#include <CTrajectoryProblem.h>

Inheritance diagram for CTrajectoryProblem:

Public Member Functions
	CTrajectoryProblem (const CDataContainer *pParent=NO_PARENT)

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

virtual bool	elevateChildren ()

bool	getAutomaticStepSize () const

const C_FLOAT64 &	getDuration () const

const bool &	getOutputEvent () const

const C_FLOAT64 &	getOutputStartTime () const

bool	getStartInSteadyState () const

const unsigned C_INT32 &	getStepNumber () const

const C_FLOAT64 &	getStepSize () const

bool	getUseValues () const

std::set< C_FLOAT64 >	getValues () const

const std::string &	getValueString () const

void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::NEXT)

virtual void	printResult (std::ostream *ostream) const

void	setAutomaticStepSize (const bool &automaticStepSize)

void	setDuration (const C_FLOAT64 &duration)

void	setOutputEvent (const bool &outputEvent)

void	setOutputStartTime (const C_FLOAT64 &endTime)

void	setStartInSteadyState (bool flag)

void	setStepNumber (const unsigned C_INT32 &stepNumber)

void	setStepSize (const C_FLOAT64 &stepSize)

void	setTimeSeriesRequested (bool flag)

void	setUseValues (bool flag)

void	setValues (const std::string &values)

void	setValues (const std::vector< C_FLOAT64 > &values)

bool	timeSeriesRequested () const

	~CTrajectoryProblem ()

Public Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src, const CDataContainer *pParent)

virtual void	clearCallBack ()

CCopasiProblem *	copy () const

const CProcessReportLevel &	getCallBack () const

CMathContainer *	getMathContainer () const

virtual CCopasiTask *	getSubTask () const

const CTaskEnum::Task &	getType () const

virtual bool	initialize ()

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

virtual bool	restore (const bool &updateModel)

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setMathContainer (CMathContainer *pContainer)

virtual bool	setModel (CModel *model)

virtual	~CCopasiProblem ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

void	addParameter (CCopasiParameter *pParameter)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

index_iterator	beginIndex () const

const_name_iterator	beginName () const

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

	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")

void	clear ()

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const

index_iterator	endIndex () const

const_name_iterator	endName () const

CCopasiParameterGroup &	getElementTemplates ()

const CCopasiParameterGroup &	getElementTemplates () const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

virtual size_t	getIndex (const CDataObject *pObject) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const size_t &index) const

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

virtual const std::string &	getName (const size_t &index) const

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

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter *	getParameter (std::string name)

const CCopasiParameter *	getParameter (std::string name) const

CCopasiParameter::Type	getType (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

template<class CType >
CType &	getValue (const size_t &index)

template<class CType >
const CType &	getValue (const size_t &index) const

template<class CType >
CType &	getValue (const std::string &name)

template<class CType >
const CType &	getValue (const std::string &name) const

bool	haveTemplate () const

virtual CUndoObjectInterface *	insert (const CData &data)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

virtual bool	remove (CDataObject *pObject)

bool	removeParameter (CCopasiParameter *pParameter)

bool	removeParameter (const size_t &index)

bool	removeParameter (const std::string &name)

virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual CData	toData () const

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

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CDataContainer pParent=NO_PARENT, const std::string &objectType="Parameter")

virtual CCommonName	getCN () const override

template<class CType >
const CType &	getDefault () const

virtual const std::string &	getKey () const override

virtual std::string	getObjectDisplayName () const override

const CCopasiParameter::Type &	getType () const

const UserInterfaceFlag &	getUserInterfaceFlag () const

template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()

template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const

void *	getValidValuesPointer () const

template<class CType >
CType &	getValue ()

template<class CType >
const CType &	getValue () const

virtual void *	getValuePointer () const override

CDataObject *	getValueReference () const

bool	hasValidValues () const

bool	isBasic () const

bool	isDefault () const

bool	isEditable () const

bool	isUnsupported () const

bool	isValidValue (const bool &value) const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const CCommonName &value) const

template<class CType >
bool	isValidValue (const CType &) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setDefault (const CType &defaultValue)

bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)

virtual bool	setObjectParent (const CDataContainer *pParent) override

template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)

template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

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 objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

