mpCurrentTime))
         {
           output(COutputInterface::DURING);
         }
 
       if (mpCallBack) mpCallBack->finishItem(hProcess);
 
       output(COutputInterface::AFTER);
 
       throw CCopasiException(Exception.getMessage());
     }
 
   if (mpCallBack) mpCallBack->finishItem(hProcess);
 
   output(COutputInterface::AFTER);
 
   return true;
 }

void CTSSATask::processStart ( const bool & useInitialValues )

Starts the process of integration by calling CTSSAMethod::start

Parameters

const bool & useInitialValues

Definition at line 319 of file CTSSATask.cpp.

References CModel::applyInitialValues(), CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, mpTSSAMethod, mpTSSAProblem, CTSSAMethod::setCurrentState(), and CTSSAMethod::start().

Referenced by process().

 {
   if (useInitialValues)
     mpTSSAProblem->getModel()->applyInitialValues();
 
   *mpCurrentState = mpTSSAProblem->getModel()->getState();
 
   mpTSSAMethod->setCurrentState(mpCurrentState);
   mpTSSAMethod->start(mpCurrentState);
 
   return;
 }

bool CTSSATask::processStep ( const C_FLOAT64 & nextTime )

Integrates one step

Parameters

const C_FLOAT64 & nextTime

Returns: bool success;

Definition at line 332 of file CTSSATask.cpp.

References C_FLOAT64, CCopasiMessage::EXCEPTION, CCopasiProblem::getModel(), MCTSSAMethod, mpCurrentState, mpCurrentTime, mpTSSAMethod, mpTSSAProblem, mUpdateMoieties, CModel::setState(), CTSSAMethod::step(), and CModel::updateSimulatedValues().

Referenced by process().

 {
   C_FLOAT64 CompareTime = nextTime - 100.0 * fabs(nextTime) * std::numeric_limits< C_FLOAT64 >::epsilon();
 
   if (*mpCurrentTime <= CompareTime)
     {
       do
         {
           mpTSSAMethod->step(nextTime - *mpCurrentTime);
 
           if (*mpCurrentTime > CompareTime) break;
 
           /* Here we will do conditional event processing */
 
           /* Currently this is correct since no events are processed. */
           CCopasiMessage(CCopasiMessage::EXCEPTION, MCTSSAMethod + 3);
         }
       while (true);
 
       mpTSSAProblem->getModel()->setState(*mpCurrentState);
       mpTSSAProblem->getModel()->updateSimulatedValues(mUpdateMoieties);
 
       return true;
     }
 
   CompareTime = nextTime + 100.0 * fabs(nextTime) * std::numeric_limits< C_FLOAT64 >::epsilon();
 
   if (*mpCurrentTime >= CompareTime)
     {
       do
         {
           mpTSSAMethod->step(nextTime - *mpCurrentTime);
 
           if (*mpCurrentTime < CompareTime) break;
 
           /* Here we will do conditional event processing */
 
           /* Currently this is correct since no events are processed. */
           CCopasiMessage(CCopasiMessage::EXCEPTION, MCTSSAMethod + 3);
         }
       while (true);
 
       mpTSSAProblem->getModel()->setState(*mpCurrentState);
       mpTSSAProblem->getModel()->updateSimulatedValues(mUpdateMoieties);
 
       return true;
     }
 
   // Current time is approximately nextTime;
   return false;
 }

bool CTSSATask::restore ( )

virtual

Perform necessary cleanup procedures

Reimplemented from CCopasiTask.

Definition at line 384 of file CTSSATask.cpp.

References CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, CCopasiTask::mpProblem, CCopasiTask::mUpdateModel, mUpdateMoieties, CCopasiTask::restore(), CModel::setInitialState(), CModel::setState(), CModel::updateInitialValues(), and CModel::updateSimulatedValues().

 {
   bool success = CCopasiTask::restore();
 
   if (mUpdateModel)
     {
       CModel * pModel = mpProblem->getModel();
 
       pModel->setState(*mpCurrentState);
       pModel->updateSimulatedValues(mUpdateMoieties);
       pModel->setInitialState(pModel->getState());
       pModel->updateInitialValues();
     }
 
   return success;
 }

bool CTSSATask::setMethodType ( const int & type )

virtual

Set the method type applied to solve the task

Parameters

const CCopasiMethod::SubType & type

Returns: bool success

Reimplemented from CCopasiTask.

Definition at line 401 of file CTSSATask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), CCopasiTask::isValidMethod(), CCopasiTask::mpMethod, pdelete, and ValidMethods.

 {
   CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;
 
   if (!isValidMethod(Type, ValidMethods)) return false;
 
   if (mpMethod->getSubType() == Type) return true;
 
   pdelete(mpMethod);
   mpMethod = createMethod(Type);
   this->add(mpMethod, true);
   //mpMethod->setObjectParent(this);
 
   return true;
 }

bool CTSSATask::updateMatrices ( )

virtual

Resizes result matrices and updates array annotations for a specific task. 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 from CCopasiTask.

Definition at line 119 of file CTSSATask.cpp.

References CCopasiProblem::getModel(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CTSSAMethod::predifineAnnotation(), and CTSSAMethod::setModel().

 {
   assert(mpProblem != NULL && mpMethod != NULL);
 
   assert(dynamic_cast<CTSSAProblem *>(mpProblem) != NULL);
 
   if (!mpMethod->isValidProblem(mpProblem)) return false;
 
   CTSSAMethod * pMethod = dynamic_cast<CTSSAMethod*>(mpMethod);
 
   if (!pMethod) return false;
 
   pMethod->setModel(mpProblem->getModel());
 
   pMethod->predifineAnnotation();
 
   return true;
 }

Member Data Documentation

CState* CTSSATask::mpCurrentState

private

A pointer to the current state of the integration.

Definition at line 82 of file CTSSATask.h.

Referenced by cleanup(), getState(), initialize(), process(), processStart(), processStep(), and restore().

const C_FLOAT64* CTSSATask::mpCurrentTime

private

A pointer to the current time of the integration.

Definition at line 87 of file CTSSATask.h.

Referenced by initialize(), process(), and processStep().

CTSSAMethod* CTSSATask::mpTSSAMethod

private

A pointer to the method

Definition at line 72 of file CTSSATask.h.

Referenced by initialize(), processStart(), and processStep().

CTSSAProblem* CTSSATask::mpTSSAProblem

private

A pointer to the Problem

Definition at line 67 of file CTSSATask.h.

Referenced by initialize(), process(), processStart(), and processStep().

CTimeSeries CTSSATask::mTimeSeries

private

the time series (if requested)

Definition at line 62 of file CTSSATask.h.

Referenced by getTimeSeries(), and initialize().

bool CTSSATask::mTimeSeriesRequested

private

whether the time series should be stored in mTimeSeries

Definition at line 57 of file CTSSATask.h.

Referenced by initialize().

bool CTSSATask::mUpdateMoieties

private

Indicates whether we need to update moieties.

Definition at line 77 of file CTSSATask.h.

Referenced by CTSSATask(), initialize(), process(), processStep(), and restore().

const unsigned int CTSSATask::ValidMethods

static

Initial value:

=
{
  CCopasiMethod::tssILDM,
  CCopasiMethod::tssILDMModified,
  CCopasiMethod::tssCSP,
  CCopasiMethod::unset
}

The methods which can be selected for performing this task.

Definition at line 50 of file CTSSATask.h.

Referenced by CQTSSAWidget::init(), and setMethodType().

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

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation