CTrajectoryProblem Class Reference

#include <CTrajectoryProblem.h>

Inheritance diagram for CTrajectoryProblem:

Collaboration diagram for CTrajectoryProblem:

Public Member Functions
	CTrajectoryProblem (const CCopasiContainer *pParent=NULL)
	CTrajectoryProblem (const CTrajectoryProblem &src, const CCopasiContainer *pParent=NULL)
virtual bool	elevateChildren ()
const bool &	getContinueSimultaneousEvents () const
const C_FLOAT64 &	getDuration () const
const bool &	getOutputEvent () const
const C_FLOAT64 &	getOutputStartTime () const
const unsigned C_INT32 &	getStepNumber () const
const C_FLOAT64 &	getStepSize () const
void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::NEXT)
void	setContinueSimultaneousEvents (const bool &continueSimultaneousEvents)
void	setDuration (const C_FLOAT64 &duration)
void	setOutputEvent (const bool &outputEvent)
void	setOutputStartTime (const C_FLOAT64 &endTime)
void	setStepNumber (const unsigned C_INT32 &stepNumber)
void	setStepSize (const C_FLOAT64 &stepSize)
void	setTimeSeriesRequested (bool flag)
bool	timeSeriesRequested () const
	~CTrajectoryProblem ()
Public Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)
CModel *	getModel () const
const CCopasiTask::Type &	getType () const
virtual bool	initialize ()
virtual void	print (std::ostream *ostream) const
virtual void	printResult (std::ostream *ostream) const
virtual bool	restore (const bool &updateModel)
virtual bool	setCallBack (CProcessReport *pCallBack)
virtual bool	setModel (CModel *pModel)
virtual	~CCopasiProblem ()
Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)
bool	addParameter (const CCopasiParameter &parameter)
bool	addParameter (const std::string &name, const CCopasiParameter::Type type)
template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)
void	addParameter (CCopasiParameter *pParameter)
CCopasiParameterGroup *	assertGroup (const std::string &name)
template<class CType >
CCopasiParameter *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)
index_iterator	beginIndex () const
name_iterator	beginName () const
	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)
	CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")
void	clear ()
index_iterator	endIndex () const
name_iterator	endName () const
CCopasiParameterGroup *	getGroup (const std::string &name)
const CCopasiParameterGroup *	getGroup (const std::string &name) const
CCopasiParameterGroup *	getGroup (const size_t &index)
const CCopasiParameterGroup *	getGroup (const size_t &index) const
size_t	getIndex (const std::string &name) const
std::string	getKey (const std::string &name) const
std::string	getKey (const size_t &index) const
virtual const std::string &	getName (const size_t &index) const
virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const
CCopasiParameter *	getParameter (const std::string &name)
const CCopasiParameter *	getParameter (const std::string &name) const
CCopasiParameter *	getParameter (const size_t &index)
const CCopasiParameter *	getParameter (const size_t &index) const
CCopasiParameter::Type	getType (const std::string &name) const
CCopasiParameter::Type	getType (const size_t &index) const
std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const
const CCopasiParameter::Value &	getValue (const std::string &name) const
const CCopasiParameter::Value &	getValue (const size_t &index) const
CCopasiParameter::Value &	getValue (const std::string &name)
CCopasiParameter::Value &	getValue (const size_t &index)
CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)
bool	removeParameter (const std::string &name)
bool	removeParameter (const size_t &index)
template<class CType >
bool	setValue (const std::string &name, const CType &value)
template<class CType >
bool	setValue (const size_t &index, const CType &value)
size_t	size () const
bool	swap (const size_t &iFrom, const size_t &iTo)
bool	swap (index_iterator &from, index_iterator &to)
virtual	~CCopasiParameterGroup ()
Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)
	CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter")
virtual CCopasiObjectName	getCN () const
virtual const std::string &	getKey () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
const CCopasiParameter::Type &	getType () const
const Value &	getValue () const
Value &	getValue ()
virtual void *	getValuePointer () const
CCopasiObject *	getValueReference () const
bool	isValidValue (const C_FLOAT64 &value) const
bool	isValidValue (const C_INT32 &value) const
bool	isValidValue (const unsigned C_INT32 &value) const
bool	isValidValue (const bool &value) const
bool	isValidValue (const std::string &value) const
bool	isValidValue (const CCopasiObjectName &value) const
bool	isValidValue (const std::vector< CCopasiParameter * > &value) const
CCopasiParameter &	operator= (const CCopasiParameter &rhs)
template<class CType >
bool	setValue (const CType &value)
bool	setValue (const std::vector< CCopasiParameter * > &value)
virtual	~CCopasiParameter ()
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 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 const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () 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
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
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 ()

