COPASI API  4.16.103
CSBMLExporter Member List

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

assignSBMLIdsToReactions(CModel *pModel)CSBMLExporterprotected
check_for_spatial_size_units(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
checkForEvents(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
checkForInitialAssignments(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
checkForODESpeciesInNonfixedCompartment(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > result)CSBMLExporterprotectedstatic
checkForPiecewiseFunctions(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
checkForPiecewiseFunctions(const CEvaluationNode &node, std::vector< SBMLIncompatibility > &result, const std::string &objectName, const std::string &objectType)CSBMLExporterprotectedstatic
checkForUnsupportedFunctionCalls(const CCopasiDataModel &dataModel, unsigned int sbmlLEvel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotected
checkForUnsupportedFunctionCalls(const CEvaluationNode &node, const std::set< CEvaluationNodeFunction::SubType > &unsupportedFunctions, std::vector< SBMLIncompatibility > &result, const std::string &objectDescription)CSBMLExporterprotectedstatic
checkForUnsupportedObjectReferences(const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotected
checkForUnsupportedObjectReferences(const CEvaluationTree &expression, const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result, bool initialExpression=false, std::map< const std::string, Parameter * > *initialMap=NULL)CSBMLExporterprotectedstatic
collectIds(const CCopasiDataModel &dataModel, std::map< std::string, const SBase * > &idMap)CSBMLExporterprotected
convert_to_l1v1(std::string &l1v2_string)CSBMLExporterprotectedstatic
convertASTTreeToLevel1(const ASTNode *pNode, const ListOfFunctionDefinitions &functions, std::string &message)CSBMLExporterprotectedstatic
convertToASTNode(const CEvaluationNode *pOrig, CCopasiDataModel &dataModel)CSBMLExporterprotected
convertToLevel1()CSBMLExporterprotected
createAreaUnit(const CCopasiDataModel &dataModel)CSBMLExporterprotected
createCompartment(CCompartment &compartment)CSBMLExporterprotected
createCompartments(CCopasiDataModel &dataModel)CSBMLExporterprotected
createEvent(CEvent &event, Event *pSBMLEvent, CCopasiDataModel &dataModel)CSBMLExporterprotected
createEvents(CCopasiDataModel &dataModel)CSBMLExporterprotected
createFunctionDefinition(CFunction &function, CCopasiDataModel &dataModel)CSBMLExporterprotected
createFunctionDefinitions(CCopasiDataModel &dataModel)CSBMLExporterprotected
createFunctionSetFromFunctionNames(const std::set< std::string > &names, CFunctionDB *pFunDB)CSBMLExporterprotectedstatic
createIdMap(const Model &sbmlModel)CSBMLExporterprotected
createInitialAssignment(const CModelEntity &modelEntity, CCopasiDataModel &dataModel)CSBMLExporterprotected
createInitialAssignments(CCopasiDataModel &dataModel)CSBMLExporterprotected
createKineticExpression(CFunction *pFun, const std::vector< std::vector< std::string > > &arguments)CSBMLExporterprotected
createKineticLaw(CReaction &reaction, CCopasiDataModel &dataModel, unsigned int level, unsigned int version)CSBMLExporterprotected
createLengthUnit(const CCopasiDataModel &dataModel)CSBMLExporterprotected
createMassActionExpression(const std::vector< std::vector< std::string > > &arguments, bool isReversible)CSBMLExporterprotectedstatic
createMetabolite(CMetab &metab)CSBMLExporterprotected
createMetabolites(CCopasiDataModel &dataModel)CSBMLExporterprotected
createParameter(CModelValue &parameter)CSBMLExporterprotected
createParameters(CCopasiDataModel &dataModel)CSBMLExporterprotected
createReaction(CReaction &reaction, CCopasiDataModel &dataModel)CSBMLExporterprotected
createReactions(CCopasiDataModel &dataModel)CSBMLExporterprotected
createRule(const CModelEntity &modelEntity, CCopasiDataModel &dataModel, Rule *pOldRule)CSBMLExporterprotected
createRules(CCopasiDataModel &dataModel)CSBMLExporterprotected
createSBMLDocument(CCopasiDataModel &dataModel)CSBMLExporterprotected
createSubstanceUnit(const CCopasiDataModel &dataModel)CSBMLExporterprotected
createTimesTree(const CCopasiVector< CChemEqElement > &vect, unsigned int pos=0)CSBMLExporterprotectedstatic
createTimeUnit(const CCopasiDataModel &dataModel)CSBMLExporterprotected
createUniqueId(const std::map< std::string, const SBase * > &idMap, const std::string &prefix, bool addIndexForFirst, const std::string &separator="_")CSBMLExporterstatic
createUnits(const CCopasiDataModel &dataModel)CSBMLExporterprotected
createUnsupportedFunctionTypeSet(unsigned int sbmlLevel)CSBMLExporterprotectedstatic
createVolumeUnit(const CCopasiDataModel &dataModel)CSBMLExporterprotected
CSBMLExporter()CSBMLExporter
disownSBMLDocument()CSBMLExporter
exportEventAssignments(const CEvent &event, Event *pSBMLEvent, CCopasiDataModel &dataModel)CSBMLExporterprotected
exportModel(CCopasiDataModel &dataModel, const std::string &filename, unsigned int sbmlLevel=2, unsigned int sbmlVersion=1, bool overwrite=false)CSBMLExporter
