#include <CFunctionDB.h>

Inheritance diagram for CFunctionDB:

Public Member Functions
bool	add (CFunction *pFunction, const bool &adopt)

CFunction *	addAndAdaptName (CFunction *pFunction)

bool	appendDependentFunctions (const ObjectSet &candidates, DataObjectSet &dependentFunctions) const

	CFunctionDB (const std::string &name, const CDataContainer *pParent)

void	cleanup ()

CFunction *	findFunction (const std::string &functionName)

CFunction *	findLoadFunction (const std::string &functionName)

std::string	getFilename () const

std::vector< const CFunction * >	getUsedFunctions (const CModel *pModel) const

void	initObjects ()

bool	load ()

bool	load (const std::string &fileName)

C_INT32	load (CReadConfig &configbuffer)

CDataVectorN< CFunction > &	loadedFunctions ()

void	purgeUnusedUserDefinedFunctions ()

bool	removeFunction (const std::string &key)

bool	removeFunction (size_t index)

bool	save (const std::string &fileName)

void	setFilename (const std::string &filename)

std::vector< CFunction * >	suitableFunctions (const size_t noSubstrates, const size_t noProducts, const TriLogic reversibility)

virtual	~CFunctionDB ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

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

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

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual size_t	getIndex (const CDataObject *pObject) const

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

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

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

virtual bool	remove (CDataObject *pObject)

virtual CData	toData () const override

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 CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

virtual const std::string &	getKey () const

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

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

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

virtual void *	getValuePointer () 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

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

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CDataContainer *pParent)

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

virtual	~CUndoObjectInterface ()

Private Attributes
CMathDependencyGraph	mDependencies

std::string	mFilename

CDataVectorN< CFunction >	mLoadedFunctions

Additional Inherited Members
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 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 CDataContainer
static const CObjectInterface::ContainerList	EmptyList

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 inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Constructor & Destructor Documentation

◆ CFunctionDB()

CFunctionDB::CFunctionDB	(	const std::string &	name,
		const CDataContainer *	pParent
	)

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CDataContainer * pParent (default: NULL)

CFunctionDB

Created for Copasi by Stefan Hoops (C) Stefan Hoops 2001

References CONSTRUCTOR_TRACE, and initObjects().

◆ ~CFunctionDB()

CFunctionDB::~CFunctionDB ( )

virtual

Destructor

References cleanup(), and DESTRUCTOR_TRACE.

Member Function Documentation

◆ add()

bool CFunctionDB::add	(	CFunction *	pFunction,
		const bool &	adopt
	)

Add the function to the database

Parameters

CFunction	* pFunction
const	bool & adopt (default = false)

Returns: bool success

References CDataVectorN< CType >::add(), and mLoadedFunctions.

Referenced by addAndAdaptName(), and SBMLImporter::createCFunctionFromFunctionDefinition().

◆ addAndAdaptName()

CFunction * CFunctionDB::addAndAdaptName ( CFunction * pFunction )

Add the function to the database, if necessary adapt the name so it is unique.

References add(), C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), CDataObject::getObjectName(), mLoadedFunctions, pdelete, and CDataObject::setObjectName().

Referenced by CModel::convert2NonReversible(), and CReaction::createFunctionFromExpression().

◆ appendDependentFunctions()

bool CFunctionDB::appendDependentFunctions	(	const ObjectSet &	candidates,
		CDataObject::DataObjectSet &	dependentFunctions
	)		const

Appends pointers to function, which are dependent on any of the candidates to the list dependentFunctions.

Parameters

const	ObjectSet & candidates
std::set<	const CDataObject * > & dependentFunctions

Returns: bool functionsAppended

References CMathDependencyGraph::appendAllDependents(), and mDependencies.

Referenced by CDataContainer::appendDeletedDependentData(), and removeFunction().

◆ cleanup()

void CFunctionDB::cleanup ( )

References CDataVector< CType >::cleanup(), CMathDependencyGraph::clear(), mDependencies, and mLoadedFunctions.

Referenced by ~CFunctionDB().

◆ findFunction()

CFunction * CFunctionDB::findFunction ( const std::string & functionName )

Delete the function functionName from the database

Parameters

const string &functionName

Returns: C_INT32 Fail Search for a function among the loaded functions. If no function is found NULL is returned

Parameters

const string &functionName

Returns: CFunction *

References C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), and mLoadedFunctions.

Referenced by CEvaluationNodeCall::calls(), CEvaluationNodeCall::compile(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createFunctionSetFromFunctionNames(), CODEExporter::exportSingleFunction(), CODEExporterC::exportSingleFunction(), SBMLImporter::findCorrespondingFunction(), SBMLImporter::findFunctionCalls(), CODEExporter::findFunctionsCalls(), CEvaluationNodeCall::getCalledTree(), SBMLImporter::isConstantFlux(), CODEExporter::modifyTreeForMassAction(), SBMLImporter::restoreFunctionDB(), CODEExporterC::setExportNameOfFunction(), CSBMLExporter::setFunctionSBMLIds(), suitableFunctions(), and CEvaluationNodeCall::toAST().

◆ findLoadFunction()

CFunction * CFunctionDB::findLoadFunction ( const std::string & functionName )

Search for a function among the loaded functions. If no function is found the database is searched and the apropriate function is loaded.

Parameters

const string &functionName

Returns: CFunction * function (NULL if function is not found)

References CDataVectorN< CType >::getIndex(), mLoadedFunctions, and CDataVector< CType >::size().

Referenced by CReaction::setFunction(), CReactionInterface::setFunctionAndDoMapping(), and CReactionInterface::setFunctionWithEmptyMapping().

◆ getFilename()

std::string CFunctionDB::getFilename ( ) const

References mFilename.