Protected Attributes
bool *	mpContinueSimultaneousEvents
C_FLOAT64 *	mpDuration
bool *	mpOutputEvent
C_FLOAT64 *	mpOutputStartTime
unsigned C_INT32 *	mpStepNumber
C_FLOAT64 *	mpStepSize
bool *	mpTimeSeriesRequested
bool	mStepNumberSetLast
Protected Attributes inherited from CCopasiProblem
CProcessReport *	mpCallBack
CModel *	mpModel
CReport *	mpReport
Protected Attributes inherited from CCopasiParameter
std::string	mKey
CCopasiObject *	mpValueReference
size_t	mSize
Value	mValue
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
void	initializeParameter ()
void	initObjects ()
bool	sync ()

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator
typedef CCopasiContainer::objectMap::iterator	name_iterator
typedef std::vector < CCopasiParameter * >	parameterGroup
Public Types inherited from CCopasiParameter
enum	Type {   DOUBLE = 0, UDOUBLE, INT, UINT,   BOOL, GROUP, STRING, CN,   KEY, FILE, EXPRESSION, INVALID }
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 CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)
Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []
static const char *	XMLType []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList
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 CCopasiProblem
	CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL)
Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()
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)
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

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

Definition at line 31 of file CTrajectoryProblem.h.

Constructor & Destructor Documentation

CTrajectoryProblem::CTrajectoryProblem

(

const CCopasiContainer *

pParent = NULL

)

Default constructor.

Parameters

const

CCopasiContainer * pParent (default: NULL)

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 Default constructor.

Definition at line 37 of file CTrajectoryProblem.cpp.

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

                                                                      :
  CCopasiProblem(CCopasiTask::timeCourse, pParent),
  mpDuration(NULL),
  mpStepSize(NULL),
  mpStepNumber(NULL),
  mpTimeSeriesRequested(NULL),
  mpOutputStartTime(NULL),
  mpOutputEvent(NULL),
  mpContinueSimultaneousEvents(NULL),
  mStepNumberSetLast(true)
{
  initializeParameter();
  initObjects();
  CONSTRUCTOR_TRACE;
}

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

Copy constructor.

Parameters

const

CTrajectoryProblem & src CCopasiContainer * pParent (default: NULL)

Copy constructor.

Parameters

const CTrajectoryProblem &

src

Definition at line 57 of file CTrajectoryProblem.cpp.

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

                                                                        :
  CCopasiProblem(src, pParent),
  mpDuration(NULL),
  mpStepSize(NULL),
  mpStepNumber(NULL),
  mpTimeSeriesRequested(NULL),
  mpOutputStartTime(NULL),
  mpOutputEvent(NULL),
  mpContinueSimultaneousEvents(NULL),
  mStepNumberSetLast(src.mStepNumberSetLast)
{
  initializeParameter();
  initObjects();
  CONSTRUCTOR_TRACE;
}

CTrajectoryProblem::~CTrajectoryProblem

(

)

Destructor.

Definition at line 77 of file CTrajectoryProblem.cpp.

References DESTRUCTOR_TRACE.

{DESTRUCTOR_TRACE;}

Member Function Documentation

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.

Definition at line 98 of file CTrajectoryProblem.cpp.

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

{
  // If we have an old COPASI file "Duration" is not set
  // but we can fix that.
  if (*mpDuration == 1.0) // the default
    setDuration(*mpStepSize * (C_FLOAT64) *mpStepNumber);

  return true;
}

const bool & CTrajectoryProblem::getContinueSimultaneousEvents

(

)

const

Retrieve whether to continue on simultaneous events.

Returns

const bool & continueSimultaneousEvents

Definition at line 210 of file CTrajectoryProblem.cpp.

References mpContinueSimultaneousEvents.

Referenced by CTrajectoryTask::initialize(), CQTrajectoryWidget::loadTask(), and CQTrajectoryWidget::saveTask().

{
  return *mpContinueSimultaneousEvents;
}

const C_FLOAT64 & CTrajectoryProblem::getDuration

(

)

const

Retrieve the end time.

