CCopasiProblem Class Reference

#include <CCopasiProblem.h>

Inheritance diagram for CCopasiProblem:

Collaboration diagram for CCopasiProblem:

Public Member Functions
	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 ()
virtual bool	elevateChildren ()
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 Member Functions
	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)

Protected Attributes
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
	CCopasiProblem ()

Private Attributes
CCopasiTask::Type	mType

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

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 }
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 40 of file CCopasiProblem.h.

Constructor & Destructor Documentation

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 whithin COPASI.

Created for Copasi by Stefan Hoops 2003

Definition at line 34 of file CCopasiProblem.cpp.

                              :
    CCopasiParameterGroup("NoName", NULL, "Problem"),
    mType(CCopasiTask::unset),
    mpModel(NULL),
    mpCallBack(NULL),
    mpReport(NULL)
{}

CCopasiProblem::CCopasiProblem ( const CCopasiTask::Type &  type, const CCopasiContainer *  pParent = NULL  )

protected

Specific constructor

Parameters

const	CCopasiTask::Type & type
const	CCopasiContainer * pParent (default: NULL)

Definition at line 42 of file CCopasiProblem.cpp.

                                                                :
    CCopasiParameterGroup(CCopasiTask::TypeName[type], pParent, "Problem"),
    mType(type),
    mpModel(NULL),
    mpCallBack(NULL),
    mpReport(NULL)
{}

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

Copy constructor

Parameters

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

Definition at line 51 of file CCopasiProblem.cpp.

                                                                :
    CCopasiParameterGroup(src, pParent),
    mType(src.mType),
    mpModel(src.mpModel),
    mpCallBack(src.mpCallBack),
    mpReport(src.mpReport)
{}

CCopasiProblem::~CCopasiProblem ( )

virtual

Destructor

Definition at line 60 of file CCopasiProblem.cpp.

{}

Member Function Documentation

CModel * CCopasiProblem::getModel

(

)

const

Retrieve the model of the problem

Returns

CModel * pModel

Definition at line 70 of file CCopasiProblem.cpp.

References mpModel.

Referenced by CLyapWolfMethod::calculate(), COutputAssistant::createDefaultOutput(), CCrossSectionTask::createEvent(), CQTSSAResultSubWidget::displayResult(), CSensMethod::do_target_calculation(), CLyapWolfMethod::evalF(), CHybridMethodLSODA::evalF(), CCrossSectionTask::eventCallBack(), CCrossSectionTask::finish(), CEFMTask::getInternalSpecies(), CEFMTask::getNetReaction(), CEFMTask::getReactionEquation(), CQTSSAResultSubWidget::init(), CScanMethod::init(), CSSAMethod::initialize(), CLNATask::initialize(), CSensMethod::initialize(), CEFMAlgorithm::initialize(), CMCATask::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CNewtonMethod::initialize(), CSteadyStateTask::initialize(), CSteadyStateMethod::initialize(), CCrossSectionTask::initialize(), CCopasiTask::initialize(), CHybridMethodODE45::initMethod(), CHybridMethodLSODA::initMethod(), CHybridMethodLSODA::integrateDeterministicPart(), CTSSAMethod::integrationMethodStart(), CSteadyStateMethod::isEquilibrium(), CEFMMethod::isValidProblem(), CNewtonMethod::isValidProblem(), CLyapMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CCopasiMethod::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CLNAMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CStochMethod::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), operator<<(), CHybridMethodLSODA::partitionSystem(), CLNATask::printResult(), CMCATask::printResult(), CMoietiesMethod::process(), CSensTask::process(), CLNATask::process(), CScanTask::process(), CLyapTask::process(), CMCATask::process(), CTrajectoryTask::process(), CTSSATask::process(), CSteadyStateTask::process(), CCrossSectionTask::process(), CTrajectoryTask::processStart(), CTSSATask::processStart(), CCrossSectionTask::processStart(), CTrajectoryTask::processStep(), CTSSATask::processStep(), CCrossSectionTask::processStep(), CCrossSectionTask::removeEvent(), CMoietiesTask::restore(), CLyapTask::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), CCrossSectionTask::restore(), CCopasiTask::restore(), CSteadyStateTask::setInitialState(), CQEFMSpeciesDM::setTask(), CQSteadyStateResult::slotUpdateModel(), CTauLeapMethod::start(), CHybridMethod::start(), CHybridMethodLSODA::start(), CStochDirectMethod::start(), CHybridMethodODE45::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CLsodaMethod::start(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CSensTask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), CTSSATask::updateMatrices(), and CSteadyStateTask::updateMatrices().

{return mpModel;}

const CCopasiTask::Type & CCopasiProblem::getType

(

void

)

const

Retrieve the type of the problem

Returns

const string & type

Definition at line 62 of file CCopasiProblem.cpp.

References mType.

