CTimeSensTask Class Reference

#include <CTimeSensTask.h>

Inheritance diagram for CTimeSensTask:

Public Member Functions
	CTimeSensTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::timeSens)
	CTimeSensTask (const CTimeSensTask &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 void	output (const COutputInterface::Activity &activity)
virtual bool	process (const bool &useInitialValues)
bool	processStart (const bool &useInitialValues)
bool	processStep (const C_FLOAT64 &nextTime, const bool &final=false)
virtual bool	updateMatrices ()
	~CTimeSensTask ()
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 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

Protected Member Functions
virtual void	signalMathContainerChanged ()
virtual void	signalMethodChanged ()
Protected Member Functions inherited from CCopasiTask
bool	isTaskValid () const
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
CVectorCore< C_FLOAT64 >	mContainerState
C_FLOAT64	mOutputStartTime
C_FLOAT64 *	mpContainerStateTime
bool(*	mpLess )(const C_FLOAT64 &, const C_FLOAT64 &)
bool(*	mpLessOrEqual )(const C_FLOAT64 &, const C_FLOAT64 &)
bool	mProceed
CSteadyStateTask *	mpSteadyState
CTimeSensMethod *	mpTimeSensMethod
CTimeSensProblem *	mpTimeSensProblem
CTimeSeries	mTimeSeries
bool	mTimeSeriesRequested
bool	mUpdateMoieties
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

Private Member Functions
void	cleanup ()
	CTimeSensTask ()

Static Private Member Functions
static bool	bl (const C_FLOAT64 &d1, const C_FLOAT64 &d2)
static bool	ble (const C_FLOAT64 &d1, const C_FLOAT64 &d2)
static bool	fl (const C_FLOAT64 &d1, const C_FLOAT64 &d2)
static bool	fle (const C_FLOAT64 &d1, const C_FLOAT64 &d2)

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

Constructor & Destructor Documentation

CTimeSensTask() [1/3]

CTimeSensTask::CTimeSensTask ( )

private

Default constructor

CTimeSensTask() [2/3]

CTimeSensTask::CTimeSensTask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = CTaskEnum::Task::timeSens
	)

Specific constructor

Parameters

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

References CMethodFactory::create(), CCopasiTask::getType(), CCopasiTask::mpMethod, mUpdateMoieties, signalMathContainerChanged(), and CTaskEnum::timeSensLsoda.

CTimeSensTask() [3/3]

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

Copy constructor

Parameters

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

References CCopasiTask::mpMethod, mUpdateMoieties, and signalMathContainerChanged().

~CTimeSensTask()

CTimeSensTask::~CTimeSensTask

(

)

Destructor

References cleanup().

Member Function Documentation

bl()

bool CTimeSensTask::bl ( const C_FLOAT64 &  d1, const C_FLOAT64 &  d2  )

staticprivate

Referenced by process().

ble()

bool CTimeSensTask::ble ( const C_FLOAT64 &  d1, const C_FLOAT64 &  d2  )

staticprivate

Referenced by process().

cleanup()

void CTimeSensTask::cleanup ( )

private

cleanup()

Referenced by ~CTimeSensTask().

fl()

bool CTimeSensTask::fl ( const C_FLOAT64 &  d1, const C_FLOAT64 &  d2  )

staticprivate

Referenced by process().

fle()

bool CTimeSensTask::fle ( const C_FLOAT64 &  d1, const C_FLOAT64 &  d2  )

staticprivate

Referenced by process().

getTimeSeries()

const CTimeSeries & CTimeSensTask::getTimeSeries

(

)

const

gets a reference to the time series

Returns

time series

References mTimeSeries.

getValidMethods()

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

virtual

Retrieve the list of valid methods

Returns

const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References ValidMethods.

initialize()

bool CTimeSensTask::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(), CTimeSeries::clear(), CDataObject::getObjectDataModel(), CTrajectoryProblem::getStartInSteadyState(), CTrajectoryProblem::getStepNumber(), CDataModel::getTaskList(), CCopasiTask::initialize(), CSteadyStateTask::initialize(), CTimeSensMethod::integrateReducedModel(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpSteadyState, mpTimeSensMethod, mpTimeSensProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CTimeSensMethod::setProblem(), signalMathContainerChanged(), CCopasiTask::TIME_SERIES, CTrajectoryProblem::timeSeriesRequested(), and updateMatrices().

Referenced by CFitProblem::initialize().

output()

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

virtual

Perform an output event for the current activity

Parameters

const

Activity & activity

Reimplemented from CCopasiTask.

References CTimeSensMethod::copySensitivitiesToResultMatrix(), mpTimeSensMethod, and CCopasiTask::output().