Returns

"const C_FLOAT64 &" duration

Definition at line 178 of file CTrajectoryProblem.cpp.

References mpDuration.

Referenced by CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CTauLeapMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CStochMethod::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CQTrajectoryWidget::loadTask(), CTrajectoryTask::process(), CCrossSectionTask::process(), and CQTrajectoryWidget::saveTask().

{return *mpDuration;}

const bool & CTrajectoryProblem::getOutputEvent

(

)

const

Retrieve whether to do additional output for events.

Definition at line 202 of file CTrajectoryProblem.cpp.

References mpOutputEvent.

Referenced by CQTrajectoryWidget::loadTask(), CTrajectoryTask::processStep(), and CQTrajectoryWidget::saveTask().

{return *mpOutputEvent;}

const C_FLOAT64 & CTrajectoryProblem::getOutputStartTime

(

)

const

Retrieve the end time.

Returns

"const C_FLOAT64 &" endTime

Definition at line 186 of file CTrajectoryProblem.cpp.

References mpOutputStartTime.

Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporter::exportExpression(), CQCrossSectionTaskWidget::loadTask(), CQTrajectoryWidget::loadTask(), CTrajectoryTask::process(), CCrossSectionTask::process(), CQTrajectoryWidget::saveTask(), and CQCrossSectionTaskWidget::updateValues().

{return *mpOutputStartTime;}

const unsigned C_INT32 & CTrajectoryProblem::getStepNumber

(

)

const

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

Returns

"const unsigned C_INT32 &" stepNumber

Definition at line 138 of file CTrajectoryProblem.cpp.

References mpStepNumber.

Referenced by CSEDMLExporter::createTimeCourseTask(), CTrajectoryTask::initialize(), CQTrajectoryWidget::loadTask(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotDuration(), and CQTrajectoryWidget::slotIntervalSize().

{return *mpStepNumber;}

const C_FLOAT64 & CTrajectoryProblem::getStepSize

(

)

const

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

Returns

"const C_FLOAT64 &" stepSize

Definition at line 158 of file CTrajectoryProblem.cpp.

References mpStepSize.

Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CQTrajectoryWidget::loadTask(), CTrajectoryTask::process(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotDuration(), CQTrajectoryWidget::slotIntervals(), and CQTrajectoryWidget::slotIntervalSize().

{return *mpStepSize;}

void CTrajectoryProblem::initializeParameter ( )

private

Initialize the method parameter

Definition at line 80 of file CTrajectoryProblem.cpp.

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameter::getValue(), mpContinueSimultaneousEvents, mpDuration, mpOutputEvent, mpOutputStartTime, mpStepNumber, mpStepSize, mpTimeSeriesRequested, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.

Referenced by CTrajectoryProblem().

{
  mpStepNumber =
    assertParameter("StepNumber", CCopasiParameter::UINT, (unsigned C_INT32) 100)->getValue().pUINT;
  mpStepSize =
    assertParameter("StepSize", CCopasiParameter::DOUBLE, (C_FLOAT64) 0.01)->getValue().pDOUBLE;;
  mpDuration =
    assertParameter("Duration", CCopasiParameter::DOUBLE, (C_FLOAT64) 1.0)->getValue().pDOUBLE;;
  mpTimeSeriesRequested =
    assertParameter("TimeSeriesRequested", CCopasiParameter::BOOL, (bool) true)->getValue().pBOOL;
  mpOutputStartTime =
    assertParameter("OutputStartTime", CCopasiParameter::DOUBLE, (C_FLOAT64) 0.0)->getValue().pDOUBLE;
  mpOutputEvent =
    assertParameter("Output Event", CCopasiParameter::BOOL, (bool) false)->getValue().pBOOL;
  mpContinueSimultaneousEvents =
    assertParameter("Continue on Simultaneous Events", CCopasiParameter::BOOL, (bool) false)->getValue().pBOOL;
}

void CTrajectoryProblem::initObjects ( )

private

Definition at line 108 of file CTrajectoryProblem.cpp.

References C_INT32, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValueReference(), setDuration(), setStepNumber(), setStepSize(), and CCopasiObject::setUpdateMethod().

Referenced by CTrajectoryProblem().

