CSBMLExporter Member List

This is the complete list of members for CSBMLExporter, including all inherited members.

addInitialAssignmentsToModel(const CDataModel &dataModel)	CSBMLExporter	protected
assignSBMLIdsToReactions(CModel *pModel)	CSBMLExporter	protected
checkForEvents(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
checkForInitialAssignments(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
checkForODESpeciesInNonfixedCompartment(const CDataModel &dataModel, std::vector< SBMLIncompatibility > result)	CSBMLExporter	protectedstatic
checkForPiecewiseFunctions(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
checkForPiecewiseFunctions(const CEvaluationNode &node, std::vector< SBMLIncompatibility > &result, const std::string &objectName, const std::string &objectType)	CSBMLExporter	protectedstatic
checkForUnsupportedFunctionCalls(const CDataModel &dataModel, unsigned int sbmlLEvel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protected
checkForUnsupportedFunctionCalls(const CEvaluationNode &node, const std::set< CEvaluationNode::SubType > &unsupportedFunctions, std::vector< SBMLIncompatibility > &result, const std::string &objectDescription)	CSBMLExporter	protectedstatic
checkForUnsupportedObjectReferences(const CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protected
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)	CSBMLExporter	protectedstatic
clearCallBack()	CSBMLExporter	virtual
collectIds(const CDataModel &dataModel, std::map< std::string, const SBase * > &idMap)	CSBMLExporter	protected
convert_to_l1v1(std::string &l1v2_string)	CSBMLExporter	protectedstatic
convertASTTreeToLevel1(const ASTNode *pNode, const ListOfFunctionDefinitions &functions, std::string &message)	CSBMLExporter	protectedstatic
convertToASTNode(const CEvaluationNode *pOrig, CDataModel &dataModel)	CSBMLExporter	protected
convertToLevel1()	CSBMLExporter	protected
createAreaUnit(const CDataModel &dataModel)	CSBMLExporter	protected
createAvogadroIfNeeded(const CDataModel &dataModel)	CSBMLExporter	protected
createCompartment(const CCompartment &compartment)	CSBMLExporter	protected
createCompartments(CDataModel &dataModel)	CSBMLExporter	protected
createEvent(const CEvent &event, Event *pSBMLEvent, CDataModel &dataModel)	CSBMLExporter	protected
createEvents(CDataModel &dataModel)	CSBMLExporter	protected
createFunctionDefinition(CFunction &function, CDataModel &dataModel)	CSBMLExporter	protected
createFunctionDefinitions(CDataModel &dataModel)	CSBMLExporter	protected
createFunctionSetFromFunctionNames(const std::set< std::string > &names, CFunctionDB *pFunDB)	CSBMLExporter	protectedstatic
createIdMap(const Model &sbmlModel)	CSBMLExporter	protected
createInitialAssignment(const CModelEntity &modelEntity, CDataModel &dataModel)	CSBMLExporter	protected
createInitialAssignments(CDataModel &dataModel)	CSBMLExporter	protected
createKineticExpression(CFunction *pFun, const std::vector< std::vector< const CDataObject * > > &arguments)	CSBMLExporter	protected
createKineticLaw(const CReaction &reaction, CDataModel &dataModel, unsigned int level, unsigned int version)	CSBMLExporter	protected
createLengthUnit(const CDataModel &dataModel)	CSBMLExporter	protected
createMassActionExpression(const std::vector< std::vector< const CDataObject * > > &arguments, bool isReversible)	CSBMLExporter	protectedstatic
createMetabolite(const CMetab &metab)	CSBMLExporter	protected
createMetabolites(CDataModel &dataModel)	CSBMLExporter	protected
