COPASI API  4.16.103
SBMLImporter Member List

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

applyStoichiometricExpressions(std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)SBMLImporterprotected
areApproximatelyEqual(const double &x, const double &y, const double &t=1e-9)SBMLImporterprotectedstatic
areEqualFunctions(const CFunction *pFun, const CFunction *pFun2)SBMLImporterstatic
areEqualSubtrees(const CEvaluationNode *pNode1, const CEvaluationNode *pNode2)SBMLImporterstatic
areRulesUnique(const Model *copasiMode)SBMLImporterprotected
areSBMLUnitDefinitionsIdentical(const UnitDefinition *pUdef1, const UnitDefinition *pUdef2)SBMLImporterstatic
checkElementUnits(const Model *pSBMLModel, CModel *pCopasiModel, int level, int version)SBMLImporterprotected
checkRuleMathConsistency(const Rule *pRule, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
containsVolume(const ASTNode *pNode, const std::string &compartmentCN)SBMLImporterprotected
convertSBMLCubicmetresToLitres(const Unit *pU)SBMLImporterprotectedstatic
createBVarMap(const ASTNode *uDefFunction, const ASTNode *function)SBMLImporterprotected
createCCompartmentFromCompartment(const Compartment *sbmlComp, CModel *copasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, const Model *pSBMLModel)SBMLImporterprotected
createCFunctionFromFunctionDefinition(const FunctionDefinition *sbmlFunction, CFunctionDB *pTmpFunctionDB, Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
createCFunctionFromFunctionTree(const FunctionDefinition *pSBMLFunction, Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
createCMetabFromSpecies(const Species *sbmlSpecies, CModel *copasiModel, CCompartment *copasiCompartment, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, const Model *pSBMLModel)SBMLImporterprotected
createCModelFromSBMLDocument(SBMLDocument *doc, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
createCModelValueFromParameter(const Parameter *sbmlParameter, CModel *copasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
createCReactionFromReaction(Reaction *sbmlReaction, Model *sbmlModel, CModel *cmodel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CFunctionDB *pTmpFunctionDB)SBMLImporterprotected
createDelayFunctionDefinition()SBMLImporterprotected
createExpressionFromFunction(const CFunction *pFun, const std::vector< std::vector< std::string > > &functionArgumentCNs)SBMLImporterprotected
createHasOnlySubstanceUnitFactor(Model *pSBMLModel, double factor, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
deleteCopasiModel()SBMLImporter
divideByObject(const CEvaluationNode *pOrigNode, const CCopasiObject *pObject)SBMLImporterstatic
doMapping(CReaction *pCopasiReaction, const CEvaluationNodeCall *pCallNode)SBMLImporterprotected
find_local_parameters_in_delay(ASTNode *pNode, Reaction *pSBMLReaction, Model *pModel, std::map< std::string, std::string > &localReplacementMap, const std::set< std::string > &localIds, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
findAvogadroConstant(Model *pSBMLModel, double factor)SBMLImporterprotected
findCorrespondingFunction(const CExpression *pExpression, const CReaction *reaction)SBMLImporterprotected
findDirectDependencies(const FunctionDefinition *pFunDef, std::map< const FunctionDefinition *, std::set< std::string > > &dependencies)SBMLImporterprotectedstatic
findDirectDependencies(const ASTNode *pNode, std::set< std::string > &dependencies)SBMLImporterprotectedstatic
findFunctionCalls(const CEvaluationNode *pNode, std::set< std::string > &functionNameSet)SBMLImporterprotected