{
  getParameter("StepNumber")->getValueReference()
  ->setUpdateMethod(this,
                    (void (CTrajectoryProblem::*)(const C_INT32 &)) &CTrajectoryProblem::setStepNumber);

  getParameter("StepSize")->getValueReference()
  ->setUpdateMethod(this, &CTrajectoryProblem::setStepSize);

  getParameter("Duration")->getValueReference()
  ->setUpdateMethod(this, &CTrajectoryProblem::setDuration);
}

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

Definition at line 219 of file CTrajectoryProblem.cpp.

References CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CReadConfig::getVariable(), CReadConfig::getVersion(), CReadConfig::LOOP, mpDuration, CCopasiProblem::mpModel, mpStepNumber, mStepNumberSetLast, and sync().

{
  if (configBuffer.getVersion() < "4.0")
    {
      CCopasiDataModel* pDataModel = getObjectDataModel();
      assert(pDataModel != NULL);
      mpModel = pDataModel->getModel();
      configBuffer.getVariable("EndTime", "C_FLOAT64",
                               mpDuration,
                               CReadConfig::LOOP);
      configBuffer.getVariable("Points", "C_INT32",
                               mpStepNumber);
      mStepNumberSetLast = true;

      sync();
    }
}

void CTrajectoryProblem::setContinueSimultaneousEvents

(

const bool &

continueSimultaneousEvents

)

Set whether to continue on simultaneous events

Parameters

const

bool & continueSimultaneousEvents

Definition at line 205 of file CTrajectoryProblem.cpp.

References mpContinueSimultaneousEvents.

Referenced by CQTrajectoryWidget::saveTask(), and SEDMLImporter::updateCopasiTaskForSimulation().

{
  *mpContinueSimultaneousEvents = continueSimultaneousEvents;
}

void CTrajectoryProblem::setDuration

(

const C_FLOAT64 &

duration

)

Set the end time.

Parameters

const C_FLOAT64 &

duration bool success

Definition at line 166 of file CTrajectoryProblem.cpp.

References mpDuration, and sync().

Referenced by CNewtonMethod::doIntegration(), elevateChildren(), initObjects(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotDuration(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().

{
  *mpDuration = duration;
  sync();

  return;
}

void CTrajectoryProblem::setOutputEvent

(

const bool &

outputEvent

)

Set whether to output events in addition to the normal steps

Parameters

const

bool & outputEvent

Definition at line 197 of file CTrajectoryProblem.cpp.

References mpOutputEvent.

Referenced by CQTrajectoryWidget::saveTask().

{
  *mpOutputEvent = outputEvent;
}

void CTrajectoryProblem::setOutputStartTime

(

const C_FLOAT64 &

endTime

)

Set the end time.

Parameters

const C_FLOAT64 &

endTime

Definition at line 181 of file CTrajectoryProblem.cpp.

References mpOutputStartTime.

Referenced by CQCrossSectionTaskWidget::commitInput(), CQCrossSectionTaskWidget::saveTask(), CQTrajectoryWidget::saveTask(), CQCrossSectionTaskWidget::slotOutputDelay(), and SEDMLImporter::updateCopasiTaskForSimulation().

{
  *mpOutputStartTime = startTime;
}

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 bool success

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

Parameters

const unsigned C_INT32 &

stepNumber

Definition at line 125 of file CTrajectoryProblem.cpp.

References mpStepNumber, mStepNumberSetLast, and sync().

Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::initialize(), initObjects(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotIntervals(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().

{
  *mpStepNumber = stepNumber;
  mStepNumberSetLast = true;
  sync();

  return;
}

void CTrajectoryProblem::setStepSize

(

const C_FLOAT64 &

stepSize

)

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

Parameters

const C_FLOAT64 &

stepSize bool success

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

Parameters

const C_FLOAT64 &

stepSize

Definition at line 145 of file CTrajectoryProblem.cpp.

References mpStepSize, mStepNumberSetLast, and sync().

Referenced by initObjects(), CQTrajectoryWidget::saveTask(), and CQTrajectoryWidget::slotIntervalSize().

{
  *mpStepSize = stepSize;
  mStepNumberSetLast = false;
  sync();

  return;
}

void CTrajectoryProblem::setTimeSeriesRequested

(

bool

flag

)

Definition at line 189 of file CTrajectoryProblem.cpp.

References mpTimeSeriesRequested.

Referenced by CQTrajectoryWidget::saveTask(), and test000087::test_simulate_reaction_flux_reference_1().

