#include <CCrossSectionTask.h>

Inheritance diagram for CCrossSectionTask:

Public Member Functions
	CCrossSectionTask (const CCrossSectionTask &src, const CDataContainer *pParent)

	CCrossSectionTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::crosssection)

void	createEvent ()

virtual const CTaskEnum::Method *	getValidMethods () const override

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

virtual bool	process (const bool &useInitialValues) override

void	removeEvent ()

virtual bool	restore (const bool &updateModel=true) override

	~CCrossSectionTask ()

Public Member Functions inherited from CTrajectoryTask
	CTrajectoryTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::timeCourse)

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

const CTimeSeries &	getTimeSeries () const

void	load (CReadConfig &configBuffer)

bool	processStart (const bool &useInitialValues)

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

virtual bool	processTrajectory (const bool &useInitialValues)

virtual bool	processValues (const bool &useInitialValues)

	~CTrajectoryTask ()

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 void	separate (const COutputInterface::Activity &activity)

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setIgnoreProblemData (const bool &ignoreProblemData)

void	setMathContainer (CMathContainer *pContainer)

bool	setMethodType (const CTaskEnum::Method &type)

void	setScheduled (const bool &scheduled)

void	setType (const CTaskEnum::Task &type)

virtual void	setUpdateModel (const bool &updateModel)

virtual CData	toData () const

virtual bool	updateMatrices ()

virtual	~CCopasiTask ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

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

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual size_t	getIndex (const CDataObject *pObject) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const override

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual bool	remove (CDataObject *pObject)

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

virtual void *	getValuePointer () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

virtual void	print (std::ostream *ostream) const override

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CDataContainer *pParent)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CUndoObjectInterface ()

Private Types
enum	STATE { TRANSIENT = 0 , MAIN , FINISH }

Private Member Functions
	CCrossSectionTask ()

void	eventCallBack (void pData, void pCaller)

void	finish ()

void	initObjects ()

C_FLOAT64	relativeDifferenceOfStates (const CVectorCore< C_FLOAT64 > &s1, const CVectorCore< C_FLOAT64 > &s2)

void	setEventCallback (const bool &set)

Private Attributes
C_FLOAT64	mAverageFreq

C_FLOAT64	mAveragePeriod

C_FLOAT64	mFreq

size_t	mhProgress

C_FLOAT64	mLastFreq

C_FLOAT64	mLastPeriod

size_t	mMaxNumCrossings

size_t	mNumCrossings

size_t	mOutputStartNumCrossings

CCrossSectionProblem *	mpCrossSectionProblem

CEvent *	mpDataEvent

C_FLOAT64	mPeriod

C_INT32	mPeriodicity

CCallbackInterface *	mpEventCallback

CMathEvent *	mpMathEvent

C_FLOAT64	mPreviousCrossingTime

C_FLOAT64	mProgressFactor

C_FLOAT64	mProgressMax

C_FLOAT64	mProgressValue

C_FLOAT64	mStartTime

STATE	mState

std::vector< CVector< C_FLOAT64 > >	mStatesRing

C_INT32	mStatesRingCounter

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

Static Public Attributes inherited from CTrajectoryTask
static const CTaskEnum::Method	ValidMethods []

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

Protected Member Functions inherited from CTrajectoryTask
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 inherited from CTrajectoryTask
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 &)

CSteadyStateTask *	mpSteadyState

CTrajectoryMethod *	mpTrajectoryMethod

CTrajectoryProblem *	mpTrajectoryProblem

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

Member Enumeration Documentation

◆ STATE

enum CCrossSectionTask::STATE

private

describes the internal state of the calculation

Enumerator
TRANSIENT
MAIN
FINISH

Constructor & Destructor Documentation

◆ CCrossSectionTask() [1/3]

CCrossSectionTask::CCrossSectionTask ( )

private

Default constructor

◆ CCrossSectionTask() [2/3]

CCrossSectionTask::CCrossSectionTask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = `CTaskEnum::Task::crosssection`
	)

Specific constructor

Parameters

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

CCrossSectionTask class.

This class implements a cross section task.

References CMethodFactory::create(), CTaskEnum::deterministic, CCopasiTask::getType(), initObjects(), and CCopasiTask::mpMethod.

◆ CCrossSectionTask() [3/3]

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

Copy constructor

Parameters

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

References initObjects().

◆ ~CCrossSectionTask()

CCrossSectionTask::~CCrossSectionTask ( )

Destructor

References mpEventCallback, and pdelete.

Member Function Documentation

◆ createEvent()

void CCrossSectionTask::createEvent ( )

References CMathContainer::addAnalysisEvent(), CEvent::Callback, CEvent::compile(), CMathContainer::getModel(), CCrossSectionProblem::getSingleObjectCN(), CCrossSectionProblem::getThreshold(), CCrossSectionProblem::isPositiveDirection(), CCopasiTask::mpContainer, mpCrossSectionProblem, mpDataEvent, mpMathEvent, CEvent::setDelayAssignment(), setEventCallback(), CEvent::setPersistentTrigger(), CEvent::setTriggerExpression(), and CEvent::setType().

Referenced by initialize(), and CScanTask::process().

◆ eventCallBack()

void CCrossSectionTask::eventCallBack	(	void *	pData,
		void *	pCaller
	)

private

This is the member function that is called by the static call back function It checks if an event describes the cut plane and does all the necessary analysis and output in this case

References C_FLOAT64, COutputInterface::DURING, FINISH, CMathContainer::getCountFixedEventTargets(), CCrossSectionProblem::getFlagLimitConvergence(), CCrossSectionProblem::getFlagLimitOutConvergence(), CCrossSectionProblem::getFlagLimitOutCrossings(), CCrossSectionProblem::getFlagLimitOutTime(), MAIN, mAverageFreq, mAveragePeriod, CTrajectoryTask::mContainerState, mFreq, mhProgress, mLastFreq, mLastPeriod, mMaxNumCrossings, mNumCrossings, mOutputStartNumCrossings, CTrajectoryTask::mOutputStartTime, CCopasiTask::mpContainer, CTrajectoryTask::mpContainerStateTime, mpCrossSectionProblem, mPeriod, mPeriodicity, mPreviousCrossingTime, CCopasiTask::mProcessReport, mProgressFactor, mProgressValue, mStartTime, mState, mStatesRing, mStatesRingCounter, CTrajectoryTask::mUpdateMoieties, CCopasiTask::output(), CProcessReportLevel::progressItem(), relativeDifferenceOfStates(), RING_SIZE, CMathContainer::setState(), TRANSIENT, and CMathContainer::updateSimulatedValues().

Referenced by setEventCallback().

◆ finish()

void CCrossSectionTask::finish ( )

private

should be called by all code paths that finish the task. -finishes progress reporting -finishes output -resets call back function

References COutputInterface::AFTER, CProcessReportLevel::finishItem(), mhProgress, CCopasiTask::mProcessReport, and CCopasiTask::output().

Referenced by process().

◆ getValidMethods()

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

overridevirtual

Retrieve the list of valid methods

Returns: const CTaskEnum::Method * pValidMethods

Reimplemented from CTrajectoryTask.

References CTaskEnum::deterministic, CTaskEnum::UnsetMethod, and CTrajectoryTask::ValidMethods.

◆ initialize()

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

overridevirtual

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