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

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 const CDataObject *	getDataObject () const override

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

CDataModel *	getObjectDataModel () const

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

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

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

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	~CUndoObjectInterface ()

Protected Member Functions
	CTrajectoryProblem (const CTaskEnum::Task &type, const CDataContainer *pParent)

	CTrajectoryProblem (const CTrajectoryProblem &src)

Protected Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src)

	CCopasiProblem (const CTaskEnum::Task &type, const CDataContainer *pParent)

virtual void	signalMathContainerChanged ()

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src)

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
bool *	mpAutomaticStepSize

C_FLOAT64 *	mpDuration

bool *	mpOutputEvent

C_FLOAT64 *	mpOutputStartTime

bool *	mpStartInSteadyState

unsigned C_INT32 *	mpStepNumber

C_FLOAT64 *	mpStepSize

bool *	mpTimeSeriesRequested

bool *	mpUseValues

std::string *	mpValueString

bool	mStepNumberSetLast

Protected Attributes inherited from CCopasiProblem
CMathContainer *	mpContainer

CReport *	mpReport

CProcessReportLevel	mProcessReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

void *	mpDefault

void *	mpValidValues

void *	mpValue

CDataObject *	mpValueReference

UserInterfaceFlag	mUserInterfaceFlag

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	initializeParameter ()

void	initObjects ()

bool	sync ()

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator

typedef std::vector< CCopasiParameter * >	elements

typedef elements::iterator	index_iterator

typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator

Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }

enum class	Type { DOUBLE = 0 , UDOUBLE , INT , UINT , BOOL , GROUP , STRING , CN , KEY , FILE , EXPRESSION , INVALID , __SIZE }

typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag

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 CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)

static void	allocateValue (const Type &type, void *&pValue)

static void	assignValue (const Type &type, void &pValue, const void pNewValue)

static void	deleteValidValues (const Type &type, void *&pValidValues)

static void	deleteValue (const Type &type, void *&pValue)

static CCopasiParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)

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 *)

Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName

static const CEnumAnnotation< std::string, Type >	XMLType

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

Detailed Description

CTrajectoryProblem class. This class describes the trajectory problem, i.e., it allows to specify for example initial conditions and number of steps.

Created for Copasi by Stefan Hoops 2002

Constructor & Destructor Documentation

◆ CTrajectoryProblem() [1/4]

CTrajectoryProblem::CTrajectoryProblem ( const CTrajectoryProblem & src )

protected

◆ CTrajectoryProblem() [2/4]

CTrajectoryProblem::CTrajectoryProblem	(	const CTaskEnum::Task &	type,
		const CDataContainer *	pParent
	)

protected

Specific constructor can be used to specify a different task type. only to be used by derived classes

CTrajectoryProblem class. This class describes the trajectory problem, i.e., it allows to specify for example initial conditions and number of steps.

Created for COPASI by Stefan Hoops 2002

References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().

◆ CTrajectoryProblem() [3/4]

CTrajectoryProblem::CTrajectoryProblem ( const CDataContainer * pParent = NO_PARENT )

Default constructor.

Parameters

const CDataContainer * pParent (default: NULL)

Default constructor.

References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().

◆ CTrajectoryProblem() [4/4]

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

Copy constructor.

Parameters

const CTrajectoryProblem & src @paramconst CDataContainer * pParent (default: NULL)

Copy constructor.

Parameters

const CTrajectoryProblem & src

References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().

◆ ~CTrajectoryProblem()

CTrajectoryProblem::~CTrajectoryProblem ( )

Destructor.

References DESTRUCTOR_TRACE.

Member Function Documentation

◆ elevateChildren()

bool CTrajectoryProblem::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

Reimplemented in CTimeSensProblem.

References C_FLOAT64, mpDuration, mpStepNumber, mpStepSize, and setDuration().

Referenced by CTimeSensProblem::elevateChildren().

◆ getAutomaticStepSize()

bool CTrajectoryProblem::getAutomaticStepSize ( ) const

Retrieve the size a integration step the trajectory method should do.

Returns: bool automaticStepSize

References mpAutomaticStepSize, and mpUseValues.