{
  *mpTimeSeriesRequested = flag;
}

bool CTrajectoryProblem::sync ( )

private

This function synchronizes step size and number

Returns

bool success

This function synchronizes step size and number

Definition at line 241 of file CTrajectoryProblem.cpp.

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

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

{
  bool success = true;

  if (fabs(*mpDuration) < std::numeric_limits< C_FLOAT64 >::min())
    return success;

  C_FLOAT64 Tmp = *mpDuration;
  C_FLOAT64 StepSize = *mpStepSize;
  C_FLOAT64 StepNumber = (C_FLOAT64) * mpStepNumber;

  if (mStepNumberSetLast)
    {
      StepSize = Tmp / (C_FLOAT64) * mpStepNumber;

      /* Assure that the step size is not to small for machine accuracy */
      if (fabs(StepSize) < 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() * fabs(*mpDuration))
        {
          CCopasiMessage(CCopasiMessage::WARNING,
                         MCTrajectoryProblem + 3, StepSize);

          StepSize = 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() * fabs(*mpDuration);
          /* Assure that the step size has the appropriate sign. */
          StepSize = (Tmp < 0.0) ? - fabs(StepSize) : fabs(StepSize);
          StepNumber = fabs(ceil(Tmp / StepSize));
        }
    }
  else
    {
      if (fabs(StepSize) < 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() * fabs(*mpDuration))
        {
          CCopasiMessage(CCopasiMessage::WARNING,
                         MCTrajectoryProblem + 3, StepSize);

          StepSize = 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() * fabs(*mpDuration);

          /* Assure that the step size has the appropriate sign. */
          StepSize = (Tmp < 0.0) ? - fabs(StepSize) : fabs(StepSize);
        }

      StepNumber = fabs(ceil(Tmp / StepSize));

      /* Protect against overflow */
      if ((C_FLOAT64) ULONG_MAX < StepNumber)
        {
          CCopasiMessage(CCopasiMessage::WARNING,
                         MCTrajectoryProblem + 2, StepNumber);

          StepNumber = (C_FLOAT64) ULONG_MAX;
          StepSize = Tmp / StepNumber;
        }

      /* Assure that the step size has the appropriate sign. */
      StepSize = (Tmp < 0.0) ? - fabs(StepSize) : fabs(StepSize);
    }

  *mpStepSize = StepSize;
  *mpStepNumber = (unsigned C_INT32) StepNumber;

  return success;
}

bool CTrajectoryProblem::timeSeriesRequested

(

)

const

Definition at line 194 of file CTrajectoryProblem.cpp.

References mpTimeSeriesRequested.

Referenced by CTrajectoryTask::initialize(), CQTrajectoryWidget::loadTask(), and CQTrajectoryWidget::saveTask().

{return *mpTimeSeriesRequested;}

Member Data Documentation

bool* CTrajectoryProblem::mpContinueSimultaneousEvents

protected

Pointer to parameter value indicating whether to continue when simultaneous events are encountered

Definition at line 206 of file CTrajectoryProblem.h.

Referenced by getContinueSimultaneousEvents(), initializeParameter(), and setContinueSimultaneousEvents().

C_FLOAT64* CTrajectoryProblem::mpDuration

protected

Pointer to parameter value for duration.

Definition at line 173 of file CTrajectoryProblem.h.

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

bool* CTrajectoryProblem::mpOutputEvent

protected

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

Definition at line 200 of file CTrajectoryProblem.h.

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

C_FLOAT64* CTrajectoryProblem::mpOutputStartTime

protected

Pointer to parameter value for output start time

Definition at line 194 of file CTrajectoryProblem.h.

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

unsigned C_INT32* CTrajectoryProblem::mpStepNumber

protected

Pointer to parameter value for step number

Definition at line 183 of file CTrajectoryProblem.h.

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

C_FLOAT64* CTrajectoryProblem::mpStepSize

protected

Pointer to parameter value for step size.

Definition at line 178 of file CTrajectoryProblem.h.

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

bool* CTrajectoryProblem::mpTimeSeriesRequested

protected

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

Definition at line 189 of file CTrajectoryProblem.h.

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

bool CTrajectoryProblem::mStepNumberSetLast

protected

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

Definition at line 211 of file CTrajectoryProblem.h.

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

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

• CTrajectoryProblem.h
• CTrajectoryProblem.cpp