#include <CSBMLExporter.h>

Public Member Functions
virtual void	clearCallBack ()

bool	createProgressStepOrStop (unsigned C_INT32 globalStep, unsigned C_INT32 currentTotal, const std::string &title)

	CSBMLExporter ()

void	disownSBMLDocument ()

bool	exportLayout (unsigned int sbmlLevel, CDataModel &dataModel)

bool	exportModel (CDataModel &dataModel, const std::string &filename, unsigned int sbmlLevel=2, unsigned int sbmlVersion=1, bool overwrite=false)

const std::string	exportModelToString (CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion)

void	finishCurrentStep ()

void	finishExport ()

const CProcessReport *	getCallBack () const

const std::map< const CDataObject , SBase > &	getCOPASI2SBMLMap () const

SBMLDocument *	getSBMLDocument ()

bool	isSetExportCOPASIMIRIAM () const

bool	reportCurrentProgressOrStop ()

void	setExportCOPASIMIRIAM (bool exportMIRIAM)

void	setHandler (CProcessReport *pProcessReport)

	~CSBMLExporter ()

Static Public Member Functions
static XMLNode *	createSBMLNotes (const std::string &notes_string)

static const std::string	createUniqueId (const std::map< std::string, const SBase * > &idMap, const std::string &prefix, bool addIndexForFirst, const std::string &separator="_")

static const std::vector< SBMLIncompatibility >	isModelSBMLCompatible (const CDataModel &pDataModel, int sbmlLevel, int sbmlVersion, std::map< std::string, const SBase * > &idMap)

Protected Member Functions
void	addInitialAssignmentsToModel (const CDataModel &dataModel)

void	assignSBMLIdsToReactions (CModel *pModel)

void	checkForUnsupportedFunctionCalls (const CDataModel &dataModel, unsigned int sbmlLEvel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)

void	checkForUnsupportedObjectReferences (const CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)

void	collectIds (const CDataModel &dataModel, std::map< std::string, const SBase * > &idMap)

ASTNode *	convertToASTNode (const CEvaluationNode *pOrig, CDataModel &dataModel)

void	convertToLevel1 ()

void	createAreaUnit (const CDataModel &dataModel)

void	createAvogadroIfNeeded (const CDataModel &dataModel)

void	createCompartment (const CCompartment &compartment)

bool	createCompartments (CDataModel &dataModel)

void	createEvent (const CEvent &event, Event *pSBMLEvent, CDataModel &dataModel)

bool	createEvents (CDataModel &dataModel)

void	createFunctionDefinition (CFunction &function, CDataModel &dataModel)

bool	createFunctionDefinitions (CDataModel &dataModel)

const std::map< std::string, const SBase * >	createIdMap (const Model &sbmlModel)

void	createInitialAssignment (const CModelEntity &modelEntity, CDataModel &dataModel)

bool	createInitialAssignments (CDataModel &dataModel)

CEvaluationNode *	createKineticExpression (CFunction pFun, const std::vector< std::vector< const CDataObject > > &arguments)

KineticLaw *	createKineticLaw (const CReaction &reaction, CDataModel &dataModel, unsigned int level, unsigned int version)

void	createLengthUnit (const CDataModel &dataModel)

void	createMetabolite (const CMetab &metab)

bool	createMetabolites (CDataModel &dataModel)

void	createParameter (const CModelValue &parameter)

bool	createParameters (CDataModel &dataModel)

void	createReaction (const CReaction &reaction, CDataModel &dataModel)

bool	createReactions (CDataModel &dataModel)

void	createRule (const CModelEntity &modelEntity, CDataModel &dataModel, Rule *pOldRule)

bool	createRules (CDataModel &dataModel)

bool	createSBMLDocument (CDataModel &dataModel)

void	createSubstanceUnit (const CDataModel &dataModel)

void	createTimeUnit (const CDataModel &dataModel)

UnitDefinition *	createUnitDefinitionFor (const CUnit &unit)
	creates and SBML UnitDefinition for the given unit More...

void	createUnits (const CDataModel &dataModel)

void	createVolumeUnit (const CDataModel &dataModel)

void	exportAndAssignUnit (const CUnit &unit, SBase *sbmlElement)
	exports the given unit to the sbmlElement More...

void	exportEventAssignments (const CEvent &event, Event *pSBMLEvent, CDataModel &dataModel)

void	findAvogadro (const CDataModel &dataModel)

bool	hasVolumeAssignment (const CDataModel &dataModel)

std::vector< const CModelEntity * >	orderRules (const CDataModel &dataModel)

void	outputIncompatibilities () const

void	removeInitialAssignment (const std::string &sbmlId)

void	removeRule (const std::string &sbmlId)

void	removeUnusedObjects ()

void	replace_local_parameters (ASTNode *pOrigNode, const CDataModel &dataModel)

XMLNode *	replaceChild (const XMLNode pParent, const XMLNode pNewChild, unsigned int index)

CEvaluationNode *	replaceSpeciesReferences (const CEvaluationNode *pOrigNode, const CDataModel &dataModel)

void	restore_local_parameters (ASTNode *pOrigNode, const CDataModel &dataModel)

void	setFunctionSBMLIds (const CEvaluationNode *pNode, CDataModel &dataModel)

void	updateCOPASI2SBMLMap (const CDataModel &dataModel)

bool	updateMIRIAMAnnotation (const CDataObject pCOPASIObject, SBase pSBMLObject, std::map< std::string, const SBase * > &metaIds)

Static Protected Member Functions
static bool	checkForEvents (const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	checkForInitialAssignments (const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	checkForODESpeciesInNonfixedCompartment (const CDataModel &dataModel, std::vector< SBMLIncompatibility > result)

static void	checkForPiecewiseFunctions (const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	checkForPiecewiseFunctions (const CEvaluationNode &node, std::vector< SBMLIncompatibility > &result, const std::string &objectName, const std::string &objectType)

static void	checkForUnsupportedFunctionCalls (const CEvaluationNode &node, const std::set< CEvaluationNode::SubType > &unsupportedFunctions, std::vector< SBMLIncompatibility > &result, const std::string &objectDescription)

static void	checkForUnsupportedObjectReferences (const CEvaluationTree &expression, const CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result, std::map< std::string, const SBase * > &idMap, bool initialExpression=false, std::map< const std::string, Parameter * > *initialMap=NULL)

static void	convert_to_l1v1 (std::string &l1v2_string)

static ASTNode *	convertASTTreeToLevel1 (const ASTNode *pNode, const ListOfFunctionDefinitions &functions, std::string &message)

static const std::set< CFunction * >	createFunctionSetFromFunctionNames (const std::set< std::string > &names, CFunctionDB *pFunDB)

static CEvaluationNode *	createMassActionExpression (const std::vector< std::vector< const CDataObject * > > &arguments, bool isReversible)

static ASTNode *	createTimesTree (const CDataVector< CChemEqElement > &vect, unsigned int pos=0)

static const std::set< CEvaluationNode::SubType >	createUnsupportedFunctionTypeSet (unsigned int sbmlLevel)

static void	findDirectlyUsedFunctions (const CEvaluationNode *pRootNode, std::set< std::string > &result)

static void	findModelEntityDependencies (const CEvaluationNode pNode, const CDataModel &dataModel, std::set< const CModelEntity > &dependencies)

static const std::vector< CFunction * >	findUsedFunctions (std::set< CFunction * > &functions, CFunctionDB *pFunctionDB)

static ASTNode *	isDividedByVolume (const ASTNode *pRootNode, const std::string &compartmentId)

static void	isEventAssignmentSBMLCompatible (const CDataObject pTarget, const CExpression pExpression, const CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, const std::string &eventName, std::vector< SBMLIncompatibility > &result, std::map< std::string, const SBase * > &idMap)

static void	isEventSBMLCompatible (const CEvent pEvent, const CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result, std::map< std::string, const SBase > &idMap)

static void	isExpressionSBMLCompatible (const CEvaluationTree &expr, const CDataModel &dataModel, int sbmlLevel, int sbmlVersion, std::vector< SBMLIncompatibility > &result, std::map< std::string, const SBase * > &idMap, const std::string &objectDescription, bool initialExression=false, std::map< const std::string, Parameter * > *initialMap=NULL)

static void	isExpressionSBMLL1Compatible (const CEvaluationTree &expr, const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	isExpressionSBMLL2V1Compatible (const CEvaluationTree &expr, const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	isExpressionSBMLL2V3Compatible (const CEvaluationTree &expression, const CDataModel &pDataModel, std::vector< SBMLIncompatibility > &result)

static void	isModelSBMLL1Compatible (const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	isModelSBMLL2V1Compatible (const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static void	isModelSBMLL2V3Compatible (const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)

static bool	isValidSId (const std::string &id)

static CEvaluationNode *	multiplyByObject (const CEvaluationNode pOrigNode, const CDataObject pObject)

static ASTNode *	replaceL1IncompatibleNodes (const ASTNode *pNode)

static bool	setSBMLNotes (SBase pSBase, const CAnnotation pAnno)

Protected Attributes
std::vector< const CModelEntity * >	mAssignmentVector

bool	mAvogadroCreated

std::string	mAvogadroId

std::map< const CDataObject , SBase >	mCOPASI2SBMLMap

unsigned C_INT32	mCurrentStepCounter

size_t	mCurrentStepHandle

unsigned C_INT32	mCurrentStepTotal

bool	mDocumentDisowned

bool	mExportCOPASIMIRIAM

ListOfFunctionDefinitions	mExportedFunctions

std::map< std::string, const CEvaluationTree * >	mFunctionIdMap

std::map< const FunctionDefinition , const CDataObject >	mFunctionMap

unsigned C_INT32	mGlobalStepCounter

size_t	mGlobalStepHandle

unsigned C_INT32	mGlobalStepTotal

std::set< SBase * >	mHandledSBMLObjects

std::map< std::string, const SBase * >	mIdMap

std::vector< SBMLIncompatibility >	mIncompatibilities

bool	mIncompleteExport

std::vector< const CModelEntity * >	mInitialAssignmentVector

std::map< const std::string, Parameter * >	mInitialValueMap

std::map< std::string, const SBase * >	mMetaIdMap

bool	mMIRIAMWarning

std::vector< const CModelEntity * >	mODEVector

std::map< std::string, Parameter * >	mParameterReplacementMap

const CModelValue *	mpAvogadro

CProcessReport *	mpProcessReport

SBMLDocument *	mpSBMLDocument

unsigned int	mSBMLLevel

unsigned int	mSBMLVersion

std::set< std::string >	mSpatialSizeUnitsSpecies

std::set< CFunction * >	mUsedFunctions

bool	mVariableVolumes

Constructor & Destructor Documentation

◆ CSBMLExporter()

CSBMLExporter::CSBMLExporter ( )

Default constructor

◆ ~CSBMLExporter()

CSBMLExporter::~CSBMLExporter ( )

Destructor

References mDocumentDisowned, mpSBMLDocument, and pdelete.

