SBMLImporter Member List

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

applyStoichiometricExpressions(std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	[protected]
areApproximatelyEqual(const double &x, const double &y, const double &t=1e-9)	SBMLImporter	[protected, static]
areEqualFunctions(const CFunction *pFun, const CFunction *pFun2)	SBMLImporter	[protected]
areEqualSubtrees(const CEvaluationNode *pNode1, const CEvaluationNode *pNode2)	SBMLImporter	[protected]
areRulesUnique(const Model *copasiMode)	SBMLImporter	[protected]
areSBMLUnitDefinitionsIdentical(const UnitDefinition *pUdef1, const UnitDefinition *pUdef2)	SBMLImporter	[static]
checkElementUnits(const Model *pSBMLModel, CModel *pCopasiModel, int level, int version)	SBMLImporter	[protected]
checkRuleMathConsistency(const Rule *pRule, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
containsVolume(const ASTNode *pNode, const std::string &compartmentCN)	SBMLImporter	[protected]
convertSBMLCubicmetresToLitres(const Unit *pU)	SBMLImporter	[protected, static]
createBVarMap(const ASTNode *uDefFunction, const ASTNode *function)	SBMLImporter	[protected]
createCCompartmentFromCompartment(const Compartment *sbmlComp, CModel *copasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, const Model *pSBMLModel)	SBMLImporter	[protected]
createCFunctionFromFunctionDefinition(const FunctionDefinition *sbmlFunction, CFunctionDB *pTmpFunctionDB, Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
createCFunctionFromFunctionTree(const FunctionDefinition *pSBMLFunction, Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
createCMetabFromSpecies(const Species *sbmlSpecies, CModel *copasiModel, CCompartment *copasiCompartment, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, const Model *pSBMLModel)	SBMLImporter	[protected]
createCModelFromSBMLDocument(SBMLDocument *doc, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
createCModelValueFromParameter(const Parameter *sbmlParameter, CModel *copasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
createCReactionFromReaction(Reaction *sbmlReaction, Model *sbmlModel, CModel *cmodel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CFunctionDB *pTmpFunctionDB)	SBMLImporter	[protected]
createDelayFunctionDefinition()	SBMLImporter	[protected]
createExpressionFromFunction(const CFunction *pFun, const std::vector< std::vector< std::string > > &functionArgumentCNs)	SBMLImporter	[protected]
createHasOnlySubstanceUnitFactor(Model *pSBMLModel, double factor, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
doMapping(CReaction *pCopasiReaction, const CEvaluationNodeCall *pCallNode)	SBMLImporter	[protected]
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)	SBMLImporter	[protected]
findAvogadroConstant(Model *pSBMLModel, double factor)	SBMLImporter	[protected]
findCorrespondingFunction(const CFunction *tree, const CReaction *reaction)	SBMLImporter	[protected]
findDirectDependencies(const FunctionDefinition *pFunDef, std::map< const FunctionDefinition *, std::set< std::string > > &dependencies)	SBMLImporter	[protected, static]
findDirectDependencies(const ASTNode *pNode, std::set< std::string > &dependencies)	SBMLImporter	[protected, static]
findFunctionCalls(const CEvaluationNode *pNode, std::set< std::string > &functionNameSet)	SBMLImporter	[protected]
findIdInASTTree(const ASTNode *pMath, const std::set< std::string > &reactionIds)	SBMLImporter
functionDB	SBMLImporter	[protected]
getFunctionDefinitionForName(const std::string name, const Model *model)	SBMLImporter	[protected]
getIdsFromNode(const ASTNode *pNode, std::set< std::string > &idSet)	SBMLImporter	[protected]
getImportCOPASIMIRIAM() const	SBMLImporter
getImportHandlerAddr()	SBMLImporter
getSBMLUnitDefinitionForId(const std::string &unitId, const Model *pSBMLModel)	SBMLImporter	[static]
handleAreaUnit(const UnitDefinition *uDef)	SBMLImporter	[protected]
handleLengthUnit(const UnitDefinition *uDef)	SBMLImporter	[protected]
handleSubstanceUnit(const UnitDefinition *uDef)	SBMLImporter	[protected]
handleTimeUnit(const UnitDefinition *uDef)	SBMLImporter	[protected]
handleVolumeUnit(const UnitDefinition *uDef)	SBMLImporter	[protected]
importEvent(const Event *pEvent, Model *pSBMLModel, CModel *pCopasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
importEvents(Model *pSBMLModel, CModel *pCopasiModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
importFunctionDefinitions(Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
importInitialAssignments(Model *pSBMLModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlMap, const CModel *pCOPASIModel)	SBMLImporter	[protected]
importMIRIAM(const SBase *pSBMLObject, CCopasiObject *pCOPASIObject)	SBMLImporter	[protected]
importRule(const Rule *rule, CModelEntity::Status ruleType, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	[protected]
importRuleForModelEntity(const Rule *rule, CModelEntity *pMV, CModelEntity::Status ruleType, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	[protected]