Referenced by CHybridMethodODE45::integrateDeterministicPart(), CTimeSensTask::process(), CTimeSensTask::processStep(), CTrajectoryTask::processStep(), CTrajectoryTask::processTrajectory(), CTimeSensLsodaMethod::start(), CLsodaMethod::start(), CLsodaMethod2::start(), CRadau5Method::start(), CHybridMethodODE45::step(), CStochasticRungeKuttaRI5::step(), CStochDirectMethod::step(), CStochMethod::step(), CTauLeapMethod::step(), and CTrajAdaptiveSA::step().

◆ getDuration()

const C_FLOAT64 & CTrajectoryProblem::getDuration ( ) const

Retrieve the end time.

Returns: "const C_FLOAT64 &" duration

References mpDuration.

Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CStochDirectMethod::isValidProblem(), CStochMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CTimeSensTask::process(), CAnalyticsTask::process(), CCrossSectionTask::process(), and CTrajectoryTask::processTrajectory().

◆ getOutputEvent()

const bool & CTrajectoryProblem::getOutputEvent ( ) const

Retrieve whether to do additional output for events.

References mpOutputEvent.

Referenced by CTimeSensTask::processStep(), and CTrajectoryTask::processStep().

◆ getOutputStartTime()

const C_FLOAT64 & CTrajectoryProblem::getOutputStartTime ( ) const

Retrieve the end time.

Returns: "const C_FLOAT64 &" endTime

References mpOutputStartTime.

Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporter::exportExpression(), CTimeSensTask::process(), CAnalyticsTask::process(), CCrossSectionTask::process(), CTrajectoryTask::processTrajectory(), CTrajectoryTask::processValues(), and SEDMLImporter::updateCopasiTaskForSimulation().

◆ getStartInSteadyState()

bool CTrajectoryProblem::getStartInSteadyState ( ) const

References mpStartInSteadyState.

Referenced by CTimeSensTask::initialize(), CTrajectoryTask::initialize(), CTimeSensTask::processStart(), and CTrajectoryTask::processStart().

◆ getStepNumber()

const unsigned C_INT32 & CTrajectoryProblem::getStepNumber ( ) const

Retrieve the number of time steps the trajectory method should integrate.

Returns: "const unsigned C_INT32 &" stepNumber

References mpStepNumber.

Referenced by CSEDMLExporter::createTimeCourseTask(), CTimeSensTask::initialize(), and CTrajectoryTask::initialize().

◆ getStepSize()

const C_FLOAT64 & CTrajectoryProblem::getStepSize ( ) const

Retrieve the size a integration step the trajectory method should do.

Returns: "const C_FLOAT64 &" stepSize

References mpStepSize.

Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CTimeSensTask::process(), and CTrajectoryTask::processTrajectory().

◆ getUseValues()

bool CTrajectoryProblem::getUseValues ( ) const

References mpUseValues.

Referenced by CTrajectoryTask::process().

◆ getValues()

std::set< C_FLOAT64 > CTrajectoryProblem::getValues ( ) const

References mpValueString, ResultParser::saveToDouble(), and ResultParser::split().

Referenced by CTrajectoryTask::processValues().

◆ getValueString()

const std::string & CTrajectoryProblem::getValueString ( ) const

References mpValueString.

◆ initializeParameter()

void CTrajectoryProblem::initializeParameter ( )

private

Initialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, mpAutomaticStepSize, mpDuration, mpOutputEvent, mpOutputStartTime, mpStartInSteadyState, mpStepNumber, mpStepSize, mpTimeSeriesRequested, mpUseValues, mpValueString, CCopasiParameter::STRING, and CCopasiParameter::UINT.

Referenced by CTrajectoryProblem().

◆ initObjects()

void CTrajectoryProblem::initObjects ( )

private

Referenced by CTrajectoryProblem().

◆ load()

void CTrajectoryProblem::load	(	CReadConfig &	configBuffer,
		CReadConfig::Mode	mode = `CReadConfig::NEXT`
	)

Load a trajectory problem

Parameters

CReadConfig &	configBuffer
"CReadConfig::Mode	mode (Default: CReadConfig::NEXT)

Load a trajectory problem

Parameters

CReadConfig & configBuffer

References CReadConfig::getVariable(), CReadConfig::getVersion(), CReadConfig::LOOP, mpDuration, mpStepNumber, mStepNumberSetLast, and sync().

