#include <CTSSATask.h>

Inheritance diagram for CTSSATask:

Public Member Functions
	CTSSATask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::tssAnalysis)

	CTSSATask (const CTSSATask &src, const CDataContainer *pParent)

const CTimeSeries &	getTimeSeries () const

virtual const CTaskEnum::Method *	getValidMethods () const

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

virtual bool	process (const bool &useInitialValues)

bool	processStart (const bool &useInitialValues)

bool	processStep (const C_FLOAT64 &nextTime)

virtual bool	updateMatrices ()

virtual	~CTSSATask ()

Public Member Functions inherited from CCopasiTask
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

const bool &	isScheduled () const

const bool &	isUpdateModel () const

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

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	~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 Attributes
static const CTaskEnum::Method	ValidMethods []

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

Private Member Functions
	CTSSATask ()

Private Attributes
CVectorCore< C_FLOAT64 >	mContainerState

C_FLOAT64 *	mpContainerStateTime

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_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

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

std::string	Warning

Protected Member Functions inherited from CCopasiTask
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 inherited from CCopasiTask
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

Constructor & Destructor Documentation

◆ CTSSATask() [1/3]

CTSSATask::CTSSATask ( )

private

Default constructor

◆ CTSSATask() [2/3]

CTSSATask::CTSSATask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = `CTaskEnum::Task::tssAnalysis`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Task & type (default: tssAnalysis)

References CMethodFactory::create(), CCopasiParameterGroup::getParameter(), CCopasiTask::getType(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, mUpdateMoieties, and CTaskEnum::tssILDM.

◆ CTSSATask() [3/3]

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

Copy constructor

Parameters

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

References CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, and mUpdateMoieties.

◆ ~CTSSATask()

CTSSATask::~CTSSATask ( )

virtual

Destructor

Member Function Documentation

◆ getTimeSeries()

const CTimeSeries & CTSSATask::getTimeSeries ( ) const

gets a reference to the time series

Returns: time series

References mTimeSeries.

◆ getValidMethods()

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

virtual

Retrieve the list of valid methods

Returns: const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References ValidMethods.

◆ initialize()

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.

References COutputHandler::addInterface(), CTimeSeries::allocate(), CVectorCore< CType >::array(), CTimeSeries::clear(), CMathContainer::getCountFixedEventTargets(), CCopasiParameterGroup::getParameter(), CMathContainer::getState(), CTSSAProblem::getStepNumber(), CCopasiParameter::getValue(), CCopasiTask::initialize(), CVectorCore< CType >::initialize(), CTSSAMethod::initializeOutput(), CCopasiMethod::isValidProblem(), mContainerState, CCopasiTask::mpContainer, mpContainerStateTime, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpTSSAMethod, mpTSSAProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CCopasiMethod::setMathContainer(), CTSSAMethod::setProblem(), and CTSSAProblem::timeSeriesRequested().

◆ process()

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.

References CProcessReportLevel::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, C_FLOAT64, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReportLevel::finishItem(), CTSSAProblem::getDuration(), CCopasiException::getMessage(), CTSSAProblem::getOutputStartTime(), CTSSAProblem::getStepSize(), MCTSSAMethod, MCTSSAProblem, CCopasiTask::mpContainer, mpContainerStateTime, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, mpTSSAMethod, mpTSSAProblem, mUpdateMoieties, CCopasiTask::output(), processStart(), processStep(), CProcessReportLevel::progressItem(), CProcessReportLevel::setName(), tbl(), tble(), tfl(), tfle(), and CMathContainer::updateSimulatedValues().

◆ processStart()

bool CTSSATask::processStart ( const bool & useInitialValues )

Starts the process of integration by calling CTSSAMethod::start

Parameters

const bool & useInitialValues

Returns: bool success

References CMathContainer::applyInitialValues(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiTask::mpContainer, mpTSSAMethod, mUpdateMoieties, and CTSSAMethod::start().

Referenced by process().

◆ processStep()

bool CTSSATask::processStep ( const C_FLOAT64 & nextTime )

Integrates one step

Parameters

const C_FLOAT64 & nextTime

Returns: bool success;

References C_FLOAT64, CCopasiMessage::EXCEPTION, MCTSSAMethod, CCopasiTask::mpContainer, mpContainerStateTime, mpTSSAMethod, mUpdateMoieties, CTSSAMethod::step(), and CMathContainer::updateSimulatedValues().

Referenced by process().

◆ updateMatrices()

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.

References CTSSAMethod::initializeOutput(), CCopasiMethod::isValidProblem(), CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::setMathContainer().

Member Data Documentation

◆ mContainerState

CVectorCore< C_FLOAT64 > CTSSATask::mContainerState

private

The current state of the integration.

Referenced by initialize(), and processStart().

◆ mpContainerStateTime

C_FLOAT64* CTSSATask::mpContainerStateTime

private

A pointer to the current time of the integration.

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

◆ mpTSSAMethod

CTSSAMethod* CTSSATask::mpTSSAMethod

private

A pointer to the method

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

◆ mpTSSAProblem

CTSSAProblem* CTSSATask::mpTSSAProblem

private

A pointer to the Problem

Referenced by initialize(), and process().

◆ mTimeSeries

CTimeSeries CTSSATask::mTimeSeries

private

the time series (if requested)

Referenced by getTimeSeries(), and initialize().

◆ mTimeSeriesRequested

bool CTSSATask::mTimeSeriesRequested

private

whether the time series should be stored in mTimeSeries

Referenced by initialize().

◆ mUpdateMoieties

bool CTSSATask::mUpdateMoieties

private

Indicates whether we need to update moieties.

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

◆ ValidMethods

const CTaskEnum::Method CTSSATask::ValidMethods

static

Initial value:

=
{
  CTaskEnum::Method::tssILDM,
  CTaskEnum::Method::tssILDMModified,
  CTaskEnum::Method::tssCSP,
  CTaskEnum::Method::UnsetMethod
}

Referenced by getValidMethods().

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

Constructor & Destructor Documentation

◆ CTSSATask() [1/3]

◆ CTSSATask() [2/3]

◆ CTSSATask() [3/3]

◆ ~CTSSATask()

Member Function Documentation

◆ getTimeSeries()

◆ getValidMethods()

◆ initialize()

◆ process()

◆ processStart()

◆ processStep()

◆ updateMatrices()

Member Data Documentation

◆ mContainerState

◆ mpContainerStateTime

◆ mpTSSAMethod

◆ mpTSSAProblem

◆ mTimeSeries

◆ mTimeSeriesRequested

◆ mUpdateMoieties

◆ ValidMethods