exportModelToString(CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion)CSBMLExporter
findAvogadro(const CCopasiDataModel &dataModel)CSBMLExporterprotected
findDirectlyUsedFunctions(const CEvaluationNode *pRootNode, std::set< std::string > &result)CSBMLExporterprotectedstatic
findModelEntityDependencies(const CEvaluationNode *pNode, const CCopasiDataModel &dataModel, std::set< const CModelEntity * > &dependencies)CSBMLExporterprotectedstatic
findUsedFunctions(std::set< CFunction * > &functions, CFunctionDB *pFunctionDB)CSBMLExporterprotectedstatic
getCOPASI2SBMLMap() const CSBMLExporter
getSBMLDocument()CSBMLExporterinline
hasVolumeAssignment(const CCopasiDataModel &dataModel)CSBMLExporterprotected
isDividedByVolume(const ASTNode *pRootNode, const std::string &compartmentId)CSBMLExporterprotectedstatic
isEventAssignmentSBMLCompatible(std::string &key, const CExpression *pExpression, const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, const std::string &eventName, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isEventSBMLCompatible(const CEvent *pEvent, const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isExpressionSBMLCompatible(const CEvaluationTree &expr, const CCopasiDataModel &dataModel, int sbmlLevel, int sbmlVersion, std::vector< SBMLIncompatibility > &result, const std::string &objectDescription, bool initialExression=false, std::map< const std::string, Parameter * > *initialMap=NULL)CSBMLExporterprotectedstatic
isExpressionSBMLL1Compatible(const CEvaluationTree &expr, const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isExpressionSBMLL2V1Compatible(const CEvaluationTree &expr, const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isExpressionSBMLL2V3Compatible(const CEvaluationTree &expression, const CCopasiDataModel &pDataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isModelSBMLCompatible(const CCopasiDataModel &pDataModel, int sbmlLevel, int sbmlVersion)CSBMLExporterstatic
isModelSBMLL1Compatible(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isModelSBMLL2V1Compatible(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isModelSBMLL2V3Compatible(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result)CSBMLExporterprotectedstatic
isSetExportCOPASIMIRIAM() const CSBMLExporter
isValidSId(const std::string &id)CSBMLExporterprotectedstatic
mAssignmentVectorCSBMLExporterprotected
mAvogadroCreatedCSBMLExporterprotected
mCOPASI2SBMLMapCSBMLExporterprotected
mDocumentDisownedCSBMLExporterprotected
mExportCOPASIMIRIAMCSBMLExporterprotected
mExportedFunctionsCSBMLExporterprotected
mFunctionIdMapCSBMLExporterprotected
mFunctionMapCSBMLExporterprotected
mHandledSBMLObjectsCSBMLExporterprotected
mHaveModelHistoryAuthorWarningCSBMLExporterprotected
mHaveModelHistoryCreationDateWarningCSBMLExporterprotected
mHaveModelHistoryModificationDateWarningCSBMLExporterprotected
mIdMapCSBMLExporterprotected
mIncompatibilitiesCSBMLExporterprotected
mIncompleteExportCSBMLExporterprotected
mInitialAssignmentVectorCSBMLExporterprotected
mInitialValueMapCSBMLExporterprotected
mMetaIdMapCSBMLExporterprotected
mMIRIAMWarningCSBMLExporterprotected
mODEVectorCSBMLExporterprotected
mParameterReplacementMapCSBMLExporterprotected
mpAvogadroCSBMLExporterprotected
mpSBMLDocumentCSBMLExporterprotected
mSBMLLevelCSBMLExporterprotected
mSBMLVersionCSBMLExporterprotected
mSpatialSizeUnitsSpeciesCSBMLExporterprotected
multiplyByObject(const CEvaluationNode *pOrigNode, const CCopasiObject *pObject)CSBMLExporterprotectedstatic
mUsedFunctionsCSBMLExporterprotected
mVariableVolumesCSBMLExporterprotected
orderRules(const CCopasiDataModel &dataModel)CSBMLExporterprotected
outputIncompatibilities() const CSBMLExporterprotected
removeInitialAssignment(const std::string &sbmlId)CSBMLExporterprotected
removeRule(const std::string &sbmlId)CSBMLExporterprotected
removeUnusedObjects()CSBMLExporterprotected
replace_local_parameters(ASTNode *pOrigNode, const CCopasiDataModel &dataModel)CSBMLExporterprotected
replaceChild(const XMLNode *pParent, const XMLNode *pNewChild, unsigned int index)CSBMLExporterprotected
replaceL1IncompatibleNodes(const ASTNode *pNode)CSBMLExporterprotectedstatic
replaceSpeciesReferences(const CEvaluationNode *pOrigNode, const CCopasiDataModel &dataModel)CSBMLExporterprotected
restore_local_parameters(ASTNode *pOrigNode, const CCopasiDataModel &dataModel)CSBMLExporterprotected
setExportCOPASIMIRIAM(bool exportMIRIAM)CSBMLExporter
setFunctionSBMLIds(const CEvaluationNode *pNode, CCopasiDataModel &dataModel)CSBMLExporterprotected
setSBMLNotes(SBase *pSBase, const CAnnotation *pAnno)CSBMLExporterprotectedstatic
updateCOPASI2SBMLMap(const CCopasiDataModel &dataModel)CSBMLExporterprotected
updateMIRIAMAnnotation(const CCopasiObject *pCOPASIObject, SBase *pSBMLObject, std::map< std::string, const SBase * > &metaIds)CSBMLExporterprotected
~CSBMLExporter()CSBMLExporter