◆ printResult()

void CTrajectoryProblem::printResult ( std::ostream * ostream ) const

virtual

This is the output method for any result of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implemented." To override this default behavior one needs to re-implement the virtual printResult function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

References CDataObject::getObjectParent(), CTrajectoryTask::getTimeSeries(), CTimeSeries::save(), and timeSeriesRequested().

◆ setAutomaticStepSize()

void CTrajectoryProblem::setAutomaticStepSize ( const bool & automaticStepSize )

Set the size a integration step the trajectory method should do.

Parameters

const bool & automaticStepSize

References mpAutomaticStepSize.

◆ setDuration()

void CTrajectoryProblem::setDuration ( const C_FLOAT64 & duration )

Set the end time.

Parameters

const C_FLOAT64 & duration

Set the end time.

Parameters

const C_FLOAT64 & duration @parem bool success

References mpDuration, and sync().

Referenced by CNewtonMethod::doIntegration(), elevateChildren(), and SEDMLImporter::updateCopasiTaskForSimulation().

◆ setOutputEvent()

void CTrajectoryProblem::setOutputEvent ( const bool & outputEvent )

Set whether to output events in addition to the normal steps

Parameters

const bool & outputEvent

References mpOutputEvent.

Referenced by CAnalyticsProblem::initializeParameter(), and CCrossSectionProblem::initializeParameter().

◆ setOutputStartTime()

void CTrajectoryProblem::setOutputStartTime ( const C_FLOAT64 & endTime )

Set the end time.

Parameters

const C_FLOAT64 & endTime

References mpOutputStartTime.

Referenced by SEDMLImporter::updateCopasiTaskForSimulation().

◆ setStartInSteadyState()

void CTrajectoryProblem::setStartInSteadyState ( bool flag )

References mpStartInSteadyState.

Referenced by CNewtonMethod::initialize().

◆ setStepNumber()

void CTrajectoryProblem::setStepNumber ( const unsigned C_INT32 & stepNumber )

Set the number of time steps the trajectory method should integrate.

Parameters

const unsigned C_INT32 & stepNumber

References mpStepNumber, mStepNumberSetLast, and sync().

Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::initialize(), and SEDMLImporter::updateCopasiTaskForSimulation().

◆ setStepSize()

void CTrajectoryProblem::setStepSize ( const C_FLOAT64 & stepSize )

Set the size a integration step the trajectory method should do.

Parameters

const C_FLOAT64 & stepSize

References mpStepSize, mStepNumberSetLast, and sync().

◆ setTimeSeriesRequested()

void CTrajectoryProblem::setTimeSeriesRequested ( bool flag )

References mpTimeSeriesRequested.

◆ setUseValues()

void CTrajectoryProblem::setUseValues ( bool flag )

References mpUseValues.

◆ setValues() [1/2]

void CTrajectoryProblem::setValues ( const std::string & values )

References mpValueString.

Referenced by setValues().

◆ setValues() [2/2]

void CTrajectoryProblem::setValues ( const std::vector< C_FLOAT64 > & values )

References C_FLOAT64, and setValues().

◆ sync()

bool CTrajectoryProblem::sync ( )

private

This function synchronizes step size and number

Returns: bool success

This function synchronizes step size and number

References C_FLOAT64, C_INT32, MCTrajectoryProblem, min, mpDuration, mpStepNumber, mpStepSize, mStepNumberSetLast, and CCopasiMessage::WARNING.

Referenced by load(), setDuration(), setStepNumber(), and setStepSize().

◆ timeSeriesRequested()

bool CTrajectoryProblem::timeSeriesRequested ( ) const

References mpTimeSeriesRequested.

Referenced by CTimeSensTask::initialize(), CTrajectoryTask::initialize(), and printResult().

Member Data Documentation

◆ mpAutomaticStepSize

bool* CTrajectoryProblem::mpAutomaticStepSize

protected

Pointer to parameter value indicating automatic step size.