Member Function Documentation

◆ addInitialAssignmentsToModel()

void CSBMLExporter::addInitialAssignmentsToModel ( const CDataModel & dataModel )

protected

References createAvogadroIfNeeded(), CMetab::getCompartment(), CDataContainer::getObject(), CDataObject::getObjectParent(), mAvogadroId, mInitialValueMap, and mpSBMLDocument.

Referenced by createSBMLDocument().

◆ assignSBMLIdsToReactions()

void CSBMLExporter::assignSBMLIdsToReactions ( CModel * pModel )

protected

Since we want to replace local reaction parameters by global parameters if they are used in an assignment, we have to create the reactions after creating the rules and events. On the other hand, a reaction flux might also be referenced in an assignment or an event and the creation of this rule or event only works if the reactions already have SBML ids. To solve this problem, the reactions have to be assigned SBML ids prior to creating rules and events.

References CDataVector< CType >::begin(), createUniqueId(), CDataVector< CType >::empty(), CDataVector< CType >::end(), CDataObject::getObjectName(), CModel::getReactions(), and mIdMap.

Referenced by createSBMLDocument().

◆ checkForEvents()

bool CSBMLExporter::checkForEvents	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks if the given datamodel contains events. This is called if SBML Level 1 is to be exported.

Returns: false if an event was used in the model, true otherwise

References CDataVector< CType >::empty(), CModel::getEvents(), and CDataModel::getModel().

Referenced by createEvents(), and isModelSBMLL1Compatible().

◆ checkForInitialAssignments()

void CSBMLExporter::checkForInitialAssignments	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

This method checks whether the given model contains any initial assignments.

References CDataVector< CType >::begin(), CDataVector< CType >::empty(), CDataVector< CType >::end(), CModel::getCompartments(), CModel::getMetabolites(), CDataModel::getModel(), CModel::getModelValues(), and CDataObject::getObjectName().

Referenced by createSBMLDocument(), isModelSBMLL1Compatible(), and isModelSBMLL2V1Compatible().

◆ checkForODESpeciesInNonfixedCompartment()

void CSBMLExporter::checkForODESpeciesInNonfixedCompartment	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility >	result
	)

staticprotected

Checks whether the model contains a metabolite that is defined by an ODE expression and that is located in a variable volume. Since COPASI interprets the expression differently from SBML, we can not correctly export this yet. See Bug 903.

References CDataVector< CType >::begin(), CDataVector< CType >::end(), CModelEntity::FIXED, CModel::getMetabolites(), CDataModel::getModel(), CDataObject::getObjectName(), CModelEntity::getStatus(), and CModelEntity::ODE.

Referenced by isModelSBMLCompatible().

◆ checkForPiecewiseFunctions() [1/2]

void CSBMLExporter::checkForPiecewiseFunctions	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks all expressions in the given datamodel for piecewise defined functions.

References CModelEntity::ASSIGNMENT, createFunctionSetFromFunctionNames(), findDirectlyUsedFunctions(), findUsedFunctions(), CModel::getCompartments(), CModelEntity::getExpressionPtr(), CReaction::getFunction(), CRootContainer::getFunctionList(), CModel::getMetabolites(), CDataModel::getModel(), CModel::getModelValues(), CDataObject::getObjectName(), CModel::getReactions(), CEvaluationTree::getRoot(), CModelEntity::getStatus(), CModelEntity::ODE, and CDataVector< CType >::size().

Referenced by checkForPiecewiseFunctions(), and isModelSBMLL1Compatible().

◆ checkForPiecewiseFunctions() [2/2]

void CSBMLExporter::checkForPiecewiseFunctions	(	const CEvaluationNode &	node,
		std::vector< SBMLIncompatibility > &	result,
		const std::string &	objectName,
		const std::string &	objectType
	)

staticprotected

Checks the given node and all it's children for the occurrence of piecewise functions.

References checkForPiecewiseFunctions(), CEvaluationNode::CHOICE, CCopasiNode< _Data >::getChild(), CCopasiNode< _Data >::getSibling(), and CEvaluationNode::mainType().

◆ checkForUnsupportedFunctionCalls() [1/2]

void CSBMLExporter::checkForUnsupportedFunctionCalls	(	const CDataModel &	dataModel,
		unsigned int	sbmlLevel,
		unsigned int	sbmlVersion,
		std::vector< SBMLIncompatibility > &	result
	)

protected

This methods checks, whether the model uses any function calls that can not be expressed in SBML like the random distribution functions.

This static methods checks, whether the model uses any function calls that can not be expressed in SBML like the random distribution functions.

References createUnsupportedFunctionTypeSet(), CModelEntity::getExpressionPtr(), CModelEntity::getInitialExpressionPtr(), CDataObject::getObjectName(), CDataObject::getObjectType(), CEvaluationTree::getRoot(), mAssignmentVector, mInitialAssignmentVector, mODEVector, and mUsedFunctions.

Referenced by checkForUnsupportedFunctionCalls(), and isExpressionSBMLCompatible().

◆ checkForUnsupportedFunctionCalls() [2/2]

void CSBMLExporter::checkForUnsupportedFunctionCalls	(	const CEvaluationNode &	node,
		const std::set< CEvaluationNode::SubType > &	unsupportedFunctions,
		std::vector< SBMLIncompatibility > &	result,
		const std::string &	objectDescription
	)

staticprotected

This static methods checks recursively, whether the given CEvaluationNode contains any function calls that can not be expressed in SBML like the random distribution functions.

This static methods checks recursively, whether the given CEvaluationNode constains any function calls that can not be expressed in SBML like the random distribution functions.

References checkForUnsupportedFunctionCalls(), CEvaluationNode::FUNCTION, CCopasiNode< _Data >::getChild(), CCopasiNode< _Data >::getData(), CCopasiNode< _Data >::getSibling(), CEvaluationNode::mainType(), and CEvaluationNode::subType().

◆ checkForUnsupportedObjectReferences() [1/2]

void CSBMLExporter::checkForUnsupportedObjectReferences	(	const CDataModel &	dataModel,
		unsigned int	sbmlLevel,
		unsigned int	sbmlVersion,
		std::vector< SBMLIncompatibility > &	result
	)

protected

Checks all assignments (initial and transient) for references to objects that can not be exported to SBML.

References CModelEntity::getExpressionPtr(), CModelEntity::getInitialExpressionPtr(), CDataModel::getModel(), mAssignmentVector, mIdMap, mInitialAssignmentVector, mInitialValueMap, and mODEVector.

Referenced by isExpressionSBMLCompatible().

◆ checkForUnsupportedObjectReferences() [2/2]

void CSBMLExporter::checkForUnsupportedObjectReferences	(	const CEvaluationTree &	expression,
		const CDataModel &	dataModel,
		unsigned int	sbmlLevel,
		unsigned int	sbmlVersion,
		std::vector< SBMLIncompatibility > &	result,
		std::map< std::string, const SBase * > &	idMap,
		bool	initialExpression = `false`,
		std::map< const std::string, Parameter * > *	initialMap = `NULL`
	)

staticprotected

Checks the given expression for references to objects that can not be exported to SBML.

References addParticleNumberToInitialValueMap(), addToInitialValueMap(), createUniqueId(), CObjectInterface::DataObject(), CDataObject::getCN(), CDataModel::getModel(), CEvaluationTree::getNodeList(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectFromCN(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::getObjectType(), CDataObject::getValuePointer(), CDataObject::hasFlag(), CEvaluationNode::mainType(), CEvaluationNode::OBJECT, CDataObject::Reference, and CCopasiMessage::WARNING.

◆ clearCallBack()

void CSBMLExporter::clearCallBack ( )

virtual

resets the currently set callback by calling setHandler(NULL)

References setHandler().

◆ collectIds()

void CSBMLExporter::collectIds	(	const CDataModel &	dataModel,
		std::map< std::string, const SBase * > &	idMap
	)

protected

This method goes through the given datamodel and collects all SBML ids.

References CModel::getCompartments(), CModel::getEvents(), CRootContainer::getFunctionList(), CModel::getMetabolites(), CDataModel::getModel(), CModel::getModelValues(), CModel::getReactions(), CFunction::getSBMLId(), CEvent::getSBMLId(), CModelEntity::getSBMLId(), CReaction::getSBMLId(), CFunctionDB::loadedFunctions(), and CDataVector< CType >::size().

Referenced by createSBMLDocument().

