CCopasiMethod Class Reference

#include <CCopasiMethod.h>

Inheritance diagram for CCopasiMethod:

Public Member Functions
	CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)
virtual void	clearCallBack ()
const CProcessReportLevel &	getCallBack () const
CMathContainer *	getMathContainer () const
const CTaskEnum::Method &	getSubType () const
const CTaskEnum::Task &	getType () const
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
CCopasiMethod &	operator= (const CCopasiMethod &rhs)
virtual void	print (std::ostream *ostream) const
virtual void	printResult (std::ostream *ostream) const
virtual bool	setCallBack (CProcessReportLevel callBack)
void	setMathContainer (CMathContainer *pContainer)
virtual	~CCopasiMethod ()
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
virtual bool	elevateChildren ()
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
	CCopasiMethod (const CCopasiMethod &src)
	CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)
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
CMathContainer *	mpContainer
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
	CCopasiMethod ()

Private Attributes
CTaskEnum::Method	mSubType
CTaskEnum::Task	mTaskType

Friends
std::ostream &	operator<< (std::ostream &os, const CCopasiMethod &o)

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

Constructor & Destructor Documentation

CCopasiMethod() [1/4]

CCopasiMethod::CCopasiMethod ( )

private

Default constructor

CCopasiMethod() [2/4]

CCopasiMethod::CCopasiMethod ( const CDataContainer *  pParent, const CTaskEnum::Method &  methodType, const CTaskEnum::Task &  taskType  )

protected

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType
const	CTaskEnum::Task & taskType

CCopasiMethod class. This class is used to describe a task in COPASI. This class is intended to be used as the parent class for all methods within COPASI.

Created for COPASI by Stefan Hoops 2003

CCopasiMethod() [3/4]

CCopasiMethod::CCopasiMethod ( const CCopasiMethod &  src )

protected

CCopasiMethod() [4/4]

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

Copy constructor

Parameters

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

~CCopasiMethod()

CCopasiMethod::~CCopasiMethod ( )

virtual

Destructor

Member Function Documentation

clearCallBack()

void CCopasiMethod::clearCallBack ( )

virtual

resets the currently set callback by calling setCallBack(NULL)

References setCallBack().

getCallBack()

const CProcessReportLevel & CCopasiMethod::getCallBack

(

)

const

Returns

the currently set callback

References mProcessReport.

getMathContainer()

CMathContainer * CCopasiMethod::getMathContainer

(

)

const

Retrieve the model of the problem

Returns

CMathContainer * pContainer

References mpContainer.

getSubType()

const CTaskEnum::Method & CCopasiMethod::getSubType

(

)

const

Retrieve the sub type of the method

Returns

CTaskEnum::Method & subType

References mSubType.

Referenced by CCopasiTask::applyData(), CMethodFactory::copy(), CCopasiTask::createUndoData(), CSEDMLExporter::exportAlgorithm(), CEFMTask::getFluxModeDescription(), CEFMTask::getReactionEquation(), COptPopulationMethod::initialize(), COptProblem::initialize(), CNewtonMethod::initialize(), COptPopulationMethod::initObjects(), CHybridMethod::isValidProblem(), CStochMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CTSSAMethod::isValidProblem(), MethodHandler::processStart(), CCopasiXML::saveTaskList(), CTSSAMethod::schur(), CCopasiTask::setMethodType(), and CCopasiTask::toData().

getType()

const CTaskEnum::Task & CCopasiMethod::getType

(

void

)

const

Retrieve the type of the method

Returns

const string & type

References mTaskType.

Referenced by COptMethodSS::initialize().

isValidProblem()

bool CCopasiMethod::isValidProblem ( const CCopasiProblem *  pProblem )

virtual

Check if the method is suitable for this problem

Returns

bool suitability of the method

Reimplemented in CSensMethod, CTSSAMethod, CTrajectoryMethodDsaLsodar, CTrajectoryMethod, CTrajAdaptiveSA, CTauLeapMethod, CStochMethod, CStochDirectMethod, CHybridMethodODE45, CHybridMethod, CTimeSensMethod, CSteadyStateMethod, CNewtonMethod, CMCAMethod, CScanMethod, COscillationMethod, COptMethod, CLyapWolfMethod, CLyapMethod, CLNAMethod, CEFMMethod, CCrossSectionMethod, and CAnalyticsMethod.

References CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CMathContainer::getEvents(), CTaskEnum::lna, CTaskEnum::lyap, MCCopasiMethod, mpContainer, mTaskType, CVectorCore< CType >::size(), and CTaskEnum::tssAnalysis.

Referenced by CEFMTask::initialize(), CLyapTask::initialize(), CScanTask::initialize(), CTimeSensTask::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CLNATask::initialize(), CMoietiesTask::initialize(), CMCATask::initialize(), CAnalyticsMethod::isValidProblem(), CCrossSectionMethod::isValidProblem(), CEFMMethod::isValidProblem(), CLNAMethod::isValidProblem(), CLyapMethod::isValidProblem(), COptMethod::isValidProblem(), COscillationMethod::isValidProblem(), CScanMethod::isValidProblem(), CMCAMethod::isValidProblem(), CSteadyStateMethod::isValidProblem(), CTimeSensMethod::isValidProblem(), CTrajectoryMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CSensMethod::isValidProblem(), COscillationTask::process(), CSensTask::process(), COptTask::process(), CFitTask::process(), CTSSATask::updateMatrices(), CLNATask::updateMatrices(), and CMCATask::updateMatrices().

load()

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

virtual

Load a list of parameters

Parameters

CReadConfig &	configBuffer
CReadConfig::Mode	mode Default(CReadConfig::SEARCH)

Reimplemented in CNewtonMethod.

References fatalError.

operator=()

CCopasiMethod & CCopasiMethod::operator=

(

const CCopasiMethod &

rhs

)

References mpContainer, mProcessReport, mSubType, mTaskType, and CCopasiParameterGroup::operator=().

print()

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

virtual

This is the output method for any object. The default implementation provided with CDataObject uses the ostream operator<< of the object to print the object.To overide this default behaviour one needs to reimplement the virtual print function.

Parameters

std::ostream

* ostream

Reimplemented from CCopasiParameterGroup.

Reimplemented in COptPopulationMethod.

Referenced by COptPopulationMethod::print().

printResult()

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

virtual

This is the output method for any result of a method. The default implementation provided with CCopasiMethod. Does only print "Not implmented." To overide this default behaviour one needs to reimplement the virtual printResult function.

Parameters

std::ostream

* ostream

Reimplemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

Referenced by CTSSAProblem::printResult().

setCallBack()

bool CCopasiMethod::setCallBack ( CProcessReportLevel  callBack )

virtual

Set the call back of the problem

Parameters

CProcessReport

* pCallBack

Returns

bool success

Reimplemented in CSensMethod.

References mProcessReport.

Referenced by clearCallBack(), CEFMTask::setCallBack(), CCopasiTask::setCallBack(), CMoietiesTask::setCallBack(), COscillationTask::setCallBack(), CFitTask::setCallBack(), and CSensMethod::setCallBack().

setMathContainer()

void CCopasiMethod::setMathContainer

(

CMathContainer *

pContainer

)

Set the model of the problem

Parameters

CMathContainer

* pContainer

References mpContainer, and signalMathContainerChanged().

Referenced by CMethodFactory::copy(), CMethodFactory::create(), CTSSATask::initialize(), CCopasiTask::setMathContainer(), CHybridNextReactionLSODAMethod::start(), CTSSAMethod::start(), and CTSSATask::updateMatrices().

signalMathContainerChanged()

void CCopasiMethod::signalMathContainerChanged ( )

protectedvirtual

Signal that the math container has changed

Reimplemented in CTrajectoryMethod, CTimeSensMethod, and COptMethod.

Referenced by setMathContainer().

