SBMLImporter Member List

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

applyConversionFactors()	SBMLImporter
applyStoichiometricExpressions(std::map< const CDataObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	protected
areApproximatelyEqual(const double &x, const double &y, const double &t=1e-9)	SBMLImporter	static
areEqualFunctions(const CFunction *pFun, const CFunction *pFun2)	SBMLImporter	static
areEqualSubtrees(const CEvaluationNode *pNode1, const CEvaluationNode *pNode2)	SBMLImporter	static
areRulesUnique(const Model *copasiMode)	SBMLImporter	protected
areSBMLUnitDefinitionsIdentical(const SUnitInfo &unitInfo1, const SUnitInfo &unitInfo2)	SBMLUnitSupport	static
checkElementUnits(const Model *pSBMLModel, CModel *pCopasiModel)	SBMLUnitSupport
checkForSpatialSizeUnits(const CDataModel &dataModel, std::vector< SBMLIncompatibility > &result)	SBMLUnitSupport	static
checkForUnitsOnNumbers(const ASTNode *pNode)	SBMLImporter	static
checkRuleMathConsistency(const Rule *pRule, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
checkValidityOfSourceDocument(SBMLDocument *sbmlDoc)	SBMLImporter	protected
clearCallBack()	SBMLImporter	virtual
containsVolume(const ASTNode *pNode, const std::string &compartmentCN)	SBMLImporter	protected
createBVarMap(const ASTNode *uDefFunction, const ASTNode *function)	SBMLImporter	protected
createCCompartmentFromCompartment(const Compartment *sbmlComp, CModel *copasiModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, const Model *pSBMLModel)	SBMLImporter	protected
createCFunctionFromFunctionDefinition(const FunctionDefinition *sbmlFunction, Model *pSBMLModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
createCFunctionFromFunctionTree(const FunctionDefinition *pSBMLFunction, Model *pSBMLModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
createCMetabFromSpecies(const Species *sbmlSpecies, CModel *copasiModel, CCompartment *copasiCompartment, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, const Model *pSBMLModel)	SBMLImporter	protected
createCModelFromSBMLDocument(SBMLDocument *doc, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
createCModelValueFromParameter(const Parameter *sbmlParameter, CModel *copasiModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
createCReactionFromReaction(Reaction *sbmlReaction, Model *sbmlModel, CModel *cmodel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	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< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
createProgressStepOrStop(unsigned C_INT32 globalStep, unsigned C_INT32 currentTotal, const std::string &title)	SBMLImporter	protected
createUnitExpressionFor(SUnitInfo &unitInfo) const	SBMLUnitSupport
deleteCopasiModel()	SBMLImporter
divideByObject(const CEvaluationNode *pOrigNode, const CDataObject *pObject)	SBMLImporter	static
divideByVolume(ASTNode *node, const std::string &compartmentSBMLId)	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< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
findAvogadroConstant(Model *pSBMLModel, double factor)	SBMLImporter	protected
findCorrespondingFunction(const CExpression *pExpression, const CReaction *reaction)	SBMLImporter	protected
findDirectDependencies(const FunctionDefinition *pFunDef, std::map< const FunctionDefinition *, std::set< std::string > > &dependencies)	SBMLImporter	protectedstatic
findDirectDependencies(const ASTNode *pNode, std::set< std::string > &dependencies)	SBMLImporter	protectedstatic
findFunctionCalls(const CEvaluationNode *pNode, std::set< std::string > &functionNameSet)	SBMLImporter	protected
findIdInASTTree(const ASTNode *pMath, const std::set< std::string > &reactionIds)	SBMLImporter
findIdInASTTree(const ASTNode *pMath, const std::map< std::string, double > &reactionIds)	SBMLImporter
finishCurrentStep()	SBMLImporter	protected
finishImport()	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
getProcessReport() const	SBMLImporter
importEvent(const Event *pEvent, Model *pSBMLModel, CModel *pCopasiModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
importEvents(Model *pSBMLModel, CModel *pCopasiModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
importFunctionDefinitions(Model *pSBMLModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
importInitialAssignments(Model *pSBMLModel, std::map< const CDataObject *, SBase * > &copasi2sbmlMap, const CModel *pCOPASIModel)	SBMLImporter	protected
importMIRIAM(const SBase *pSBMLObject, CDataObject *pCOPASIObject)	SBMLImporter	protected
importNotes(CAnnotation *pAnno, const SBase *pSBase)	SBMLImporter	static
importRule(const Rule *rule, CModelEntity::Status ruleType, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	protected
importRuleForModelEntity(const Rule *rule, const CModelEntity *pMV, CModelEntity::Status ruleType, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	protected
importSBMLRule(const Rule *sbmlRule, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, Model *pSBMLModel)	SBMLImporter	protected