◆ convert_to_l1v1()

void CSBMLExporter::convert_to_l1v1 ( std::string & l1v2_string )

staticprotected

Converts the SBML model given in SBML Level 1 Version 2 format to SBML Level 1 Version 1. The method basically removes the namespace attribute on the sbml element and changes the version from 2 to 1. It also renames all "species" elements to "specie". All other changes between SBML Level 1 Version 2 and Level 1 Version 1 should not be relevant here.

References CCopasiMessage::EXCEPTION.

◆ convertASTTreeToLevel1()

ASTNode * CSBMLExporter::convertASTTreeToLevel1	(	const ASTNode *	pNode,
		const ListOfFunctionDefinitions &	functions,
		std::string &	message
	)

staticprotected

Creates an ASTNode based tree where all occurrences of nodes that are not supported in SBML Level 1 are replaced by supported constructs. On error an exception is created. The caller is responsible for freeing the memory of the returned object.

References CCopasiMessage::EXCEPTION, MCSBML, and replaceL1IncompatibleNodes().

Referenced by convertToLevel1().

◆ convertToASTNode()

ASTNode * CSBMLExporter::convertToASTNode	(	const CEvaluationNode *	pOrig,
		CDataModel &	dataModel
	)

protected

This converts an CEvaluationNode based tree to an ASTNode tree. It makes sure that all functions used in function calls already have a unique SBML id.

References adjustNames(), mIdMap, mpSBMLDocument, setFunctionSBMLIds(), and CEvaluationNode::toAST().

Referenced by createEvent(), createFunctionDefinition(), createInitialAssignment(), createKineticLaw(), createRule(), and exportEventAssignments().

◆ convertToLevel1()

void CSBMLExporter::convertToLevel1 ( )

protected

This method takes care of expanding all function calls in all expressions and converting functions that are not supported in Level 1 as well as constants that were not supported in Level 1

References convertASTTreeToLevel1(), fatalError, mExportedFunctions, and mpSBMLDocument.

Referenced by createSBMLDocument().

◆ createAreaUnit()

void CSBMLExporter::createAreaUnit ( const CDataModel & dataModel )

protected

Creates the volume unit for the SBML model.

Creates the area unit for the SBML model.

References createUnitDefinitionFor(), CModel::getAreaUnit(), CDataModel::getModel(), CModelEntity::getModel(), mpSBMLDocument, and pdelete.

Referenced by createUnits().

◆ createAvogadroIfNeeded()

void CSBMLExporter::createAvogadroIfNeeded ( const CDataModel & dataModel )

protected

References createUniqueId(), CDataModel::getModel(), CDataObject::getObjectName(), CModel::getQuantity2NumberFactor(), mAvogadroCreated, mAvogadroId, mCOPASI2SBMLMap, mHandledSBMLObjects, mIdMap, mpAvogadro, and mpSBMLDocument.

Referenced by addInitialAssignmentsToModel(), and replaceSpeciesReferences().

◆ createCompartment()

void CSBMLExporter::createCompartment ( const CCompartment & compartment )

protected

Creates the compartment for the given COPASI compartment.

References CModelEntity::ASSIGNMENT, createUniqueId(), CCompartment::getDimensionality(), CModelEntity::getInitialExpression(), CModelEntity::getInitialValue(), CDataObject::getObjectName(), CModelEntity::getSBMLId(), CModelEntity::getStatus(), INIT_DEFAULTS, mAssignmentVector, mCOPASI2SBMLMap, mHandledSBMLObjects, mIdMap, mInitialAssignmentVector, mMetaIdMap, mODEVector, mpSBMLDocument, mSBMLLevel, CModelEntity::ODE, removeInitialAssignment(), removeRule(), CModelEntity::setSBMLId(), setSBMLNotes(), and updateMIRIAMAnnotation().

Referenced by createCompartments().

◆ createCompartments()

bool CSBMLExporter::createCompartments ( CDataModel & dataModel )

protected

Creates the compartments for the model.

References CDataVector< CType >::begin(), createCompartment(), CDataVector< CType >::end(), CModel::getCompartments(), CDataModel::getModel(), CModelEntity::getModel(), mCurrentStepCounter, and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createEvent()

void CSBMLExporter::createEvent	(	const CEvent &	event,
		Event *	pSBMLEvent,
		CDataModel &	dataModel
	)

protected

Creates an SBML Event for the given COPASI event.

References convertExpression(), convertToASTNode(), createFunctionSetFromFunctionNames(), createUniqueId(), CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, exportEventAssignments(), findDirectlyUsedFunctions(), CEvent::getDelayAssignment(), CEvent::getFireAtInitialTime(), CRootContainer::getFunctionList(), CEvaluationTree::getInfix(), CDataObject::getObjectName(), CEvent::getPersistentTrigger(), CEvaluationTree::getRoot(), CEvent::getSBMLId(), CEvaluationNode::INVALID, isExpressionSBMLCompatible(), CEvaluationNode::mainType(), mCOPASI2SBMLMap, MCSBML, mIdMap, mIncompatibilities, mIncompleteExport, mInitialValueMap, mMetaIdMap, mpSBMLDocument, mSBMLLevel, mSBMLVersion, mUsedFunctions, outputIncompatibilities(), replace_local_parameters(), replaceSpeciesReferences(), CEvaluationTree::setInfix(), setSBMLNotes(), updateMIRIAMAnnotation(), and CCopasiMessage::WARNING.

Referenced by createEvents().

◆ createEvents()

bool CSBMLExporter::createEvents ( CDataModel & dataModel )

protected

Creates the events for the given data model.

References CDataVector< CType >::begin(), checkForEvents(), createEvent(), CDataVector< CType >::end(), CCopasiMessage::ERROR, CModel::getEvents(), CDataModel::getModel(), mCOPASI2SBMLMap, mCurrentStepCounter, mIncompatibilities, mpSBMLDocument, mSBMLLevel, and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createFunctionDefinition()

void CSBMLExporter::createFunctionDefinition	(	CFunction &	function,
		CDataModel &	dataModel
	)

protected

Create the SBML function definition from the given COPASI function.

References convertToASTNode(), createUniqueId(), CCopasiMessage::EXCEPTION, CDataObject::getObjectName(), isExpressionSBMLCompatible(), isValidSId(), mCOPASI2SBMLMap, MCSBML, mExportedFunctions, mFunctionMap, mIdMap, mIncompatibilities, mMetaIdMap, mpSBMLDocument, mSBMLLevel, mSBMLVersion, nameToSbmlId(), renameAstNodes(), setSBMLNotes(), CFunctionParameters::size(), updateMIRIAMAnnotation(), and CCopasiMessage::WARNING.

Referenced by createFunctionDefinitions().

◆ createFunctionDefinitions()

bool CSBMLExporter::createFunctionDefinitions ( CDataModel & dataModel )

protected

Create all function definitions.

References createFunctionDefinition(), fatalError, findUsedFunctions(), CRootContainer::getFunctionList(), CDataObject::getObjectName(), CUndoObjectInterface::insert(), CDataContainer::insert(), mCOPASI2SBMLMap, mExportedFunctions, mFunctionMap, mpSBMLDocument, mUsedFunctions, and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createFunctionSetFromFunctionNames()

const std::set< CFunction * > CSBMLExporter::createFunctionSetFromFunctionNames	(	const std::set< std::string > &	names,
		CFunctionDB *	pFunDB
	)

staticprotected

References CCopasiMessage::ERROR, CFunctionDB::findFunction(), and MCSBML.

Referenced by checkForPiecewiseFunctions(), createEvent(), createInitialAssignment(), createRule(), exportEventAssignments(), and findUsedFunctions().

◆ createIdMap()

const std::map< std::string, const SBase * > CSBMLExporter::createIdMap ( const Model & sbmlModel )

protected

Goes through the given SBML model and puts all ids with the corresponding object into a map.

◆ createInitialAssignment()

void CSBMLExporter::createInitialAssignment	(	const CModelEntity &	modelEntity,
		CDataModel &	dataModel
	)

protected

◆ createInitialAssignments()

bool CSBMLExporter::createInitialAssignments ( CDataModel & dataModel )

protected

Creates the initial assignments for the model.

References createInitialAssignment(), mInitialAssignmentVector, and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createKineticExpression()

CEvaluationNode * CSBMLExporter::createKineticExpression	(	CFunction *	pFun,
		const std::vector< std::vector< const CDataObject * > > &	arguments
	)

protected

Creates an expression from a given node and a set of parameter mappings by replacing the function arguments with the parameters. static CEvaluationNode* createExpressionTree(const CEvaluationNode* const pNode, const std::map<std::string, std::string>& parameterMap, const CDataModel& dataModel); Creates an expression from a given function and a set of parameters by replacing the function arguments with the parameters. static CEvaluationNode* createExpressionTree(const CFunction* const pFun, const std::vector<std::vector<std::string> >& arguments, const CDataModel& dataModel); Create an expression that corresponds to a kinetic law. If the kinetic law was mass action, the expression is a mass action term , otherwise it is a function call.

References CEvaluationNodeCall::addChild(), CEvaluationNode::CN, createMassActionExpression(), fatalError, CEvaluationNode::FUNCTION, CDataObject::getCN(), CDataObject::getObjectName(), CEvaluationTree::getType(), CFunction::getVariables(), CFunction::isReversible(), CEvaluationTree::MassAction, mUsedFunctions, CFunctionParameters::size(), and TriTrue.

Referenced by createKineticLaw().

◆ createKineticLaw()

KineticLaw * CSBMLExporter::createKineticLaw	(	const CReaction &	reaction,
		CDataModel &	dataModel,
		unsigned int	level,
		unsigned int	version
	)

protected

Create the kinetic law for the given reaction. On failure NULL is returned.