createParameter(const CModelValue &parameter)	CSBMLExporter	protected
createParameters(CDataModel &dataModel)	CSBMLExporter	protected
createProgressStepOrStop(unsigned C_INT32 globalStep, unsigned C_INT32 currentTotal, const std::string &title)	CSBMLExporter
createReaction(const CReaction &reaction, CDataModel &dataModel)	CSBMLExporter	protected
createReactions(CDataModel &dataModel)	CSBMLExporter	protected
createRule(const CModelEntity &modelEntity, CDataModel &dataModel, Rule *pOldRule)	CSBMLExporter	protected
createRules(CDataModel &dataModel)	CSBMLExporter	protected
createSBMLDocument(CDataModel &dataModel)	CSBMLExporter	protected
createSBMLNotes(const std::string &notes_string)	CSBMLExporter	static
createSubstanceUnit(const CDataModel &dataModel)	CSBMLExporter	protected
createTimesTree(const CDataVector< CChemEqElement > &vect, unsigned int pos=0)	CSBMLExporter	protectedstatic
createTimeUnit(const CDataModel &dataModel)	CSBMLExporter	protected
createUniqueId(const std::map< std::string, const SBase * > &idMap, const std::string &prefix, bool addIndexForFirst, const std::string &separator="_")	CSBMLExporter	static
createUnitDefinitionFor(const CUnit &unit)	CSBMLExporter	protected
createUnits(const CDataModel &dataModel)	CSBMLExporter	protected
createUnsupportedFunctionTypeSet(unsigned int sbmlLevel)	CSBMLExporter	protectedstatic
createVolumeUnit(const CDataModel &dataModel)	CSBMLExporter	protected
CSBMLExporter()	CSBMLExporter
disownSBMLDocument()	CSBMLExporter
exportAndAssignUnit(const CUnit &unit, SBase *sbmlElement)	CSBMLExporter	protected
exportEventAssignments(const CEvent &event, Event *pSBMLEvent, CDataModel &dataModel)	CSBMLExporter	protected
exportLayout(unsigned int sbmlLevel, CDataModel &dataModel)	CSBMLExporter
exportModel(CDataModel &dataModel, const std::string &filename, unsigned int sbmlLevel=2, unsigned int sbmlVersion=1, bool overwrite=false)	CSBMLExporter
exportModelToString(CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion)	CSBMLExporter
findAvogadro(const CDataModel &dataModel)	CSBMLExporter	protected
findDirectlyUsedFunctions(const CEvaluationNode *pRootNode, std::set< std::string > &result)	CSBMLExporter	protectedstatic
findModelEntityDependencies(const CEvaluationNode *pNode, const CDataModel &dataModel, std::set< const CModelEntity * > &dependencies)	CSBMLExporter	protectedstatic
findUsedFunctions(std::set< CFunction * > &functions, CFunctionDB *pFunctionDB)	CSBMLExporter	protectedstatic
finishCurrentStep()	CSBMLExporter
finishExport()	CSBMLExporter
getCallBack() const	CSBMLExporter
getCOPASI2SBMLMap() const	CSBMLExporter
getSBMLDocument()	CSBMLExporter
hasVolumeAssignment(const CDataModel &dataModel)	CSBMLExporter	protected
isDividedByVolume(const ASTNode *pRootNode, const std::string &compartmentId)	CSBMLExporter	protectedstatic
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)	CSBMLExporter	protectedstatic
isEventSBMLCompatible(const CEvent *pEvent, const CDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result, std::map< std::string, const SBase * > &idMap)	CSBMLExporter	protectedstatic
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)	CSBMLExporter	protectedstatic
isExpressionSBMLL1Compatible(const CEvaluationTree &expr, const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
isExpressionSBMLL2V1Compatible(const CEvaluationTree &expr, const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