Referenced by COutputAssistant::getDefaultPlotIndex(), COutputAssistant::getDefaultReportIndex(), and COptProblem::setSubtaskType().

{return mType;}

bool CCopasiProblem::initialize ( )

virtual

Sets the initial value (in case this applies to the specific problem) Do all neccessary initialization so that calls to caluclate will be successful. This is called once from CCopasiTask::process()

Returns

bool succes

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

Definition at line 80 of file CCopasiProblem.cpp.

Referenced by CEFMProblem::initialize().

{return true;}

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

virtual

calculate function for optimization

Returns

bool fullfilled calculate function for optimization

bool fullfilled This is the output method for any object. The default implementation provided with CCopasiObject 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 COptProblem, CSensProblem, CCrossSectionProblem, CLNAProblem, CMCAProblem, CFitProblem, and COscillationProblem.

Definition at line 84 of file CCopasiProblem.cpp.

Referenced by operator<<(), and CTSSAProblem::printResult().

  {*ostream << *this;}

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

virtual

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

Parameters

std::ostream

* ostream

Reimplemented in COptProblem, CTSSAProblem, CSensProblem, CLyapProblem, CFitProblem, CEFMProblem, CLNAProblem, CMCAProblem, COscillationProblem, and CMoietiesProblem.

Definition at line 87 of file CCopasiProblem.cpp.

Referenced by operator<<(), and CQTSSAResultSubWidget::saveDataToFile().

  {*ostream << "Not implemented.";}

bool CCopasiProblem::restore ( const bool &  updateModel )

virtual

Do the calculatting based on CalculateVariables and fill CalculateResults with the results.

Returns

bool succes Do all neccessary restore procedures so that the model is in the same state as before const bool & updateModel

bool succes

Reimplemented in COptProblem, and CFitProblem.

Definition at line 82 of file CCopasiProblem.cpp.

Referenced by CCopasiTask::restore().

{return true;}

bool CCopasiProblem::setCallBack ( CProcessReport *  pCallBack )

virtual

Set the call back of the problem

Parameters

CProcessReport

* pCallBack

Returns

bool succes

Reimplemented in COptProblem, CEFMProblem, CFitProblem, and COscillationProblem.

Definition at line 72 of file CCopasiProblem.cpp.

References mpCallBack.

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

{
  mpCallBack = pCallBack;
  return true;
}

bool CCopasiProblem::setModel ( CModel *  pModel )

virtual

Set the model of the problem

Parameters

CModel

* pModel

Returns

bool succes

Reimplemented in COptProblem, CLNAProblem, CMCAProblem, CFitProblem, and COscillationProblem.

Definition at line 64 of file CCopasiProblem.cpp.

References mpModel.

Referenced by CCopasiDataModel::addTask(), CSensMethod::initialize(), CNewtonMethod::initialize(), CScanTask::initSubtask(), CCopasiXMLParser::TaskElement::start(), and test000087::test_simulate_reaction_flux_reference_1().

{
  mpModel = pModel;
  return true;
}

Friends And Related Function Documentation

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

friend

Output stream operator

Parameters

ostream	& os
const	CCopasiProblem & A

Returns

ostream & os

Definition at line 90 of file CCopasiProblem.cpp.

{
  os << "Problem Description:" << std::endl;

  CCopasiParameterGroup::parameterGroup::const_iterator it =
    o.CCopasiParameter::getValue().pGROUP->begin();
  CCopasiParameterGroup::parameterGroup::const_iterator end =
    o.CCopasiParameter::getValue().pGROUP->end();

  for (; it != end; ++it)
    {
      (*it)->print(&os);
      os << std::endl;
    }

  return os;
}

Member Data Documentation

CProcessReport* CCopasiProblem::mpCallBack

protected

a pointer to the callback

Definition at line 58 of file CCopasiProblem.h.

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

CModel* CCopasiProblem::mpModel

protected

The model of the problem

Definition at line 53 of file CCopasiProblem.h.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), getModel(), COscillationProblem::initialize(), CSteadyStateProblem::initialize(), CFitProblem::initialize(), COptProblem::initialize(), CSteadyStateProblem::load(), CTrajectoryProblem::load(), CMoietiesProblem::printResult(), CEFMProblem::printResult(), COptProblem::restoreModel(), COscillationProblem::setModel(), CLNAProblem::setModel(), CMCAProblem::setModel(), COptProblem::setModel(), setModel(), and CFitProblem::updateInitialState().

CReport* CCopasiProblem::mpReport

protected

A pointer to the report

Definition at line 63 of file CCopasiProblem.h.

Referenced by COptProblem::initialize().

CCopasiTask::Type CCopasiProblem::mType

private

The type of the problem

Definition at line 47 of file CCopasiProblem.h.

Referenced by getType().

---

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

• CCopasiProblem.h
• CCopasiProblem.cpp