Referenced by getAutomaticStepSize(), initializeParameter(), and setAutomaticStepSize().

◆ mpDuration

C_FLOAT64* CTrajectoryProblem::mpDuration

protected

Pointer to parameter value for duration.

Referenced by elevateChildren(), getDuration(), CAnalyticsProblem::getTimeLimit(), CCrossSectionProblem::getTimeLimit(), initializeParameter(), load(), setDuration(), CAnalyticsProblem::setTimeLimit(), CCrossSectionProblem::setTimeLimit(), and sync().

◆ mpOutputEvent

bool* CTrajectoryProblem::mpOutputEvent

protected

Pointer to parameter value indicating whether events should be added to the output

Referenced by getOutputEvent(), initializeParameter(), and setOutputEvent().

◆ mpOutputStartTime

C_FLOAT64* CTrajectoryProblem::mpOutputStartTime

protected

Pointer to parameter value for output start time

Referenced by getOutputStartTime(), initializeParameter(), and setOutputStartTime().

◆ mpStartInSteadyState

bool* CTrajectoryProblem::mpStartInSteadyState

protected

Indicates whether a time course is supposed to start in a steady state realized as a CCopasiParameter

Referenced by getStartInSteadyState(), initializeParameter(), and setStartInSteadyState().

◆ mpStepNumber

unsigned C_INT32* CTrajectoryProblem::mpStepNumber

protected

Pointer to parameter value for step number

Referenced by elevateChildren(), getStepNumber(), initializeParameter(), load(), setStepNumber(), and sync().

◆ mpStepSize

C_FLOAT64* CTrajectoryProblem::mpStepSize

protected

Pointer to parameter value for step size.

Referenced by elevateChildren(), getStepSize(), initializeParameter(), setStepSize(), and sync().

◆ mpTimeSeriesRequested

bool* CTrajectoryProblem::mpTimeSeriesRequested

protected

Pointer to parameter value indicating whether a time series needs to be stored in memory

Referenced by initializeParameter(), setTimeSeriesRequested(), and timeSeriesRequested().

◆ mpUseValues

bool* CTrajectoryProblem::mpUseValues

protected

Indicates whether a time course is using a the normal trajectory or a list of values to integrate over

Referenced by getAutomaticStepSize(), getUseValues(), initializeParameter(), and setUseValues().

◆ mpValueString

std::string* CTrajectoryProblem::mpValueString

protected

the string with specific values to hit during integration

Referenced by getValues(), getValueString(), initializeParameter(), and setValues().

◆ mStepNumberSetLast

bool CTrajectoryProblem::mStepNumberSetLast

protected

Indicate whether the step number or step size was set last.

Referenced by load(), setStepNumber(), setStepSize(), and sync().

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CTrajectoryProblem() [1/4]

◆ CTrajectoryProblem() [2/4]

◆ CTrajectoryProblem() [3/4]

◆ CTrajectoryProblem() [4/4]

◆ ~CTrajectoryProblem()

Member Function Documentation

◆ elevateChildren()

◆ getAutomaticStepSize()

◆ getDuration()

◆ getOutputEvent()

◆ getOutputStartTime()

◆ getStartInSteadyState()

◆ getStepNumber()

◆ getStepSize()

◆ getUseValues()

◆ getValues()

◆ getValueString()

◆ initializeParameter()

◆ initObjects()

◆ load()

◆ printResult()

◆ setAutomaticStepSize()

◆ setDuration()

◆ setOutputEvent()

◆ setOutputStartTime()

◆ setStartInSteadyState()

◆ setStepNumber()

◆ setStepSize()

◆ setTimeSeriesRequested()

◆ setUseValues()

◆ setValues() [1/2]

◆ setValues() [2/2]

◆ sync()

◆ timeSeriesRequested()

Member Data Documentation

◆ mpAutomaticStepSize

◆ mpDuration

◆ mpOutputEvent

◆ mpOutputStartTime

◆ mpStartInSteadyState

◆ mpStepNumber

◆ mpStepSize

◆ mpTimeSeriesRequested

◆ mpUseValues

◆ mpValueString

◆ mStepNumberSetLast