References CReaction::ConcentrationPerTime, convertToASTNode(), createKineticExpression(), CDataVector< CType >::empty(), fatalError, CReaction::getChemEq(), CCopasiParameter::getCN(), CReaction::getEffectiveKineticLawUnitType(), CReaction::getFunction(), CReaction::getFunctionParameters(), CDataObject::getObjectName(), CReaction::getParameterObjects(), CReaction::getParameterValue(), CChemEq::getProducts(), CModelEntity::getSBMLId(), CReaction::getScalingCompartment(), CChemEq::getSubstrates(), CFunctionParameter::getUsage(), isDividedByVolume(), CReaction::isLocalParameter(), CFunction::isReversible(), mParameterReplacementMap, mpSBMLDocument, mSBMLLevel, CFunctionParameter::PARAMETER, replaceSpeciesReferences(), restore_local_parameters(), CFunctionParameters::size(), TriUnspecified, and CFunctionParameter::VARIABLE.

Referenced by createReaction().

◆ createLengthUnit()

void CSBMLExporter::createLengthUnit ( const CDataModel & dataModel )

protected

Creates the volume unit for the SBML model.

Creates the length unit for the SBML model.

References createUnitDefinitionFor(), CModel::getLengthUnit(), CDataModel::getModel(), CModelEntity::getModel(), mpSBMLDocument, and pdelete.

Referenced by createUnits().

◆ createMassActionExpression()

CEvaluationNode * CSBMLExporter::createMassActionExpression	(	const std::vector< std::vector< const CDataObject * > > &	arguments,
		bool	isReversible
	)

staticprotected

This method creates the CEvaluationNode based tree for a reversible or irreversible Mass Action call. The first parameter contains the arguments from the COPASI reaction. The second argument determines whether it is reversible or irreversible mass action.

References CCopasiNode< _Data >::addChild(), CEvaluationNode::CN, CEvaluationNode::DOUBLE, CDataObject::getCN(), CEvaluationNode::MINUS, CEvaluationNode::MULTIPLY, and CEvaluationNode::POWER.

Referenced by createKineticExpression().

◆ createMetabolite()

void CSBMLExporter::createMetabolite ( const CMetab & metab )

protected

◆ createMetabolites()

bool CSBMLExporter::createMetabolites ( CDataModel & dataModel )

protected

Creates the compartments for the model.

References CDataVector< CType >::begin(), SBMLUnitSupport::checkForSpatialSizeUnits(), createMetabolite(), CDataVector< CType >::end(), CModel::getMetabolites(), CDataModel::getModel(), CModelEntity::getModel(), MCSBML, mCurrentStepCounter, mIncompatibilities, mSBMLLevel, mSBMLVersion, mSpatialSizeUnitsSpecies, reportCurrentProgressOrStop(), and CCopasiMessage::WARNING.

Referenced by createSBMLDocument().

◆ createParameter()

void CSBMLExporter::createParameter ( const CModelValue & modelValue )

protected

Creates the parameter for the given COPASI parameter.

References CModelEntity::ASSIGNMENT, createUniqueId(), exportAndAssignUnit(), CModelEntity::getInitialExpression(), CModelEntity::getInitialValue(), CDataObject::getObjectName(), CModelEntity::getSBMLId(), CModelEntity::getStatus(), CModelEntity::getUnitExpression(), INIT_DEFAULTS, mAssignmentVector, mCOPASI2SBMLMap, mHandledSBMLObjects, mIdMap, mInitialAssignmentVector, mMetaIdMap, mODEVector, mpSBMLDocument, mSBMLLevel, CModelEntity::ODE, removeInitialAssignment(), removeRule(), CModelEntity::setSBMLId(), setSBMLNotes(), and updateMIRIAMAnnotation().

Referenced by createParameters().

◆ createParameters()

bool CSBMLExporter::createParameters ( CDataModel & dataModel )

protected

Creates the parameters for the model.

References CDataVector< CType >::begin(), createParameter(), CDataVector< CType >::end(), CDataModel::getModel(), CModelEntity::getModel(), CModel::getModelValues(), mCurrentStepCounter, and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createProgressStepOrStop()

bool CSBMLExporter::createProgressStepOrStop	(	unsigned C_INT32	globalStep,
		unsigned C_INT32	currentTotal,
		const std::string &	title
	)

This utility functions adds a new step to the progress dialog (if present)

Parameters

globalStep	the global steps that have been completed
currentTotal	the total for current task
title	the title of the current task

Returns: a boolean indicating whether processing should be stopped

References CProcessReport::addItem(), C_INVALID_INDEX, CProcessReport::finishItem(), mCurrentStepCounter, mCurrentStepHandle, mCurrentStepTotal, mGlobalStepCounter, mGlobalStepHandle, mpProcessReport, and CProcessReport::progressItem().

Referenced by createSBMLDocument(), exportLayout(), and exportModelToString().

◆ createReaction()

void CSBMLExporter::createReaction	(	const CReaction &	reaction,
		CDataModel &	dataModel
	)

protected

◆ createReactions()

bool CSBMLExporter::createReactions ( CDataModel & dataModel )

protected

Creates the reactions for the model.

References CDataVector< CType >::begin(), createReaction(), CDataVector< CType >::end(), CDataModel::getModel(), CModelEntity::getModel(), CModel::getReactions(), mCurrentStepCounter, and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createRule()

void CSBMLExporter::createRule	(	const CModelEntity &	modelEntity,
		CDataModel &	dataModel,
		Rule *	pOldRule
	)

protected

Creates the rule for the given COPASI model entity.

References CModelEntity::ASSIGNMENT, convertExpression(), convertToASTNode(), createFunctionSetFromFunctionNames(), CCopasiMessage::ERROR, findDirectlyUsedFunctions(), CModelEntity::FIXED, CMetab::getCompartment(), CModelEntity::getExpression(), CModelEntity::getExpressionPtr(), CRootContainer::getFunctionList(), CDataObject::getObjectName(), CDataObject::getObjectType(), CEvaluationTree::getRoot(), CModelEntity::getSBMLId(), CModelEntity::getStatus(), CModelEntity::getValueReference(), CEvaluationNode::INVALID, isExpressionSBMLCompatible(), CEvaluationNode::mainType(), mCOPASI2SBMLMap, MCSBML, mIdMap, mIncompatibilities, mIncompleteExport, mInitialValueMap, mpSBMLDocument, multiplyByObject(), mUsedFunctions, outputIncompatibilities(), replace_local_parameters(), replaceSpeciesReferences(), and CEvaluationTree::setInfix().

Referenced by createRules().

◆ createRules()

bool CSBMLExporter::createRules ( CDataModel & dataModel )

protected

Creates the rules for the model.

References createRule(), CModelEntity::getSBMLId(), mODEVector, mpSBMLDocument, orderRules(), and reportCurrentProgressOrStop().

Referenced by createSBMLDocument().

◆ createSBMLDocument()

bool CSBMLExporter::createSBMLDocument ( CDataModel & dataModel )

protected

Creates an SBMLDocument from the given CDataModelObject. It checks if an SBMLDocument already exists from an import and if this is the case, the old document is copied. If none exists a new one is created. Copying the old one makes sure that if something goes wrong during export, the original model is still consistent.

Returns: true, if exporting should continue, false otherwise

References addInitialAssignmentsToModel(), assignSBMLIdsToReactions(), checkForInitialAssignments(), collectIds(), SBMLUtils::collectIds(), convertToLevel1(), createCompartments(), createEvents(), createFunctionDefinitions(), createInitialAssignments(), createMetabolites(), createParameters(), createProgressStepOrStop(), createReactions(), createRules(), createUniqueId(), createUnits(), CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, fatalError, findAvogadro(), finishExport(), CModel::getCompartments(), CDataModel::getCurrentSBMLDocument(), CModel::getEvents(), CModelEntity::getKey(), CModel::getMetabolites(), CDataModel::getModel(), CModel::getModelValues(), CDataObject::getObjectName(), CModel::getReactions(), CModelEntity::getSBMLId(), hasVolumeAssignment(), mAvogadroCreated, mCOPASI2SBMLMap, mExportedFunctions, mFunctionIdMap, mFunctionMap, mIdMap, mIncompatibilities, mInitialValueMap, mpAvogadro, mpSBMLDocument, mSBMLLevel, mSBMLVersion, mVariableVolumes, outputIncompatibilities(), CModel::removeModelValue(), setSBMLNotes(), CDataVector< CType >::size(), updateCOPASI2SBMLMap(), and updateMIRIAMAnnotation().

Referenced by exportModelToString().

◆ createSBMLNotes()

XMLNode * CSBMLExporter::createSBMLNotes ( const std::string & notes_string )

static

Method to create a valid XHTML node from a CModels comments string. This method is declared public so that I can call it from the unit tests.

Method to create a valid XHTML node from a CModels comments string.

Referenced by setSBMLNotes().

◆ createSubstanceUnit()

void CSBMLExporter::createSubstanceUnit ( const CDataModel & dataModel )

protected

Creates the substance unit for the SBML model.

References createUnitDefinitionFor(), CDataModel::getModel(), CModelEntity::getModel(), CModel::getQuantityUnit(), mpSBMLDocument, mSBMLLevel, and pdelete.

Referenced by createUnits().

◆ createTimesTree()

ASTNode * CSBMLExporter::createTimesTree	(	const CDataVector< CChemEqElement > &	vect,
		unsigned int	pos = `0`
	)

staticprotected

This method creates an ASTNode tree where all the species specified in the given vector are multiplied. This is used to create the mass action kinetic law.

References CModelEntity::getSBMLId(), and CDataVector< CType >::size().

◆ createTimeUnit()

void CSBMLExporter::createTimeUnit ( const CDataModel & dataModel )

protected

Creates the time unit for the SBML model.