findIdInASTTree(const ASTNode *pMath, const std::set< std::string > &reactionIds)SBMLImporter
findIdInASTTree(const ASTNode *pMath, const std::map< std::string, double > &reactionIds)SBMLImporter
functionDBSBMLImporterprotected
getFunctionDefinitionForName(const std::string name, const Model *model)SBMLImporterprotected
getIdsFromNode(const ASTNode *pNode, std::set< std::string > &idSet)SBMLImporterprotected
getImportCOPASIMIRIAM() const SBMLImporter
getImportHandlerAddr()SBMLImporter
getSBMLUnitDefinitionForId(const std::string &unitId, const Model *pSBMLModel)SBMLImporterstatic
handleAreaUnit(const UnitDefinition *uDef)SBMLImporterprotected
handleLengthUnit(const UnitDefinition *uDef)SBMLImporterprotected
handleSubstanceUnit(const UnitDefinition *uDef)SBMLImporterprotected
handleTimeUnit(const UnitDefinition *uDef)SBMLImporterprotected
handleVolumeUnit(const UnitDefinition *uDef)SBMLImporterprotected
importEvent(const Event *pEvent, Model *pSBMLModel, CModel *pCopasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
importEvents(Model *pSBMLModel, CModel *pCopasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
importFunctionDefinitions(Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
importInitialAssignments(Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlMap, const CModel *pCOPASIModel)SBMLImporterprotected
importMIRIAM(const SBase *pSBMLObject, CCopasiObject *pCOPASIObject)SBMLImporterprotected
importNotes(CAnnotation *pAnno, const SBase *pSBase)SBMLImporterstatic
importRule(const Rule *rule, CModelEntity::Status ruleType, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)SBMLImporterprotected
importRuleForModelEntity(const Rule *rule, CModelEntity *pMV, CModelEntity::Status ruleType, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)SBMLImporterprotected
importSBMLRule(const Rule *sbmlRule, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)SBMLImporterprotected
isConstantFlux(const CEvaluationNode *pRoot, CModel *pModel, CFunctionDB *pFunctionDB)SBMLImporterprotected
isDelayFunctionUsed(ConverterASTNode *pNode)SBMLImporterprotected
isMassAction(const CEvaluationTree *pTree, const CChemEq &chemicalEquation, const CEvaluationNodeCall *pCallNode=NULL)SBMLImporterprotected
isMassActionExpression(const CEvaluationNode *pRootNode, const CChemEq &chemicalEquation)SBMLImporterprotected
isMassActionFunction(const CFunction *pFun, const CChemEq &chemicalEquation, const std::vector< std::vector< std::string > > &functionArgumentCNs)SBMLImporterprotected
isMultipliedByVolume(const ASTNode *node, const std::string &compartmentSBMLId)SBMLImporterprotected
isSimpleFunctionCall(const CEvaluationNode *pRootNode)SBMLImporterprotected
isStochasticModel(const Model *pSBMLModel)SBMLImporterprotected
mAssignmentToSpeciesReferenceFoundSBMLImporterprotected
mAvogadroCreatedSBMLImporterprotected
mAvogadroSetSBMLImporterprotected
mDelayFoundSBMLImporterprotected
mDelayNodeMapSBMLImporterprotected
mDivisionByCompartmentReactionsSBMLImporterprotected
mExplicitelyTimeDependentFunctionDefinitionsSBMLImporterprotected
mFastReactionsSBMLImporterprotected
mFunctionNameMappingSBMLImporterprotected
mhImportStepSBMLImporterprotected
mIgnoredParameterUnitsSBMLImporterprotected
mIgnoredSBMLMessagesSBMLImporterprotected
mImportCOPASIMIRIAMSBMLImporterprotected
mImportStepSBMLImporterprotected
mIncompleteModelSBMLImporterprotected
mKnownCustomUserDefinedFunctionsSBMLImporterprotected
mKnownInitalValuesSBMLImporterprotected
mLevelSBMLImporterprotected
mOriginalLevelSBMLImporterprotected
mpCopasiModelSBMLImporterprotected
mpDataModelSBMLImporterprotected