importSBMLRule(const Rule *sbmlRule, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	[protected]
isConstantFlux(const CEvaluationNode *pRoot, CModel *pModel, CFunctionDB *pFunctionDB)	SBMLImporter	[protected, static]
isDelayFunctionUsed(ConverterASTNode *pNode)	SBMLImporter	[protected]
isMassAction(const CEvaluationTree *pTree, const CChemEq &chemicalEquation, const CEvaluationNodeCall *pCallNode=NULL)	SBMLImporter	[protected]
isMassActionExpression(const CEvaluationNode *pRootNode, const CChemEq &chemicalEquation)	SBMLImporter	[protected]
isMassActionFunction(const CFunction *pFun, const CChemEq &chemicalEquation, const std::vector< std::vector< std::string > > &functionArgumentCNs)	SBMLImporter	[protected]
isMultipliedByVolume(const ASTNode *node, const std::string &compartmentSBMLId)	SBMLImporter	[protected]
isSimpleFunctionCall(const CEvaluationNode *pRootNode)	SBMLImporter	[protected]
isStochasticModel(const Model *pSBMLModel)	SBMLImporter	[protected]
mAssignmentToSpeciesReferenceFound	SBMLImporter	[protected]
mAvogadroCreated	SBMLImporter	[protected]
mDelayFound	SBMLImporter	[protected]
mDelayNodeMap	SBMLImporter	[protected]
mDivisionByCompartmentReactions	SBMLImporter	[protected]
mExplicitelyTimeDependentFunctionDefinitions	SBMLImporter	[protected]
mFastReactions	SBMLImporter	[protected]
mFunctionNameMapping	SBMLImporter	[protected]
mhImportStep	SBMLImporter	[protected]
mIgnoredParameterUnits	SBMLImporter	[protected]
mIgnoredSBMLMessages	SBMLImporter	[protected]
mImportCOPASIMIRIAM	SBMLImporter	[protected]
mImportStep	SBMLImporter	[protected]
mIncompleteModel	SBMLImporter	[protected]
mLevel	SBMLImporter	[protected]
mOriginalLevel	SBMLImporter	[protected]
mpCopasiModel	SBMLImporter	[protected]
mpDataModel	SBMLImporter	[protected]
mpImportHandler	SBMLImporter	[protected]
mPotentialAvogadroNumbers	SBMLImporter	[protected]
mReactionsWithReplacedLocalParameters	SBMLImporter	[protected]
mStoichiometricExpressionMap	SBMLImporter	[protected]
mSubstanceOnlySpecies	SBMLImporter	[protected]
mTotalSteps	SBMLImporter	[protected]
multiplySubstanceOnlySpeciesByVolume(ConverterASTNode *pNode)	SBMLImporter	[protected]
mUnitOnNumberFound	SBMLImporter	[protected]
mUnsupportedAssignmentRuleFound	SBMLImporter	[protected]
mUnsupportedRateRuleFound	SBMLImporter	[protected]
mUnsupportedRuleFound	SBMLImporter	[protected]
mUsedFunctions	SBMLImporter	[protected]
mUsedSBMLIds	SBMLImporter	[protected]
mUsedSBMLIdsPopulated	SBMLImporter	[protected]
mVersion	SBMLImporter	[protected]
normalizeSBMLUnit(Unit *pU)	SBMLImporter	[protected, static]
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)	SBMLImporter	[protected]
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)	SBMLImporter	[protected]
renameMassActionParameters(CEvaluationNodeCall *pCallNode)	SBMLImporter	[protected]
replace_delay_nodes(ConverterASTNode *pNode, Model *pModel, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, Reaction *pSBMLReaction, std::map< std::string, std::string > &localReplacementMap)	SBMLImporter	[protected]
replace_name_nodes(ASTNode *pNode, const std::map< std::string, std::string > &replacementMap)	SBMLImporter	[protected]
replace_time_with_initial_time(ASTNode *pNode, const CModel *pCOPASIModel)	SBMLImporter	[protected]
replaceAmountReferences(ConverterASTNode *pNode, Model *pSBMLModel, double factor, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
replaceBvars(const ASTNode *node, std::map< std::string, ASTNode * > bvarMap)	SBMLImporter	[protected]
replaceCallNodeNames(ASTNode *pNode)	SBMLImporter	[protected]
replaceLog(ConverterASTNode *sourceNode)	SBMLImporter	[protected]
replaceObjectNames(ASTNode *pNode, const std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, bool initialExpression=false)	SBMLImporter	[protected]
replacePowerFunctionNodes(ASTNode *node)	SBMLImporter	[protected]
replaceRoot(ConverterASTNode *sourceNode)	SBMLImporter	[protected]
replaceTimeDependentFunctionCalls(ASTNode *root)	SBMLImporter	[protected]
replaceTimeNodeNames(ASTNode *pNode)	SBMLImporter	[protected]
replaceTimeNodesInFunctionDefinition(ASTNode *root, std::string newNodeName)	SBMLImporter	[protected]
restoreFunctionDB()	SBMLImporter
round(const C_FLOAT64 &x)	SBMLImporter	[protected, static]
sbmlId2CopasiCN(ASTNode *pNode, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CCopasiParameterGroup &pParamGroup)	SBMLImporter	[protected]
sbmlIdMap	SBMLImporter	[protected]
SBMLImporter()	SBMLImporter
separateProductArguments(const CEvaluationNode *pRootNode, std::vector< const CEvaluationNode * > &arguments)	SBMLImporter	[protected]
setCorrectUsage(CReaction *pCopasiReaction, const CEvaluationNodeCall *pCallNode)	SBMLImporter	[protected]
setImportCOPASIMIRIAM(bool import)	SBMLImporter
setImportHandler(CProcessReport *pHandler)	SBMLImporter
setInitialValues(CModel *pModel, const std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	[protected]
speciesMap	SBMLImporter	[protected]
variables2objects(const CEvaluationNode *pOrigNode, const std::map< std::string, std::string > &replacementMap)	SBMLImporter	[protected]
~SBMLImporter()	SBMLImporter