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  os, const CCopasiMethod &  o  )

friend

Output stream operator

Parameters

ostream	& os
const	CCopasiMethod & A

Returns

ostream & os

Member Data Documentation

mpContainer

CMathContainer* CCopasiMethod::mpContainer

protected

The model of the problem

Referenced by CSteadyStateMethod::allPositive(), CLyapWolfMethod::calculate(), CScanMethod::calculate(), CTimeSensMethod::calculate_dAssignments_dPar(), CTimeSensMethod::calculate_dAssignments_dState(), CTimeSensMethod::calculate_dInitialState_dPar(), CTimeSensMethod::calculate_dRate_dPar(), CLNAMethod::calculateCovarianceMatrixFull(), CLNAMethod::calculateCovarianceMatrixReduced(), CHybridMethod::calculateDerivative(), CTSSAMethod::calculateDerivatives(), CNewtonMethod::calculateDerivativesX(), CSteadyStateMethod::calculateJacobian(), CMCAMethod::calculateUnscaledElasticities(), CHybridMethodODE45::checkRoots(), CStochDirectMethod::checkRoots(), CNewtonMethod::containsNaN(), CMCAMethod::createLinkMatrix(), CTimeSensLsodaMethod::createRootMask(), CHybridMethodODE45::createRootMask(), CLsodaMethod::createRootMask(), CLsodaMethod2::createRootMask(), CRadau5Method::createRootMask(), CStochasticRungeKuttaRI5::createRootMask(), CCSPMethod::CSPImportanceIndex(), CCSPMethod::CSPOutput(), CCSPMethod::CSPParticipationIndex(), CCSPMethod::CSPradicalPointer(), CCSPMethod::cspstep(), CLsodaMethod2::destroyRootMask(), CStochasticRungeKuttaRI5::destroyRootMask(), CILDMMethod::deuflhard(), CSensMethod::do_target_calculation(), CNewtonMethod::doIntegration(), CSteadyStateMethod::doJacobian(), CTrajAdaptiveSA::doSingleSSAStep(), CStochDirectMethod::doSingleStep(), CStochNextReactionMethod::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CLyapWolfMethod::evalF(), CTimeSensLsodaMethod::evalF(), CHybridMethodODE45::evalF(), CLsodaMethod::evalF(), CLsodaMethod2::evalF(), CRadau5Method::evalF(), CTrajectoryMethodDsaLsodar::evalF(), CStochasticRungeKuttaRI5::evalNoise(), CTimeSensLsodaMethod::evalR(), CLsodaMethod::evalR(), CRadau5Method::evalR(), CHybridMethodODE45::evalR(), CStochasticRungeKuttaRI5::evalRate(), CLsodaMethod2::evalRoot(), CStochasticRungeKuttaRI5::evalRoot(), CHybridMethodODE45::fireReaction(), CTrajectoryMethodDsaLsodar::fireReaction(), getMathContainer(), CMCAMethod::getModel(), CTimeSensLsodaMethod::hasStateChanged(), CLsodaMethod::hasStateChanged(), CRadau5Method::hasStateChanged(), CScanMethod::init(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CEFMAlgorithm::initialize(), CNewtonMethod::initialize(), CSteadyStateMethod::initialize(), CSensMethod::initialize(), CTimeSensMethod::initializeDerivativesCalculations(), CCSPMethod::initializeOutput(), CTimeSensMethod::initResult(), CHybridMethodODE45::integrateDeterministicPart(), CHybridNextReactionRKMethod::integrateDeterministicPart(), CTrajectoryMethodDsaLsodar::integrateDeterministicPart(), CStochasticRungeKuttaRI5::internalStep(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), CSteadyStateMethod::isEquilibrium(), CEFMMethod::isValidProblem(), CLNAMethod::isValidProblem(), CLyapMethod::isValidProblem(), CMCAMethod::isValidProblem(), CNewtonMethod::isValidProblem(), CHybridMethod::isValidProblem(), CStochDirectMethod::isValidProblem(), CStochMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CTSSAMethod::isValidProblem(), isValidProblem(), CILDMMethod::newton(), operator=(), CTimeSensMethod::output(), CTrajectoryMethod::output(), CHybridMethodODE45::partitionSystem(), CTimeSensLsodaMethod::peekAhead(), CLsodaMethod::peekAhead(), CLsodaMethod2::peekAhead(), CRadau5Method::peekAhead(), CCSPMethod::printResult(), CILDMModifiedMethod::printResult(), CMoietiesMethod::process(), CLNAMethod::resizeAllMatrices(), CMCAMethod::resizeAllMatrices(), CSteadyStateMethod::returnProcess(), CStochDirectMethod::rootValue(), CMCAMethod::scaleMCA(), CCSPMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CILDMModifiedMethod::setAnnotationM(), setMathContainer(), CTimeSensLsodaMethod::setRootMaskType(), CLsodaMethod::setRootMaskType(), CRadau5Method::setRootMaskType(), CHybridMethod::setupDependencyGraph(), CCSPMethod::setVectors(), CILDMMethod::setVectors(), CCSPMethod::setVectorsToNaN(), COptMethod::signalMathContainerChanged(), CTimeSensMethod::signalMathContainerChanged(), CTrajectoryMethod::signalMathContainerChanged(), CLyapWolfMethod::start(), CTimeSensLsodaMethod::start(), CHybridMethod::start(), CHybridMethodODE45::start(), CHybridNextReactionLSODAMethod::start(), CLsodaMethod::start(), CLsodaMethod2::start(), CRadau5Method::start(), CStochasticRungeKuttaRI5::start(), CStochDirectMethod::start(), CStochMethod::start(), CTauLeapMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethod::start(), CTrajectoryMethodDsaLsodar::start(), CCSPMethod::start(), CTSSAMethod::start(), CTimeSensLsodaMethod::stateChange(), CLsodaMethod::stateChange(), CLsodaMethod2::stateChange(), CRadau5Method::stateChange(), CStochDirectMethod::stateChange(), CLsodaMethod2::step(), CCSPMethod::step(), CILDMMethod::step(), CILDMModifiedMethod::step(), CTimeSensLsodaMethod::step(), CHybridMethod::step(), CLsodaMethod::step(), CRadau5Method::step(), CTauLeapMethod::step(), CNewtonMethod::targetFunction(), CNewtonMethod::targetFunctionDistance(), CNewtonMethod::targetFunctionRate(), and CHybridMethod::updatePriorityQueue().

