CCopasiProblem Class Reference

#include <CCopasiProblem.h>

Inheritance diagram for CCopasiProblem:

Public Member Functions
	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 void	printResult (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
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
	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
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
	CCopasiProblem ()

Private Attributes
CTaskEnum::Task	mType

Friends
std::ostream &	operator<< (std::ostream &os, const CCopasiProblem &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

CCopasiProblem() [1/4]

CCopasiProblem::CCopasiProblem ( )

private

Default constructor

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

Created for COPASI by Stefan Hoops 2003

CCopasiProblem() [2/4]

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

protected

Specific constructor

Parameters

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

References CCopasiTask::getMathContainer(), and setMathContainer().

CCopasiProblem() [3/4]

CCopasiProblem::CCopasiProblem ( const CCopasiProblem &  src )

protected

CCopasiProblem() [4/4]

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

Copy constructor

Parameters

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

References CCopasiTask::getMathContainer(), CDataObject::getObjectParent(), and setMathContainer().

~CCopasiProblem()

CCopasiProblem::~CCopasiProblem ( )

virtual

Destructor

Member Function Documentation

clearCallBack()

void CCopasiProblem::clearCallBack ( )

virtual

resets the currently set callback by calling setCallBack(NULL)

References setCallBack().

copy()

CCopasiProblem * CCopasiProblem::copy

(

)

const

copy

References CProblemFactory::copy().

getCallBack()

const CProcessReportLevel & CCopasiProblem::getCallBack

(

)

const

Returns

the currently set callback

References mProcessReport.

getMathContainer()

CMathContainer * CCopasiProblem::getMathContainer

(

)

const

Retrieve the model of the problem

Returns

CMathContainer * pContainer

References mpContainer.

Referenced by ResultData::applyToModelStateFromOptTask().

getSubTask()

CCopasiTask * CCopasiProblem::getSubTask ( ) const

virtual

Retrieve the optional sub task

Returns

CCopasiTask* * pSubTask

Reimplemented in CMCAProblem, CSensProblem, CScanProblem, COptProblem, and CLNAProblem.

Referenced by CCopasiTask::isTaskValid(), CLNATask::process(), CMCATask::process(), CLNATask::setCallBack(), and CMCATask::setCallBack().

getType()

const CTaskEnum::Task & CCopasiProblem::getType

(

void

)

const

Retrieve the type of the problem

Returns

const string & type

References mType.

Referenced by CProblemFactory::copy(), COutputAssistant::getDefaultPlotIndex(), and COutputAssistant::getDefaultReportIndex().

initialize()

bool CCopasiProblem::initialize ( )

virtual

Do all necessary initialization so that calls to calculate will be successful. This is called once from CCopasiTask::process()

Returns

bool success

Reimplemented in CFitProblem, COptProblem, CEFMProblem, CSteadyStateProblem, and COscillationProblem.

Referenced by CEFMProblem::initialize().

print()

void CCopasiProblem::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 override this default behavior one needs to re-implement the virtual print function.

Parameters

std::ostream

* ostream

Reimplemented from CCopasiParameterGroup.

Reimplemented in CMCAProblem, CSensProblem, CFitProblem, COptProblem, CLNAProblem, COscillationProblem, CCrossSectionProblem, and CAnalyticsProblem.

Referenced by CTSSAProblem::printResult().

printResult()

void CCopasiProblem::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 in CMoietiesProblem, CMCAProblem, CSensProblem, CFitProblem, COptProblem, CLNAProblem, CEFMProblem, CTSSAProblem, CTrajectoryProblem, COscillationProblem, and CLyapProblem.

restore()

bool CCopasiProblem::restore ( const bool &  updateModel )

virtual

Do all necessary restore procedures so that the model is in the same state as before

Parameters

const

bool & updateModel

Returns

bool success

Reimplemented in CScanProblem, CFitProblem, and COptProblem.

Referenced by CCopasiTask::restore().

setCallBack()

bool CCopasiProblem::setCallBack ( CProcessReportLevel  callBack )

virtual

Set the call back of the problem

Parameters

CProcessReport

* pCallBack

Returns

bool success

Reimplemented in CFitProblem, COscillationProblem, COptProblem, and CEFMProblem.

References mProcessReport.

Referenced by clearCallBack(), CEFMTask::setCallBack(), CEFMProblem::setCallBack(), CMoietiesTask::setCallBack(), COptProblem::setCallBack(), COptTask::setCallBack(), COscillationProblem::setCallBack(), COscillationTask::setCallBack(), and CFitTask::setCallBack().

setMathContainer()

void CCopasiProblem::setMathContainer

(

CMathContainer *

pContainer

)

Set the model of the problem

Parameters

CMathContainer

* pContainer

Returns

bool success

References mpContainer, and signalMathContainerChanged().

Referenced by CCopasiProblem(), CProblemFactory::copy(), CProblemFactory::create(), CCopasiTask::setMathContainer(), and setModel().

setModel()

bool CCopasiProblem::setModel ( CModel *  model )

virtual

convenience method that sets the models math continer as the mathcontainer for this problem

Parameters

model

the model whose mathcontainer to set

Returns

bool success

References CModel::getMathContainer(), and setMathContainer().

signalMathContainerChanged()

void CCopasiProblem::signalMathContainerChanged ( )

protectedvirtual

Signal that the math container has changed

Referenced by setMathContainer().

Friends And Related Function Documentation

operator<<

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

friend

Output stream operator

Parameters

ostream	& os
const	CCopasiProblem & A

Returns

ostream & os

Member Data Documentation

mpContainer

CMathContainer* CCopasiProblem::mpContainer

protected

The model of the problem

Referenced by COptProblem::adjustStartValue(), COptProblem::adjustStartValuesForIntervals(), COptProblem::calculate(), CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COptProblem::calculateStatistics(), COptProblem::checkFunctionalConstraints(), COptProblem::checkIntervals(), CFitProblem::createParameterSet(), CFitProblem::createParameterSets(), COptProblem::evalMinimizeIntervals(), getMathContainer(), COscillationProblem::initialize(), CSteadyStateProblem::initialize(), COptProblem::initialize(), CFitProblem::initialize(), COptProblem::initializeSubtaskBeforeOutput(), CEFMProblem::printResult(), CMoietiesProblem::printResult(), COptProblem::randomizeStartValues(), COptProblem::restore(), CFitProblem::restore(), setMathContainer(), and CFitProblem::updateInitialState().

mpReport

CReport* CCopasiProblem::mpReport

protected

A pointer to the report

Referenced by COptProblem::initialize().

mProcessReport

CProcessReportLevel CCopasiProblem::mProcessReport

protected

a pointer to the callback

Referenced by COptProblem::calculate(), CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), getCallBack(), COptProblem::incrementCounters(), COscillationProblem::initialize(), CFitProblem::initialize(), COptProblem::initializeSubtaskBeforeOutput(), setCallBack(), COptProblem::setCallBack(), CFitProblem::setCallBack(), and COptProblem::setSolution().

mType

CTaskEnum::Task CCopasiProblem::mType

private

The type of the problem

Referenced by getType().

---

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

• CCopasiProblem.h
• CCopasiProblem.cpp