References createUnitDefinitionFor(), CDataModel::getModel(), CModelEntity::getModel(), CModel::getTimeUnit(), mpSBMLDocument, and pdelete.

Referenced by createUnits().

◆ createUniqueId()

const std::string CSBMLExporter::createUniqueId	(	const std::map< std::string, const SBase * > &	idMap,
		const std::string &	prefix,
		bool	addIndexForFirst,
		const std::string &	separator = `"_"`
	)

static

Create a unique id for an SBML object. I can't just take the Copasi key of the object since this might conflict with an already existing sbml id which came from the sbmlid attribute in a copasi file or directly by importing an SBML file.

Create a unique id for an SBML object. I can't just take the COPASI key of the object since this might conflict with an already existing SBML id which came from the sbmlid attribute in a COPASI file or directly by importing an SBML file.

References nameToSbmlId().

Referenced by addParticleNumberToInitialValueMap(), addToInitialValueMap(), assignSBMLIdsToReactions(), checkForUnsupportedObjectReferences(), createAvogadroIfNeeded(), createCompartment(), createEvent(), createFunctionDefinition(), createFunctionDefinitonForURI(), createMetabolite(), createParameter(), createReaction(), createSBMLDocument(), CLGraphicalObject::exportToSBML(), CLayout::exportToSBML(), replace_local_parameters(), setFunctionSBMLIds(), and updateMIRIAMAnnotation().

◆ createUnitDefinitionFor()

UnitDefinition * CSBMLExporter::createUnitDefinitionFor ( const CUnit & unit )

protected

creates and SBML UnitDefinition for the given unit

Parameters

unit	the COPASI unit element

Returns: the SBML UnitDefinition

References addCUnitComponentToUnitDefinition(), addSymbolComponentToUnitDefinition(), CUnit::getComponents(), CUnit::getExpression(), CUnit::getSymbolComponents(), CUnit::isUndefined(), mIdMap, and mpSBMLDocument.

Referenced by createAreaUnit(), createLengthUnit(), createSubstanceUnit(), createTimeUnit(), createVolumeUnit(), and exportAndAssignUnit().

◆ createUnits()

void CSBMLExporter::createUnits ( const CDataModel & dataModel )

protected

Creates the units for the SBML model.

References createAreaUnit(), createLengthUnit(), createSubstanceUnit(), createTimeUnit(), and createVolumeUnit().

Referenced by createSBMLDocument().

◆ createUnsupportedFunctionTypeSet()

const std::set< CEvaluationNode::SubType > CSBMLExporter::createUnsupportedFunctionTypeSet ( unsigned int sbmlLevel )

staticprotected

Creates a set of all function subtypes that can not be exported for a certain SBML level.

References CEvaluationNode::ARCCOTH, CEvaluationNode::MAX, and CEvaluationNode::MIN.

Referenced by checkForUnsupportedFunctionCalls(), and isExpressionSBMLCompatible().

◆ createVolumeUnit()

void CSBMLExporter::createVolumeUnit ( const CDataModel & dataModel )

protected

Creates the volume unit for the SBML model.

References createUnitDefinitionFor(), CDataModel::getModel(), CModelEntity::getModel(), CModel::getVolumeUnit(), mpSBMLDocument, and pdelete.

Referenced by createUnits().

◆ disownSBMLDocument()

void CSBMLExporter::disownSBMLDocument ( )

This method assures that the SBMLDocument is not deleted by the destructor of the exporter. This allows us to get the SBMLDocument from the exporter and store it in the data model without having to copy it.

References mDocumentDisowned.

Referenced by CDataModel::exportSBML(), and CDataModel::exportSBMLToString().

◆ exportAndAssignUnit()

void CSBMLExporter::exportAndAssignUnit	(	const CUnit &	unit,
		SBase *	sbmlElement
	)

protected

exports the given unit to the sbmlElement

Parameters

unit	the unit to export
sbmlElement	the sbml element that the unit should be assigned to

References createUnitDefinitionFor(), CUnit::isUndefined(), and mpSBMLDocument.

Referenced by createParameter().

◆ exportEventAssignments()

void CSBMLExporter::exportEventAssignments	(	const CEvent &	event,
		Event *	pSBMLEvent,
		CDataModel &	dataModel
	)

protected

This method creates the individual event assignments for the given event.

References CDataVector< CType >::begin(), convertExpression(), convertToASTNode(), createFunctionSetFromFunctionNames(), CObjectInterface::DataObject(), CDataVector< CType >::end(), CCopasiMessage::EXCEPTION, fatalError, findDirectlyUsedFunctions(), CMetab::getCompartment(), CRootContainer::getFunctionList(), CEvaluationTree::getInfix(), CDataModel::getModel(), CDataContainer::getObject(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::getObjectType(), CModel::getQuantity2NumberFactor(), CEvaluationTree::getRoot(), CEvent::getSBMLId(), CModelEntity::getSBMLId(), CModelEntity::getValueReference(), CEvaluationNode::INVALID, isExpressionSBMLCompatible(), CEvaluationNode::mainType(), mCOPASI2SBMLMap, MCSBML, mHandledSBMLObjects, mIdMap, mIncompatibilities, mIncompleteExport, mInitialValueMap, mSBMLLevel, mSBMLVersion, multiplyByObject(), mUsedFunctions, outputIncompatibilities(), replace_local_parameters(), replaceSpeciesReferences(), CEvaluationTree::setInfix(), and CCopasiMessage::WARNING.

Referenced by createEvent().

◆ exportLayout()

bool CSBMLExporter::exportLayout	(	unsigned int	sbmlLevel,
		CDataModel &	dataModel
	)

Export the model to SBML. The SBML model is returned as a string. In case of an error, an empty string is returned.

References createProgressStepOrStop(), CListOfLayouts::exportToSBML(), finishExport(), getDefaultStyle(), CDataModel::getListOfLayouts(), getNumDefaultStyles(), mCOPASI2SBMLMap, mIdMap, mpSBMLDocument, and CLGlobalRenderInformation::toSBML().

Referenced by exportModelToString().

◆ exportModel()

bool CSBMLExporter::exportModel	(	CDataModel &	dataModel,
		const std::string &	filename,
		unsigned int	sbmlLevel = `2`,
		unsigned int	sbmlVersion = `1`,
		bool	overwrite = `false`
	)

Export the model to SBML. The model is written to the file given by filename. If the export fails, false is returned.

References CCopasiMessage::ERROR, exportModelToString(), CLocaleString::fromUtf8(), and MCDirEntry.

Referenced by CDataModel::exportSBML().

◆ exportModelToString()

const std::string CSBMLExporter::exportModelToString	(	CDataModel &	dataModel,
		unsigned int	sbmlLevel,
		unsigned int	sbmlVersion
	)

Export the model to SBML. The SBML model is returned as a string. In case of an error, an empty string is returned.

References CProcessReport::addItem(), createProgressStepOrStop(), createSBMLDocument(), exportLayout(), finishExport(), mGlobalStepCounter, mGlobalStepHandle, mGlobalStepTotal, mHandledSBMLObjects, mpProcessReport, mpSBMLDocument, mSBMLLevel, mSBMLVersion, pdelete, removeStickyTagFromElements(), removeUnusedObjects(), CProcessReport::setName(), and CVersion::VERSION.

Referenced by exportModel(), and CDataModel::exportSBMLToString().

◆ findAvogadro()

void CSBMLExporter::findAvogadro ( const CDataModel & dataModel )

protected

Try to find a global parameter that represents avogadros number.

References CDataVector< CType >::begin(), CDataVector< CType >::end(), CModelEntity::FIXED, CDataModel::getModel(), CModel::getModelValues(), CModel::getQuantity2NumberFactor(), and mpAvogadro.

Referenced by createSBMLDocument().

◆ findDirectlyUsedFunctions()

void CSBMLExporter::findDirectlyUsedFunctions	(	const CEvaluationNode *	pRootNode,
		std::set< std::string > &	result
	)

staticprotected

Go through a CEvaluationNode base tree and add the names of all functions directly called in this tree to the set.

References CEvaluationNode::CALL, CCopasiNode< _Data >::getChild(), CCopasiNode< _Data >::getData(), CCopasiNode< _Data >::getSibling(), and CEvaluationNode::mainType().

Referenced by checkForPiecewiseFunctions(), createEvent(), createInitialAssignment(), createRule(), exportEventAssignments(), findUsedFunctions(), isEventAssignmentSBMLCompatible(), isEventSBMLCompatible(), and isModelSBMLCompatible().

◆ findModelEntityDependencies()

void CSBMLExporter::findModelEntityDependencies	(	const CEvaluationNode *	pNode,
		const CDataModel &	dataModel,
		std::set< const CModelEntity * > &	dependencies
	)

staticprotected

Find all ModelEntities for which the given node and its children contains references.

References CObjectInterface::DataObject(), fatalError, CCopasiNode< _Data >::getChild(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectFromCN(), CDataObject::getObjectParent(), CCopasiNode< _Data >::getSibling(), CDataObject::hasFlag(), CDataContainer::insert(), CEvaluationNode::mainType(), CEvaluationNode::OBJECT, and CDataObject::Reference.

Referenced by orderRules().

◆ findUsedFunctions()

const std::vector< CFunction * > CSBMLExporter::findUsedFunctions	(	std::set< CFunction * > &	functions,
		CFunctionDB *	pFunctionDB
	)

staticprotected

Takes a set of functions and recursively finds functions used by those functions

References createFunctionSetFromFunctionNames(), CCopasiMessage::EXCEPTION, findDirectlyUsedFunctions(), and CEvaluationTree::getRoot().