mProcessReport

CProcessReportLevel CCopasiMethod::mProcessReport

protected

a pointer to the callback

Referenced by CBitPatternMethod::calculate(), CBitPatternTreeMethod::calculate(), CEFMAlgorithm::calculate(), CSSAMethod::calculate(), CLyapWolfMethod::calculate(), CEFMAlgorithm::calculateFluxModes(), CEFMAlgorithm::calculateNextTableau(), CBitPatternTreeMethod::combine(), CBitPatternMethod::combine(), CSensMethod::do_target_calculation(), CNewtonMethod::doIntegration(), getCallBack(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CEFMAlgorithm::initialize(), CSSAMethod::initialize(), COptMethodCoranaWalk::initialize(), COptMethodDE::initialize(), COptMethodGA::initialize(), COptMethodHookeJeeves::initialize(), COptMethodLevenbergMarquardt::initialize(), COptMethodNelderMead::initialize(), COptMethodPS::initialize(), COptMethodSA::initialize(), COptMethodSS::initialize(), COptPopulationMethod::initialize(), operator=(), COptMethodCoranaWalk::optimise(), COptMethodDE::optimise(), COptMethodEP::optimise(), COptMethodGA::optimise(), COptMethodGASR::optimise(), COptMethodHookeJeeves::optimise(), COptMethodLevenbergMarquardt::optimise(), COptMethodNelderMead::optimise(), COptMethodPS::optimise(), COptMethodSA::optimise(), COptMethodSRES::optimise(), COptMethodSS::optimise(), CMoietiesMethod::process(), CSensMethod::process(), CSteadyStateMethod::process(), CNewtonMethod::processInternal(), CNewtonMethod::processNewton(), setCallBack(), and CSensMethod::setCallBack().

mSubType

CTaskEnum::Method CCopasiMethod::mSubType

private

The type of the method

Referenced by getSubType(), and operator=().

mTaskType

CTaskEnum::Task CCopasiMethod::mTaskType

private

The type of the method

Referenced by getType(), isValidProblem(), and operator=().

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

• CCopasiMethod.h
• CCopasiMethod.cpp