COPASI API
4.16.103
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This is the complete list of members for CSBMLExporter, including all inherited members.
assignSBMLIdsToReactions(CModel *pModel) | CSBMLExporter | protected |
check_for_spatial_size_units(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
checkForEvents(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
checkForInitialAssignments(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
checkForODESpeciesInNonfixedCompartment(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > result) | CSBMLExporter | protectedstatic |
checkForPiecewiseFunctions(const CCopasiDataModel &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 CCopasiDataModel &dataModel, unsigned int sbmlLEvel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protected |
checkForUnsupportedFunctionCalls(const CEvaluationNode &node, const std::set< CEvaluationNodeFunction::SubType > &unsupportedFunctions, std::vector< SBMLIncompatibility > &result, const std::string &objectDescription) | CSBMLExporter | protectedstatic |
checkForUnsupportedObjectReferences(const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protected |
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) | CSBMLExporter | protectedstatic |
collectIds(const CCopasiDataModel &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, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
convertToLevel1() | CSBMLExporter | protected |
createAreaUnit(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createCompartment(CCompartment &compartment) | CSBMLExporter | protected |
createCompartments(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createEvent(CEvent &event, Event *pSBMLEvent, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createEvents(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createFunctionDefinition(CFunction &function, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createFunctionDefinitions(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createFunctionSetFromFunctionNames(const std::set< std::string > &names, CFunctionDB *pFunDB) | CSBMLExporter | protectedstatic |
createIdMap(const Model &sbmlModel) | CSBMLExporter | protected |
createInitialAssignment(const CModelEntity &modelEntity, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createInitialAssignments(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createKineticExpression(CFunction *pFun, const std::vector< std::vector< std::string > > &arguments) | CSBMLExporter | protected |
createKineticLaw(CReaction &reaction, CCopasiDataModel &dataModel, unsigned int level, unsigned int version) | CSBMLExporter | protected |
createLengthUnit(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createMassActionExpression(const std::vector< std::vector< std::string > > &arguments, bool isReversible) | CSBMLExporter | protectedstatic |
createMetabolite(CMetab &metab) | CSBMLExporter | protected |
createMetabolites(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createParameter(CModelValue ¶meter) | CSBMLExporter | protected |
createParameters(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createReaction(CReaction &reaction, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createReactions(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createRule(const CModelEntity &modelEntity, CCopasiDataModel &dataModel, Rule *pOldRule) | CSBMLExporter | protected |
createRules(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createSBMLDocument(CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createSubstanceUnit(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createTimesTree(const CCopasiVector< CChemEqElement > &vect, unsigned int pos=0) | CSBMLExporter | protectedstatic |
createTimeUnit(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createUniqueId(const std::map< std::string, const SBase * > &idMap, const std::string &prefix, bool addIndexForFirst, const std::string &separator="_") | CSBMLExporter | static |
createUnits(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
createUnsupportedFunctionTypeSet(unsigned int sbmlLevel) | CSBMLExporter | protectedstatic |
createVolumeUnit(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
CSBMLExporter() | CSBMLExporter | |
disownSBMLDocument() | CSBMLExporter | |
exportEventAssignments(const CEvent &event, Event *pSBMLEvent, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
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) | CSBMLExporter | protected |
findDirectlyUsedFunctions(const CEvaluationNode *pRootNode, std::set< std::string > &result) | CSBMLExporter | protectedstatic |
findModelEntityDependencies(const CEvaluationNode *pNode, const CCopasiDataModel &dataModel, std::set< const CModelEntity * > &dependencies) | CSBMLExporter | protectedstatic |
findUsedFunctions(std::set< CFunction * > &functions, CFunctionDB *pFunctionDB) | CSBMLExporter | protectedstatic |
getCOPASI2SBMLMap() const | CSBMLExporter | |
getSBMLDocument() | CSBMLExporter | inline |
hasVolumeAssignment(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
isDividedByVolume(const ASTNode *pRootNode, const std::string &compartmentId) | CSBMLExporter | protectedstatic |
isEventAssignmentSBMLCompatible(std::string &key, const CExpression *pExpression, const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, const std::string &eventName, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isEventSBMLCompatible(const CEvent *pEvent, const CCopasiDataModel &dataModel, unsigned int sbmlLevel, unsigned int sbmlVersion, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
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) | CSBMLExporter | protectedstatic |
isExpressionSBMLL1Compatible(const CEvaluationTree &expr, const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isExpressionSBMLL2V1Compatible(const CEvaluationTree &expr, const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isExpressionSBMLL2V3Compatible(const CEvaluationTree &expression, const CCopasiDataModel &pDataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isModelSBMLCompatible(const CCopasiDataModel &pDataModel, int sbmlLevel, int sbmlVersion) | CSBMLExporter | static |
isModelSBMLL1Compatible(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isModelSBMLL2V1Compatible(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isModelSBMLL2V3Compatible(const CCopasiDataModel &dataModel, std::vector< SBMLIncompatibility > &result) | CSBMLExporter | protectedstatic |
isSetExportCOPASIMIRIAM() const | CSBMLExporter | |
isValidSId(const std::string &id) | CSBMLExporter | protectedstatic |
mAssignmentVector | CSBMLExporter | protected |
mAvogadroCreated | CSBMLExporter | protected |
mCOPASI2SBMLMap | CSBMLExporter | protected |
mDocumentDisowned | CSBMLExporter | protected |
mExportCOPASIMIRIAM | CSBMLExporter | protected |
mExportedFunctions | CSBMLExporter | protected |
mFunctionIdMap | CSBMLExporter | protected |
mFunctionMap | CSBMLExporter | protected |
mHandledSBMLObjects | CSBMLExporter | protected |
mHaveModelHistoryAuthorWarning | CSBMLExporter | protected |
mHaveModelHistoryCreationDateWarning | CSBMLExporter | protected |
mHaveModelHistoryModificationDateWarning | 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 |
mpSBMLDocument | CSBMLExporter | protected |
mSBMLLevel | CSBMLExporter | protected |
mSBMLVersion | CSBMLExporter | protected |
mSpatialSizeUnitsSpecies | CSBMLExporter | protected |
multiplyByObject(const CEvaluationNode *pOrigNode, const CCopasiObject *pObject) | CSBMLExporter | protectedstatic |
mUsedFunctions | CSBMLExporter | protected |
mVariableVolumes | CSBMLExporter | protected |
orderRules(const CCopasiDataModel &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 CCopasiDataModel &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 CCopasiDataModel &dataModel) | CSBMLExporter | protected |
restore_local_parameters(ASTNode *pOrigNode, const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
setExportCOPASIMIRIAM(bool exportMIRIAM) | CSBMLExporter | |
setFunctionSBMLIds(const CEvaluationNode *pNode, CCopasiDataModel &dataModel) | CSBMLExporter | protected |
setSBMLNotes(SBase *pSBase, const CAnnotation *pAnno) | CSBMLExporter | protectedstatic |
updateCOPASI2SBMLMap(const CCopasiDataModel &dataModel) | CSBMLExporter | protected |
updateMIRIAMAnnotation(const CCopasiObject *pCOPASIObject, SBase *pSBMLObject, std::map< std::string, const SBase * > &metaIds) | CSBMLExporter | protected |
~CSBMLExporter() | CSBMLExporter |