Referenced by checkForPiecewiseFunctions(), and createFunctionDefinitions().

◆ finishCurrentStep()

void CSBMLExporter::finishCurrentStep ( )

Notifies the progress dialog that a step finished

References C_INVALID_INDEX, CProcessReport::finishItem(), mCurrentStepHandle, and mpProcessReport.

Referenced by finishExport().

◆ finishExport()

void CSBMLExporter::finishExport ( )

Notifies the progress dialog that the overall exporting is complete

References finishCurrentStep(), CProcessReport::finishItem(), mGlobalStepHandle, and mpProcessReport.

Referenced by createSBMLDocument(), exportLayout(), and exportModelToString().

◆ getCallBack()

const CProcessReport * CSBMLExporter::getCallBack ( ) const

Returns: the currently set callback handler

References mpProcessReport.

◆ getCOPASI2SBMLMap()

const std::map< const CDataObject *, SBase * > & CSBMLExporter::getCOPASI2SBMLMap ( ) const

Returns a const pointer to the COPASI2SBMLMap.

References mCOPASI2SBMLMap.

Referenced by CDataModel::exportSBML(), and CDataModel::exportSBMLToString().

◆ getSBMLDocument()

SBMLDocument * CSBMLExporter::getSBMLDocument ( )

References mpSBMLDocument.

Referenced by CDataModel::exportSBML(), and CDataModel::exportSBMLToString().

◆ hasVolumeAssignment()

bool CSBMLExporter::hasVolumeAssignment ( const CDataModel & dataModel )

protected

This method goes through all compartments and events and checks if there is an assignment to a volume.

References CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), CObjectInterface::DataObject(), CDataVector< CType >::empty(), CDataVector< CType >::end(), CModel::getCompartments(), CModel::getEvents(), CDataModel::getModel(), CModelEntity::getModel(), CDataContainer::getObject(), CDataObject::getObjectParent(), CDataObject::getObjectType(), mSBMLLevel, mSBMLVersion, and CModelEntity::ODE.

Referenced by createSBMLDocument().

◆ isDividedByVolume()

ASTNode * CSBMLExporter::isDividedByVolume	(	const ASTNode *	pRootNode,
		const std::string &	compartmentId
	)

staticprotected

checks if the given ASTNode based tree is divided by the volume of the compartment identified by the given id string.

Referenced by createKineticLaw().

◆ isEventAssignmentSBMLCompatible()

void CSBMLExporter::isEventAssignmentSBMLCompatible	(	const CDataObject *	pTarget,
		const CExpression *	pExpression,
		const CDataModel &	dataModel,
		unsigned int	sbmlLevel,
		unsigned int	sbmlVersion,
		const std::string &	eventName,
		std::vector< SBMLIncompatibility > &	result,
		std::map< std::string, const SBase * > &	idMap
	)

staticprotected

This method checks if the given event assignment object is SBML compatible.

References CModelEntity::ASSIGNMENT, findDirectlyUsedFunctions(), CModelEntity::FIXED, CDataObject::getObjectName(), CDataObject::getObjectType(), CEvaluationTree::getRoot(), CModelEntity::getStatus(), CEvaluationNode::INVALID, isExpressionSBMLCompatible(), CEvaluationNode::mainType(), and CCopasiMessage::RAW.

Referenced by isEventSBMLCompatible().

◆ isEventSBMLCompatible()

void CSBMLExporter::isEventSBMLCompatible	(	const CEvent *	pEvent,
		const CDataModel &	dataModel,
		unsigned int	sbmlLevel,
		unsigned int	sbmlVersion,
		std::vector< SBMLIncompatibility > &	result,
		std::map< std::string, const SBase * > &	idMap
	)

staticprotected

This method checks if the given event object is SBML compatible.

References CDataVector< CType >::begin(), CObjectInterface::DataObject(), CDataVector< CType >::end(), findDirectlyUsedFunctions(), CEvent::getAssignments(), CEvent::getDelayExpressionPtr(), CDataContainer::getObject(), CDataObject::getObjectName(), CEvaluationTree::getRoot(), CEvent::getTriggerExpressionPtr(), isEventAssignmentSBMLCompatible(), isExpressionSBMLCompatible(), and CCopasiMessage::RAW.

Referenced by isModelSBMLCompatible().

◆ isExpressionSBMLCompatible()

void CSBMLExporter::isExpressionSBMLCompatible	(	const CEvaluationTree &	expr,
		const CDataModel &	dataModel,
		int	sbmlLevel,
		int	sbmlVersion,
		std::vector< SBMLIncompatibility > &	result,
		std::map< std::string, const SBase * > &	idMap,
		const std::string &	objectDescription,
		bool	initialExpression = `false`,
		std::map< const std::string, Parameter * > *	initialMap = `NULL`
	)

staticprotected

Checks whether the rule in the given model entity can be exported to the specified version of SBML. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

References checkForUnsupportedFunctionCalls(), checkForUnsupportedObjectReferences(), createUnsupportedFunctionTypeSet(), and CEvaluationTree::getRoot().

Referenced by createEvent(), createFunctionDefinition(), createInitialAssignment(), createRule(), exportEventAssignments(), isEventAssignmentSBMLCompatible(), isEventSBMLCompatible(), and isModelSBMLCompatible().

◆ isExpressionSBMLL1Compatible()

static void CSBMLExporter::isExpressionSBMLL1Compatible	(	const CEvaluationTree &	expr,
		const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks whether the rule in the given model entity can be exported to SBML Level2 Version1. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

◆ isExpressionSBMLL2V1Compatible()

static void CSBMLExporter::isExpressionSBMLL2V1Compatible	(	const CEvaluationTree &	expr,
		const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks whether the rule in the given model entity can be exported to SBML Level2 Version1. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

◆ isExpressionSBMLL2V3Compatible()

static void CSBMLExporter::isExpressionSBMLL2V3Compatible	(	const CEvaluationTree &	expression,
		const CDataModel &	pDataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks whether the rule in the given model entity can be exported to SBML Level2 Version3. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

◆ isModelSBMLCompatible()

const std::vector< SBMLIncompatibility > CSBMLExporter::isModelSBMLCompatible	(	const CDataModel &	dataModel,
		int	sbmlLevel,
		int	sbmlVersion,
		std::map< std::string, const SBase * > &	idMap
	)

static

Checks wether the given data model can be exported to a certain version of SBML. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

Checks whether the given data model can be exported to a certain version of SBML. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

References CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), checkForODESpeciesInNonfixedCompartment(), CDataVector< CType >::end(), findDirectlyUsedFunctions(), CModel::getCompartments(), CModel::getEvents(), CModel::getMetabolites(), CDataModel::getModel(), CModel::getModelValues(), CDataObject::getObjectName(), CEvaluationTree::getRoot(), isEventSBMLCompatible(), isExpressionSBMLCompatible(), isModelSBMLL1Compatible(), isModelSBMLL2V1Compatible(), isModelSBMLL2V3Compatible(), and CModelEntity::ODE.

◆ isModelSBMLL1Compatible()

void CSBMLExporter::isModelSBMLL1Compatible	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks whether the given data model can be exported to SBML Level1 If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

References checkForEvents(), checkForInitialAssignments(), and checkForPiecewiseFunctions().

Referenced by isModelSBMLCompatible().

◆ isModelSBMLL2V1Compatible()

void CSBMLExporter::isModelSBMLL2V1Compatible	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks whether the given data model can be exported to SBML Level2 Version1. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

References checkForInitialAssignments().

Referenced by isModelSBMLCompatible().

◆ isModelSBMLL2V3Compatible()

void CSBMLExporter::isModelSBMLL2V3Compatible	(	const CDataModel &	dataModel,
		std::vector< SBMLIncompatibility > &	result
	)

staticprotected

Checks whether the given data model can be exported to SBML Level2 Version3. If it can be exported, the result vector will be empty, otherwise it will contain a number of messages that specify why it can't be exported.

References SBMLUnitSupport::checkForSpatialSizeUnits().

Referenced by isModelSBMLCompatible().

◆ isSetExportCOPASIMIRIAM()

bool CSBMLExporter::isSetExportCOPASIMIRIAM ( ) const

Returns whether the exporter is supposed to export COPASIs MIRIAM annotation in addition to SBML MIRIAM.

References mExportCOPASIMIRIAM.

◆ isValidSId()

bool CSBMLExporter::isValidSId ( const std::string & id )

staticprotected

Checks if the given string is a valid SId

Referenced by createFunctionDefinition(), and setFunctionSBMLIds().

◆ multiplyByObject()

CEvaluationNode * CSBMLExporter::multiplyByObject	(	const CEvaluationNode *	pOrigNode,
		const CDataObject *	pObject
	)

staticprotected

This method multiplies a given expression by the given object. The caller is responsible for freeing the memory for the new expression.

References CCopasiNode< _Data >::addChild(), CEvaluationNode::CN, CEvaluationNode::copyBranch(), CEvaluationNode::DIVIDE, CCopasiNode< _Data >::getChild(), CDataObject::getCN(), CEvaluationNode::mainType(), CEvaluationNode::MULTIPLY, CEvaluationNode::OBJECT, CEvaluationNode::OPERATOR, and CEvaluationNode::subType().

Referenced by createInitialAssignment(), createRule(), and exportEventAssignments().

◆ orderRules()

std::vector< const CModelEntity * > CSBMLExporter::orderRules ( const CDataModel & dataModel )

protected

Sorts the rules.

References CCopasiMessage::EXCEPTION, findModelEntityDependencies(), CEvaluationTree::getRoot(), and mAssignmentVector.

Referenced by createRules().

◆ outputIncompatibilities()

void CSBMLExporter::outputIncompatibilities ( ) const

protected

Creates error messages from the list of incompatibilities and thows an exception.