mpImportHandlerSBMLImporterprotected
mPotentialAvogadroNumbersSBMLImporterprotected
mReactionsWithReplacedLocalParametersSBMLImporterprotected
mStoichiometricExpressionMapSBMLImporterprotected
mSubstanceOnlySpeciesSBMLImporterprotected
mTotalStepsSBMLImporterprotected
multiplySubstanceOnlySpeciesByVolume(ConverterASTNode *pNode)SBMLImporterprotected
mUnitOnNumberFoundSBMLImporterprotected
mUnsupportedAssignmentRuleFoundSBMLImporterprotected
mUnsupportedRateRuleFoundSBMLImporterprotected
mUnsupportedRuleFoundSBMLImporterprotected
mUsedFunctionsSBMLImporterprotected
mUsedSBMLIdsSBMLImporterprotected
mUsedSBMLIdsPopulatedSBMLImporterprotected
mVersionSBMLImporterprotected
normalizeSBMLUnit(Unit *pU)SBMLImporterprotectedstatic
parseSBML(const std::string &sbmlDocumentText, CFunctionDB *funDB, SBMLDocument *&pSBMLDocument, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CListOfLayouts *&prLol, CCopasiDataModel *pDataModel)SBMLImporter
preprocessNode(ConverterASTNode *pNode, Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Reaction *pSBMLReaction=NULL)SBMLImporterprotected
readSBML(std::string filename, CFunctionDB *funDB, SBMLDocument *&pSBMLDocument, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CListOfLayouts *&prLol, CCopasiDataModel *pDataModel)SBMLImporter
removeUnusedFunctions(CFunctionDB *pTmpFunctionDB, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
renameMassActionParameters(CEvaluationNodeCall *pCallNode)SBMLImporterprotected
replace_delay_nodes(ConverterASTNode *pNode, Model *pModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Reaction *pSBMLReaction, std::map< std::string, std::string > &localReplacementMap)SBMLImporterprotected
replace_name_nodes(ASTNode *pNode, const std::map< std::string, std::string > &replacementMap)SBMLImporterprotected
replace_time_with_initial_time(ASTNode *pNode, const CModel *pCOPASIModel)SBMLImporterprotected
replaceAmountReferences(ConverterASTNode *pNode, Model *pSBMLModel, double factor, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
replaceCallNodeNames(ASTNode *pNode)SBMLImporterprotected
replaceLog(ConverterASTNode *sourceNode)SBMLImporterprotected
replaceObjectNames(ASTNode *pNode, const std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, bool initialExpression=false)SBMLImporterprotected
replacePowerFunctionNodes(ASTNode *node)SBMLImporterprotected
replaceRoot(ConverterASTNode *sourceNode)SBMLImporterprotected
replaceTimeAndAvogadroNodeNames(ASTNode *pNode)SBMLImporterprotected
replaceTimeDependentFunctionCalls(ASTNode *root)SBMLImporterprotected
replaceTimeNodesInFunctionDefinition(ASTNode *root, std::string newNodeName)SBMLImporterprotected
restoreFunctionDB()SBMLImporter
round(const C_FLOAT64 &x)SBMLImporterprotectedstatic
sbmlId2CopasiCN(ASTNode *pNode, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CCopasiParameterGroup &pParamGroup)SBMLImporterprotected
sbmlIdMapSBMLImporterprotected
SBMLImporter()SBMLImporter
separateProductArguments(const CEvaluationNode *pRootNode, std::vector< const CEvaluationNode * > &arguments)SBMLImporterprotected
setCorrectUsage(CReaction *pCopasiReaction, const CEvaluationNodeCall *pCallNode)SBMLImporterprotected
setImportCOPASIMIRIAM(bool import)SBMLImporter
setImportHandler(CProcessReport *pHandler)SBMLImporter
setInitialValues(CModel *pModel, const std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)SBMLImporterprotected
speciesMapSBMLImporterprotected
variables2objects(const CEvaluationNode *pOrigNode, const std::map< std::string, std::string > &replacementMap)SBMLImporterprotected
~SBMLImporter()SBMLImporter