Referenced by CTimeSensMethod::output(), process(), and processStep().

process()

bool CTimeSensTask::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, bl(), ble(), C_FLOAT64, C_INT32, C_INVALID_INDEX, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReportLevel::finishItem(), fl(), fle(), CTrajectoryProblem::getAutomaticStepSize(), CTrajectoryProblem::getDuration(), CCopasiException::getMessage(), CTrajectoryProblem::getOutputStartTime(), CMathContainer::getState(), CTrajectoryProblem::getStepSize(), mContainerState, MCTrajectoryMethod, MCTrajectoryProblem, min, mOutputStartTime, CCopasiTask::mpContainer, mpContainerStateTime, mpLess, mpLessOrEqual, mProceed, CCopasiTask::mProcessReport, mpTimeSensMethod, mpTimeSensProblem, mUpdateMoieties, output(), CMathContainer::processQueue(), processStart(), processStep(), CProcessReportLevel::progressItem(), CMathContainer::pushAllTransientValues(), CProcessReportLevel::setName(), CMathContainer::setState(), CTimeSensMethod::stateChange(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().

processStart()

bool CTimeSensTask::processStart

(

const bool &

useInitialValues

)

Starts the process of integration by calling CTimeSensMethod::start

Parameters

const

bool & useInitialValues

Returns

bool success

References CMathContainer::applyInitialValues(), CVectorCore< CType >::array(), CCopasiMessage::ERROR, CMathContainer::getCountFixedEventTargets(), CTrajectoryProblem::getStartInSteadyState(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiTask::mpContainer, mpContainerStateTime, mpSteadyState, mpTimeSensMethod, mpTimeSensProblem, mUpdateMoieties, CSteadyStateTask::process(), and CTimeSensMethod::start().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().

processStep()

bool CTimeSensTask::processStep	(	const C_FLOAT64 &	nextTime,
		const bool &	final = false
	)

Integrates one step

Parameters

const	C_FLOAT64 & nextTime
const	bool & final (default: false)

Returns

bool success;

References C_FLOAT64, COutputInterface::DURING, CCopasiMessage::EXCEPTION, CTimeSensMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), CTrajectoryProblem::getOutputEvent(), CMathContainer::getProcessQueueExecutionTime(), CTimeSensMethod::getRoots(), CMathContainer::getState(), mContainerState, MCTrajectoryMethod, min, mOutputStartTime, CCopasiTask::mpContainer, mpContainerStateTime, mpLessOrEqual, mProceed, CCopasiTask::mProcessReport, mpTimeSensMethod, mpTimeSensProblem, mUpdateMoieties, CFlags< eStateChange >::None, CTimeSensMethod::NORMAL, output(), CProcessReportLevel::proceed(), CMathContainer::processQueue(), CMathContainer::processRoots(), CTimeSensMethod::ROOT, CMathContainer::setState(), CTimeSensMethod::stateChange(), CTimeSensMethod::step(), CMathContainer::updateRootValues(), and CMathContainer::updateSimulatedValues().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().

signalMathContainerChanged()

void CTimeSensTask::signalMathContainerChanged ( )

protectedvirtual

Signal that the math container has changed

Reimplemented from CCopasiTask.

References CVectorCore< CType >::array(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiTask::mpContainer, mpContainerStateTime, and mUpdateMoieties.

Referenced by CTimeSensTask(), and initialize().

signalMethodChanged()

void CTimeSensTask::signalMethodChanged ( )

protectedvirtual

Signal that the method has changed

Reimplemented from CCopasiTask.

References CCopasiTask::mpMethod, and mUpdateMoieties.

updateMatrices()

bool CTimeSensTask::updateMatrices ( )

virtual

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 from CCopasiTask.

References CTimeSensMethod::initResult(), and CCopasiTask::mpMethod.

Referenced by initialize().

Member Data Documentation

mContainerState

CVectorCore< C_FLOAT64 > CTimeSensTask::mContainerState

protected

The current state of the integration.

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

mOutputStartTime

C_FLOAT64 CTimeSensTask::mOutputStartTime

protected

A pointer to the time at which the output starts.

Referenced by process(), and processStep().

mpContainerStateTime

C_FLOAT64* CTimeSensTask::mpContainerStateTime

protected

A pointer to the current time of the integration.

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

mpLess

bool(* CTimeSensTask::mpLess) (const C_FLOAT64 &, const C_FLOAT64 &)

protected

A pointer to less comparison

Referenced by process().

mpLessOrEqual

bool(* CTimeSensTask::mpLessOrEqual) (const C_FLOAT64 &, const C_FLOAT64 &)

protected

A pointer to lessOrEqual comparison

Referenced by process(), and processStep().

mProceed

bool CTimeSensTask::mProceed

protected

A Boolean flag indication whether to proceed with the integration

Referenced by process(), and processStep().

mpSteadyState

CSteadyStateTask* CTimeSensTask::mpSteadyState

protected

Pointer to CSteadyStateTask. To be used in processStart() to start simulation in steady state

Referenced by initialize(), and processStart().

mpTimeSensMethod

CTimeSensMethod* CTimeSensTask::mpTimeSensMethod

protected

A pointer to the time sensitivities method

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

mpTimeSensProblem

CTimeSensProblem* CTimeSensTask::mpTimeSensProblem

protected

A pointer to the time sensitivities Problem

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

mTimeSeries

CTimeSeries CTimeSensTask::mTimeSeries

protected

the time series (if requested)

Referenced by getTimeSeries(), and initialize().

mTimeSeriesRequested

bool CTimeSensTask::mTimeSeriesRequested

protected

whether the time series should be stored in mTimeSeries

Referenced by initialize().

mUpdateMoieties

bool CTimeSensTask::mUpdateMoieties

protected

Indicates whether we need to update moieties.

Referenced by CTimeSensTask(), initialize(), process(), processStart(), processStep(), signalMathContainerChanged(), and signalMethodChanged().

ValidMethods

const CTaskEnum::Method CTimeSensTask::ValidMethods

static

Initial value:

=
{
  CTaskEnum::Method::timeSensLsoda,
  CTaskEnum::Method::UnsetMethod
}

Referenced by getValidMethods().

---

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

• CTimeSensTask.h
• CTimeSensTask.cpp