References SBMLIncompatibility::getDetails(), SBMLIncompatibility::getMessage(), mIncompatibilities, SBMLIncompatibility::minSBMLLevel(), SBMLIncompatibility::minSBMLVersion(), and CCopasiMessage::RAW.

Referenced by createEvent(), createInitialAssignment(), createRule(), createSBMLDocument(), and exportEventAssignments().

◆ removeInitialAssignment()

void CSBMLExporter::removeInitialAssignment ( const std::string & sbmlId )

protected

Remove the initial assignment for the entity with the given id if there is any.

References mpSBMLDocument.

Referenced by createCompartment(), createMetabolite(), and createParameter().

◆ removeRule()

void CSBMLExporter::removeRule ( const std::string & sbmlId )

protected

Remove the rule for the entity with the given id if there is any.

References mpSBMLDocument.

Referenced by createCompartment(), createMetabolite(), and createParameter().

◆ removeUnusedObjects()

void CSBMLExporter::removeUnusedObjects ( )

protected

Remove all compartments, species, parameters and reactions that did not end up in mHandledSBMLObjects during an export.

Remove all compartments, species, parameters and reactions and initial assignments that did not end up in mHandledSBMLObjects during an export.

References mCOPASI2SBMLMap, mHandledSBMLObjects, and mpSBMLDocument.

Referenced by exportModelToString().

◆ replace_local_parameters()

void CSBMLExporter::replace_local_parameters	(	ASTNode *	pOrigNode,
		const CDataModel &	dataModel
	)

protected

Goes through the expression tree and tries to find occurences of local parameters. If one is found, a global parameter is created and all references to the local parameters are substituted.

References C_FLOAT64, createUniqueId(), CObjectInterface::DataObject(), CCopasiParameter::getCN(), CDataObject::getObjectFromCN(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CCopasiParameter::getValue(), mHandledSBMLObjects, mIdMap, mParameterReplacementMap, and mpSBMLDocument.

Referenced by createEvent(), createInitialAssignment(), createRule(), and exportEventAssignments().

◆ replaceChild()

XMLNode * CSBMLExporter::replaceChild	(	const XMLNode *	pParent,
		const XMLNode *	pNewChild,
		unsigned int	index
	)

protected

This method creates a copy of parent where the child with the given index is replaced by the new child given as the second argument. If index is greater than the number of children - 1, NULL is returned.

This method creates a copy of parent where the child with the given index is replaced by the new child given as the second argument. If index is greater than the number of children - 1, NULL is returned. If the new child is a null pointer, this method deleted the old node at the given index.

Referenced by updateMIRIAMAnnotation().

◆ replaceL1IncompatibleNodes()

ASTNode * CSBMLExporter::replaceL1IncompatibleNodes ( const ASTNode * pNode )

staticprotected

This method goes through the ASTNode based tree rooted at pNode and replaces all unsupported nodes with constructs supported by SBML Level 1 The caller is responsible for freeing the memory of the returned object.

References fatalError, max, and ConverterASTNode::shallowCopy().

Referenced by convertASTTreeToLevel1().

◆ replaceSpeciesReferences()

CEvaluationNode * CSBMLExporter::replaceSpeciesReferences	(	const CEvaluationNode *	pOrigNode,
		const CDataModel &	dataModel
	)

protected

Replaces references to species with reference to species divided by volume if it is a reference to a concentration or by a reference to the species times avogadros number if it is a reference to the amount. The method also takes into consideration the substance units of the model.

References CCopasiNode< _Data >::addChild(), addRateOfIfItDoesNotExist(), CEvaluationNode::CN, CEvaluationNode::copyBranch(), CEvaluationNode::copyNode(), createAvogadroIfNeeded(), CObjectInterface::DataObject(), CEvaluationNode::DIVIDE, CEvaluationNode::DOUBLE, CEvaluationNode::ENOTATION, fatalError, CModelEntity::FIXED, CCopasiNode< _Data >::getChild(), CDataObject::getCN(), CMetab::getCompartment(), CMetab::getConcentrationReference(), CCopasiNode< _Data >::getData(), CDataModel::getModel(), CDataContainer::getObject(), CEvaluationNodeObject::getObjectCN(), CDataObject::getObjectFromCN(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CModel::getQuantity2NumberFactor(), CModel::getQuantityUnit(), CCopasiNode< _Data >::getSibling(), CModelEntity::getStatus(), CModelEntity::getValue(), CModelEntity::getValueReference(), CDataObject::hasFlag(), CEvaluationNode::INVALID, CEvaluationNode::mainType(), mIdMap, mpAvogadro, mpSBMLDocument, CEvaluationNode::MULTIPLY, mVariableVolumes, CEvaluationNode::NUMBER, CEvaluationNode::OBJECT, CEvaluationNode::OPERATOR, CDataObject::Reference, and CEvaluationNode::subType().

Referenced by createEvent(), createInitialAssignment(), createKineticLaw(), createRule(), and exportEventAssignments().

◆ reportCurrentProgressOrStop()

bool CSBMLExporter::reportCurrentProgressOrStop ( )

Notifies the progress dialog of local progress

Returns: a boolean indicating whether processing should be stopped

References mCurrentStepHandle, mpProcessReport, and CProcessReport::progressItem().

Referenced by createCompartments(), createEvents(), createFunctionDefinitions(), createInitialAssignments(), createMetabolites(), createParameters(), createReactions(), and createRules().

◆ restore_local_parameters()

void CSBMLExporter::restore_local_parameters	(	ASTNode *	pOrigNode,
		const CDataModel &	dataModel
	)

protected

This method goes through the expression tree and tries to find node names that correspond to common names of local parameters. If the common name also occurs in the replacement map, the node name has to be set to the id of the corresponding global parameter, otherwise the name has to be set to the object name of the parameter.

References CObjectInterface::DataObject(), CDataObject::getObjectFromCN(), CDataObject::getObjectName(), and mParameterReplacementMap.

Referenced by createKineticLaw().

◆ setExportCOPASIMIRIAM()

void CSBMLExporter::setExportCOPASIMIRIAM ( bool exportMIRIAM )

Sets whether the exporter is supposed to export COPASIs MIRIAM annotation in addition to SBML MIRIAM.

References mExportCOPASIMIRIAM.

Referenced by CDataModel::exportSBML(), and CDataModel::exportSBMLToString().

◆ setFunctionSBMLIds()

void CSBMLExporter::setFunctionSBMLIds	(	const CEvaluationNode *	pNode,
		CDataModel &	dataModel
	)

protected

This method traverse a CEvaluationTree and set the SBML id on all functions that are used in function calls in the tree.

References CEvaluationNode::CALL, createUniqueId(), fatalError, CFunctionDB::findFunction(), CCopasiNode< _Data >::getChild(), CRootContainer::getFunctionList(), CDataObject::getObjectName(), CFunction::getSBMLId(), CCopasiNode< _Data >::getSibling(), isValidSId(), CEvaluationNode::mainType(), mFunctionIdMap, mIdMap, and CFunction::setSBMLId().

Referenced by convertToASTNode().

◆ setHandler()

void CSBMLExporter::setHandler ( CProcessReport * pProcessReport )

Sets the progress handler to be used while exporting set to NULL, to stop reporting

Parameters

pHandler the progress handler to be used, or NULL

References mpProcessReport.

Referenced by clearCallBack(), CDataModel::exportSBML(), and CDataModel::exportSBMLToString().

◆ setSBMLNotes()

bool CSBMLExporter::setSBMLNotes	(	SBase *	pSBase,
		const CAnnotation *	pAnno
	)

staticprotected

This is a general method to set the notes of an SBase object based on a COPASI Annotation. This will allow us to export notes on objects other than just the model.

References createSBMLNotes(), CAnnotation::getNotes(), CAnnotation::getUnsupportedAnnotations(), and CCopasiMessage::WARNING.

Referenced by createCompartment(), createEvent(), createFunctionDefinition(), createMetabolite(), createParameter(), createReaction(), and createSBMLDocument().

◆ updateCOPASI2SBMLMap()

void CSBMLExporter::updateCOPASI2SBMLMap ( const CDataModel & dataModel )

protected

Creates a new COPASI2SBMLMap based on the old map and the copied SBMLDocument.

References mCOPASI2SBMLMap, and mIdMap.

Referenced by createSBMLDocument().

◆ updateMIRIAMAnnotation()

bool CSBMLExporter::updateMIRIAMAnnotation	(	const CDataObject *	pCOPASIObject,
		SBase *	pSBMLObject,
		std::map< std::string, const SBase * > &	metaIds
	)

protected

This method gets the MIRIAM annotation from the given COPASI object and sets it on the given SBML object.

This method updates the MIRIAM annotation on different model entities like the model itself, compartments, species, reactions, functions and global parameters

Referenced by createCompartment(), createEvent(), createFunctionDefinition(), createMetabolite(), createParameter(), createReaction(), and createSBMLDocument().

Member Data Documentation

◆ mAssignmentVector

std::vector<const CModelEntity*> CSBMLExporter::mAssignmentVector

protected

Referenced by checkForUnsupportedFunctionCalls(), checkForUnsupportedObjectReferences(), createCompartment(), createMetabolite(), createParameter(), and orderRules().

◆ mAvogadroCreated

bool CSBMLExporter::mAvogadroCreated

protected

Referenced by createAvogadroIfNeeded(), and createSBMLDocument().

◆ mAvogadroId

std::string CSBMLExporter::mAvogadroId

protected

Referenced by addInitialAssignmentsToModel(), and createAvogadroIfNeeded().