◆ getUsedFunctions()

std::vector< const CFunction * > CFunctionDB::getUsedFunctions ( const CModel * pModel ) const

Retrieves a list of all functions used in the model

Returns: std::vector< const CFunction * > usedFunctions

References CModel::appendAllDependents(), CDataVector< CType >::begin(), CFunction::completeFunctionList(), CDataVector< CType >::end(), and mLoadedFunctions.

Referenced by CCopasiXML::buildFunctionList(), and purgeUnusedUserDefinedFunctions().

◆ initObjects()

void CFunctionDB::initObjects ( )

References CDataContainer::addObjectReference(), CUnit::Avogadro, and mFilename.

Referenced by CFunctionDB().

◆ load() [1/3]

bool CFunctionDB::load ( )

References mLoadedFunctions, and CCopasiXML::setFunctionList().

Referenced by CRootContainer::initializeChildren().

◆ load() [2/3]

bool CFunctionDB::load ( const std::string & fileName )

References CCopasiXML::load(), mLoadedFunctions, and CCopasiXML::setFunctionList().

◆ load() [3/3]

C_INT32 CFunctionDB::load ( CReadConfig & configbuffer )

Loads an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

pconfigbuffer reference to a CReadConfig object.

Returns: mFail

References CDataVectorN< CType >::add(), C_INT32, CEvaluationTree::compile(), fatalError, CEvaluationTree::Function, CCopasiMessage::getLastMessage(), CEvaluationTree::getType(), CReadConfig::getVariable(), CFunction::load(), CReadConfig::LOOP, CEvaluationTree::MassAction, MCDataVector, mLoadedFunctions, NO_PARENT, pdelete, CCopasiMessage::peekLastMessage(), CEvaluationTree::PreDefined, and CEvaluationTree::UserDefined.

◆ loadedFunctions()

CDataVectorN< CFunction > & CFunctionDB::loadedFunctions ( )

Retrieves the vector of loaded functions.

Returns: "CDataVectorNS < CFunction > &" loadedFunctions

References mLoadedFunctions.

Referenced by CSBMLExporter::collectIds(), CFunction::completeFunctionList(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCReactionFromReaction(), COptProblem::elevateChildren(), CDataModel::removeSBMLIdFromFunctions(), and SBMLImporter::removeUnusedFunctions().

◆ purgeUnusedUserDefinedFunctions()

void CFunctionDB::purgeUnusedUserDefinedFunctions ( )

Purge all unused user defined functions from the data base

References CDataObject::DataModel, CRootContainer::getDatamodelList(), getUsedFunctions(), and mLoadedFunctions.

◆ removeFunction() [1/2]

bool CFunctionDB::removeFunction ( const std::string & key )

References C_INVALID_INDEX, CKeyFactory::get(), CRootContainer::getKeyFactory(), mLoadedFunctions, and removeFunction().

◆ removeFunction() [2/2]

bool CFunctionDB::removeFunction ( size_t index )

References appendDependentFunctions(), CDataVector< CType >::begin(), C_INVALID_INDEX, CDataVector< CType >::end(), CRootContainer::getDatamodelList(), CDataVector< CType >::insert(), and mLoadedFunctions.

Referenced by removeFunction(), and SBMLImporter::restoreFunctionDB().

◆ save()

bool CFunctionDB::save ( const std::string & fileName )

References CDirEntry::dirName(), mLoadedFunctions, and CCopasiXML::setFunctionList().

◆ setFilename()

void CFunctionDB::setFilename ( const std::string & filename )

References mFilename.

◆ suitableFunctions()

std::vector< CFunction * > CFunctionDB::suitableFunctions	(	const size_t	noSubstrates,
		const size_t	noProducts,
		const TriLogic	reversibility
	)

Retrieves the vector of functions that are suitable for a number of substrates, products and reversibility status. Note: The returns CDataVector has to be deleted after use!

Parameters

const size_t	noSubstrates the number of substrates
const size_t	noProducts the number of products
const TriLogic	reversible the reversibility status

Returns: "std::vector<CFunction*> " suitableFunctions

References fatalError, findFunction(), CFunction::isSuitable(), mLoadedFunctions, CDataVector< CType >::size(), and TriTrue.

Referenced by CReactionInterface::getListOfPossibleFunctions().

Member Data Documentation

◆ mDependencies

CMathDependencyGraph CFunctionDB::mDependencies

private

The function dependencies

Referenced by appendDependentFunctions(), and cleanup().

◆ mFilename

std::string CFunctionDB::mFilename

private

Filename which contains the function database

Referenced by getFilename(), initObjects(), and setFilename().

◆ mLoadedFunctions

CDataVectorN< CFunction > CFunctionDB::mLoadedFunctions

private

Vector of the currently loaded functions

Referenced by add(), addAndAdaptName(), cleanup(), findFunction(), findLoadFunction(), getUsedFunctions(), load(), loadedFunctions(), purgeUnusedUserDefinedFunctions(), removeFunction(), save(), and suitableFunctions().

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

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CFunctionDB()

◆ ~CFunctionDB()

Member Function Documentation

◆ add()

◆ addAndAdaptName()

◆ appendDependentFunctions()

◆ cleanup()

◆ findFunction()

◆ findLoadFunction()

◆ getFilename()

◆ getUsedFunctions()

◆ initObjects()

◆ load() [1/3]

◆ load() [2/3]

◆ load() [3/3]

◆ loadedFunctions()

◆ purgeUnusedUserDefinedFunctions()

◆ removeFunction() [1/2]

◆ removeFunction() [2/2]

◆ save()

◆ setFilename()

◆ suitableFunctions()

Member Data Documentation

◆ mDependencies

◆ mFilename

◆ mLoadedFunctions