isExpressionSBMLL2V3Compatible(const CEvaluationTree &expression, const CDataModel &pDataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
isModelSBMLCompatible(const CDataModel &pDataModel, int sbmlLevel, int sbmlVersion, std::map< std::string, const SBase * > &idMap)	CSBMLExporter	static
isModelSBMLL1Compatible(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
isModelSBMLL2V1Compatible(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
isModelSBMLL2V3Compatible(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	CSBMLExporter	protectedstatic
isSetExportCOPASIMIRIAM() const	CSBMLExporter
isValidSId(const std::string &id)	CSBMLExporter	protectedstatic
mAssignmentVector	CSBMLExporter	protected
mAvogadroCreated	CSBMLExporter	protected
mAvogadroId	CSBMLExporter	protected
mCOPASI2SBMLMap	CSBMLExporter	protected
mCurrentStepCounter	CSBMLExporter	protected
mCurrentStepHandle	CSBMLExporter	protected
mCurrentStepTotal	CSBMLExporter	protected
mDocumentDisowned	CSBMLExporter	protected
mExportCOPASIMIRIAM	CSBMLExporter	protected
mExportedFunctions	CSBMLExporter	protected
mFunctionIdMap	CSBMLExporter	protected
mFunctionMap	CSBMLExporter	protected
mGlobalStepCounter	CSBMLExporter	protected
mGlobalStepHandle	CSBMLExporter	protected
mGlobalStepTotal	CSBMLExporter	protected
mHandledSBMLObjects	CSBMLExporter	protected
mIdMap	CSBMLExporter	protected
mIncompatibilities	CSBMLExporter	protected
mIncompleteExport	CSBMLExporter	protected
mInitialAssignmentVector	CSBMLExporter	protected
mInitialValueMap	CSBMLExporter	protected
mMetaIdMap	CSBMLExporter	protected
mMIRIAMWarning	CSBMLExporter	protected
mODEVector	CSBMLExporter	protected
mParameterReplacementMap	CSBMLExporter	protected
mpAvogadro	CSBMLExporter	protected
mpProcessReport	CSBMLExporter	protected
mpSBMLDocument	CSBMLExporter	protected
mSBMLLevel	CSBMLExporter	protected
mSBMLVersion	CSBMLExporter	protected
mSpatialSizeUnitsSpecies	CSBMLExporter	protected
multiplyByObject(const CEvaluationNode *pOrigNode, const CDataObject *pObject)	CSBMLExporter	protectedstatic
mUsedFunctions	CSBMLExporter	protected
mVariableVolumes	CSBMLExporter	protected
orderRules(const CDataModel &dataModel)	CSBMLExporter	protected
outputIncompatibilities() const	CSBMLExporter	protected
removeInitialAssignment(const std::string &sbmlId)	CSBMLExporter	protected
removeRule(const std::string &sbmlId)	CSBMLExporter	protected
removeUnusedObjects()	CSBMLExporter	protected
replace_local_parameters(ASTNode *pOrigNode, const CDataModel &dataModel)	CSBMLExporter	protected
replaceChild(const XMLNode *pParent, const XMLNode *pNewChild, unsigned int index)	CSBMLExporter	protected
replaceL1IncompatibleNodes(const ASTNode *pNode)	CSBMLExporter	protectedstatic
replaceSpeciesReferences(const CEvaluationNode *pOrigNode, const CDataModel &dataModel)	CSBMLExporter	protected
reportCurrentProgressOrStop()	CSBMLExporter
restore_local_parameters(ASTNode *pOrigNode, const CDataModel &dataModel)	CSBMLExporter	protected
setExportCOPASIMIRIAM(bool exportMIRIAM)	CSBMLExporter
setFunctionSBMLIds(const CEvaluationNode *pNode, CDataModel &dataModel)	CSBMLExporter	protected
setHandler(CProcessReport *pProcessReport)	CSBMLExporter
setSBMLNotes(SBase *pSBase, const CAnnotation *pAnno)	CSBMLExporter	protectedstatic
updateCOPASI2SBMLMap(const CDataModel &dataModel)	CSBMLExporter	protected
updateMIRIAMAnnotation(const CDataObject *pCOPASIObject, SBase *pSBMLObject, std::map< std::string, const SBase * > &metaIds)	CSBMLExporter	protected
~CSBMLExporter()	CSBMLExporter