◆ mCOPASI2SBMLMap

std::map<const CDataObject*, SBase*> CSBMLExporter::mCOPASI2SBMLMap

protected

Referenced by createAvogadroIfNeeded(), createCompartment(), createEvent(), createEvents(), createFunctionDefinition(), createFunctionDefinitions(), createInitialAssignment(), createMetabolite(), createParameter(), createReaction(), createRule(), createSBMLDocument(), exportEventAssignments(), exportLayout(), getCOPASI2SBMLMap(), removeUnusedObjects(), and updateCOPASI2SBMLMap().

◆ mCurrentStepCounter

unsigned C_INT32 CSBMLExporter::mCurrentStepCounter

protected

current step counter for current import

Referenced by createCompartments(), createEvents(), createMetabolites(), createParameters(), createProgressStepOrStop(), and createReactions().

◆ mCurrentStepHandle

size_t CSBMLExporter::mCurrentStepHandle

protected

the current import step handle

Referenced by createProgressStepOrStop(), finishCurrentStep(), and reportCurrentProgressOrStop().

◆ mCurrentStepTotal

unsigned C_INT32 CSBMLExporter::mCurrentStepTotal

protected

total steps of current import task

Referenced by createProgressStepOrStop().

◆ mDocumentDisowned

bool CSBMLExporter::mDocumentDisowned

protected

Referenced by disownSBMLDocument(), and ~CSBMLExporter().

◆ mExportCOPASIMIRIAM

bool CSBMLExporter::mExportCOPASIMIRIAM

protected

Referenced by isSetExportCOPASIMIRIAM(), setExportCOPASIMIRIAM(), and updateMIRIAMAnnotation().

◆ mExportedFunctions

ListOfFunctionDefinitions CSBMLExporter::mExportedFunctions

protected

Referenced by convertToLevel1(), createFunctionDefinition(), createFunctionDefinitions(), and createSBMLDocument().

◆ mFunctionIdMap

std::map<std::string, const CEvaluationTree*> CSBMLExporter::mFunctionIdMap

protected

Referenced by createSBMLDocument(), and setFunctionSBMLIds().

◆ mFunctionMap

std::map<const FunctionDefinition*, const CDataObject*> CSBMLExporter::mFunctionMap

protected

Referenced by createFunctionDefinition(), createFunctionDefinitions(), and createSBMLDocument().

◆ mGlobalStepCounter

unsigned C_INT32 CSBMLExporter::mGlobalStepCounter

protected

global step counter

Referenced by createProgressStepOrStop(), and exportModelToString().

◆ mGlobalStepHandle

size_t CSBMLExporter::mGlobalStepHandle

protected

the global import step handle

Referenced by createProgressStepOrStop(), exportModelToString(), and finishExport().

◆ mGlobalStepTotal

unsigned C_INT32 CSBMLExporter::mGlobalStepTotal

protected

total step counter for global import

Referenced by exportModelToString().

◆ mHandledSBMLObjects

std::set<SBase*> CSBMLExporter::mHandledSBMLObjects

protected

Referenced by createAvogadroIfNeeded(), createCompartment(), createInitialAssignment(), createMetabolite(), createParameter(), createReaction(), exportEventAssignments(), exportModelToString(), removeUnusedObjects(), and replace_local_parameters().

◆ mIdMap

std::map<std::string, const SBase*> CSBMLExporter::mIdMap

protected

◆ mIncompatibilities

std::vector<SBMLIncompatibility> CSBMLExporter::mIncompatibilities

protected

Referenced by createEvent(), createEvents(), createFunctionDefinition(), createInitialAssignment(), createMetabolites(), createRule(), createSBMLDocument(), exportEventAssignments(), and outputIncompatibilities().

◆ mIncompleteExport

bool CSBMLExporter::mIncompleteExport

protected

Referenced by createEvent(), createInitialAssignment(), createReaction(), createRule(), and exportEventAssignments().

◆ mInitialAssignmentVector

std::vector<const CModelEntity*> CSBMLExporter::mInitialAssignmentVector

protected

Referenced by checkForUnsupportedFunctionCalls(), checkForUnsupportedObjectReferences(), createCompartment(), createInitialAssignments(), createMetabolite(), and createParameter().

◆ mInitialValueMap

std::map<const std::string, Parameter*> CSBMLExporter::mInitialValueMap

protected

Referenced by addInitialAssignmentsToModel(), checkForUnsupportedObjectReferences(), createEvent(), createInitialAssignment(), createRule(), createSBMLDocument(), and exportEventAssignments().

◆ mMetaIdMap

std::map<std::string, const SBase*> CSBMLExporter::mMetaIdMap

protected

Referenced by createCompartment(), createEvent(), createFunctionDefinition(), createMetabolite(), createParameter(), and createReaction().

◆ mMIRIAMWarning

bool CSBMLExporter::mMIRIAMWarning

protected

◆ mODEVector

std::vector<const CModelEntity*> CSBMLExporter::mODEVector

protected

Referenced by checkForUnsupportedFunctionCalls(), checkForUnsupportedObjectReferences(), createCompartment(), createMetabolite(), createParameter(), and createRules().

◆ mParameterReplacementMap

std::map<std::string, Parameter*> CSBMLExporter::mParameterReplacementMap

protected

Referenced by createKineticLaw(), replace_local_parameters(), and restore_local_parameters().

◆ mpAvogadro

const CModelValue* CSBMLExporter::mpAvogadro

protected

Referenced by createAvogadroIfNeeded(), createSBMLDocument(), findAvogadro(), and replaceSpeciesReferences().

◆ mpProcessReport

CProcessReport* CSBMLExporter::mpProcessReport

protected

the progress handler for the export

Referenced by createProgressStepOrStop(), exportModelToString(), finishCurrentStep(), finishExport(), getCallBack(), reportCurrentProgressOrStop(), and setHandler().

◆ mpSBMLDocument

SBMLDocument* CSBMLExporter::mpSBMLDocument

protected

◆ mSBMLLevel

unsigned int CSBMLExporter::mSBMLLevel

protected

Referenced by createCompartment(), createEvent(), createEvents(), createFunctionDefinition(), createKineticLaw(), createMetabolite(), createMetabolites(), createParameter(), createReaction(), createSBMLDocument(), createSubstanceUnit(), exportEventAssignments(), exportModelToString(), hasVolumeAssignment(), and updateMIRIAMAnnotation().

◆ mSBMLVersion

unsigned int CSBMLExporter::mSBMLVersion

protected

Referenced by createEvent(), createFunctionDefinition(), createMetabolite(), createMetabolites(), createSBMLDocument(), exportEventAssignments(), exportModelToString(), and hasVolumeAssignment().

◆ mSpatialSizeUnitsSpecies

std::set<std::string> CSBMLExporter::mSpatialSizeUnitsSpecies

protected

Referenced by createMetabolite(), and createMetabolites().

◆ mUsedFunctions

std::set<CFunction*> CSBMLExporter::mUsedFunctions

protected

Referenced by checkForUnsupportedFunctionCalls(), createEvent(), createFunctionDefinitions(), createInitialAssignment(), createKineticExpression(), createRule(), and exportEventAssignments().

◆ mVariableVolumes

bool CSBMLExporter::mVariableVolumes

protected

Referenced by createMetabolite(), createSBMLDocument(), and replaceSpeciesReferences().

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ CSBMLExporter()

◆ ~CSBMLExporter()

Member Function Documentation

◆ addInitialAssignmentsToModel()

◆ assignSBMLIdsToReactions()

◆ checkForEvents()

◆ checkForInitialAssignments()

◆ checkForODESpeciesInNonfixedCompartment()

◆ checkForPiecewiseFunctions() [1/2]

◆ checkForPiecewiseFunctions() [2/2]

◆ checkForUnsupportedFunctionCalls() [1/2]

◆ checkForUnsupportedFunctionCalls() [2/2]

◆ checkForUnsupportedObjectReferences() [1/2]

◆ checkForUnsupportedObjectReferences() [2/2]

◆ clearCallBack()

◆ collectIds()

◆ convert_to_l1v1()

◆ convertASTTreeToLevel1()

◆ convertToASTNode()

◆ convertToLevel1()

◆ createAreaUnit()

◆ createAvogadroIfNeeded()

◆ createCompartment()

◆ createCompartments()

◆ createEvent()

◆ createEvents()

◆ createFunctionDefinition()

◆ createFunctionDefinitions()

◆ createFunctionSetFromFunctionNames()

◆ createIdMap()

◆ createInitialAssignment()

◆ createInitialAssignments()

◆ createKineticExpression()

◆ createKineticLaw()

◆ createLengthUnit()

◆ createMassActionExpression()

◆ createMetabolite()

◆ createMetabolites()

◆ createParameter()

◆ createParameters()

◆ createProgressStepOrStop()

◆ createReaction()

◆ createReactions()

◆ createRule()

◆ createRules()

◆ createSBMLDocument()

◆ createSBMLNotes()

◆ createSubstanceUnit()

◆ createTimesTree()

◆ createTimeUnit()

◆ createUniqueId()

◆ createUnitDefinitionFor()

◆ createUnits()

◆ createUnsupportedFunctionTypeSet()

◆ createVolumeUnit()

◆ disownSBMLDocument()

◆ exportAndAssignUnit()

◆ exportEventAssignments()

◆ exportLayout()

◆ exportModel()

◆ exportModelToString()

◆ findAvogadro()

◆ findDirectlyUsedFunctions()

◆ findModelEntityDependencies()

◆ findUsedFunctions()

◆ finishCurrentStep()

◆ finishExport()

◆ getCallBack()

◆ getCOPASI2SBMLMap()

◆ getSBMLDocument()

◆ hasVolumeAssignment()

◆ isDividedByVolume()

◆ isEventAssignmentSBMLCompatible()

◆ isEventSBMLCompatible()