importUnit(const std::string unitId, const Model *pSBMLModel)	SBMLUnitSupport
importUnit(const UnitDefinition *pUnitDefinition, const bool &allocated)	SBMLUnitSupport
importUnitsFromSBMLDocument(Model *sbmlModel, CModel *pCopasiModel)	SBMLUnitSupport
isConstantFlux(const CEvaluationNode *pRoot, CModel *pModel)	SBMLImporter	protected
isDelayFunctionUsed(ConverterASTNode *pNode)	SBMLImporter	protected
isEmptyOrWhiteSpace(const std::string &name)	SBMLImporter	static
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
isSimpleFunctionCall(const CEvaluationNode *pRootNode)	SBMLImporter	protected
isStochasticModel(const Model *pSBMLModel)	SBMLImporter	protected
mAssignmentToSpeciesReferenceFound	SBMLImporter	protected
mAvogadroCreated	SBMLImporter	protected
mAvogadroSet	SBMLUnitSupport	protected
mChangedObjects	SBMLImporter	protected
mChemEqElementSpeciesIdMap	SBMLImporter	protected
mCompartmentMap	SBMLImporter	protected
mConversionFactorFound	SBMLImporter	protected
mCreatedFunctions	SBMLImporter	protected
mCurrentStepCounter	SBMLImporter	protected
mCurrentStepHandle	SBMLImporter	protected
mCurrentStepTotal	SBMLImporter	protected
mDelayFound	SBMLImporter	protected
mDelayNodeMap	SBMLImporter	protected
mDivisionByCompartmentReactions	SBMLImporter	protected
mEventAssignmentForSpeciesReferenceIgnored	SBMLImporter	protected
mExplicitelyTimeDependentFunctionDefinitions	SBMLImporter	protected
mFastReactions	SBMLImporter	protected
mFunctionNameMapping	SBMLImporter	protected
mGlobalStepCounter	SBMLImporter	protected
mGlobalStepHandle	SBMLImporter	protected
mGlobalStepTotal	SBMLImporter	protected
mIgnoredParameterUnits	SBMLImporter	protected
mIgnoredSBMLMessages	SBMLImporter	protected
mImportCOPASIMIRIAM	SBMLImporter	protected
mImportedUnits	SBMLUnitSupport	private
mIncompleteModel	SBMLImporter	protected
mKnownCustomUserDefinedFunctions	SBMLImporter	protected
mKnownInitalValues	SBMLImporter	protected
mLevel	SBMLUnitSupport	protected
mOriginalLevel	SBMLImporter	protected
mParameterFluxMap	SBMLImporter	protected
mpAreaUnit	SBMLUnitSupport	private
mpCopasiModel	SBMLImporter	protected
mpDataModel	SBMLImporter	protected
mpLengthUnit	SBMLUnitSupport	private
mpModelConversionFactor	SBMLImporter	protected
mPotentialAvogadroNumbers	SBMLImporter	protected
mpProcessReport	SBMLImporter	protected
mpSbmlCallback	SBMLImporter	protected
mpSubstanceUnit	SBMLUnitSupport	private
mpTimeUnit	SBMLUnitSupport	private
mpVolumeUnit	SBMLUnitSupport	private
mRateRuleForSpeciesReferenceIgnored	SBMLImporter	protected
mReactions	SBMLImporter	protected
mReactionsWithReplacedLocalParameters	SBMLImporter	protected
mSBMLIdModelValueMap	SBMLImporter	protected
mSBMLSpeciesReferenceIds	SBMLImporter	protected
mSpeciesConversionParameterMap	SBMLImporter	protected
mStoichiometricExpressionMap	SBMLImporter	protected
mSubstanceOnlySpecies	SBMLImporter	protected
multiplySubstanceOnlySpeciesByVolume(ConverterASTNode *pNode)	SBMLImporter	protected
mUnitOnNumberFound	SBMLImporter	protected
mUnsupportedAssignmentRuleFound	SBMLImporter	protected
mUnsupportedRateRuleFound	SBMLImporter	protected
mUnsupportedRuleFound	SBMLImporter	protected
mUsedSBMLIds	SBMLImporter	protected
mUsedSBMLIdsPopulated	SBMLImporter	protected
mVersion	SBMLUnitSupport	protected
parseSBML(const std::string &sbmlDocumentText, SBMLDocument *&pSBMLDocument, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, CListOfLayouts *&prLol, CDataModel *pDataModel)	SBMLImporter
preprocessNode(ConverterASTNode *pNode, Model *pSBMLModel, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, Reaction *pSBMLReaction=NULL)	SBMLImporter	protected
readSBML(std::string filename, SBMLDocument *&pSBMLDocument, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, CListOfLayouts *&prLol, CDataModel *pDataModel)	SBMLImporter
removeUnusedFunctions(std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
renameMassActionParameters(CEvaluationNodeCall *pCallNode)	SBMLImporter	protected
replace_delay_nodes(ConverterASTNode *pNode, Model *pModel, std::map< const CDataObject *, 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< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
replaceCallNodeNames(ASTNode *pNode)	SBMLImporter	protected
replaceLog(ConverterASTNode *sourceNode)	SBMLImporter	protected
replaceObjectNames(ASTNode *pNode, const std::map< const CDataObject *, SBase * > &copasi2sbmlmap, bool initialExpression=false)	SBMLImporter	protected
replacePowerFunctionNodes(ASTNode *node)	SBMLImporter	protected
replaceRoot(ConverterASTNode *sourceNode)	SBMLImporter	protected
replaceTimeAndAvogadroNodeNames(ASTNode *pNode)	SBMLImporter	protected
replaceTimeDependentFunctionCalls(ASTNode *root)	SBMLImporter	protected
replaceTimeNodesInFunctionDefinition(ASTNode *root, std::string newNodeName)	SBMLImporter	protected
reportCurrentProgressOrStop()	SBMLImporter	protected
restoreFunctionDB()	SBMLImporter
round(const C_FLOAT64 &x)	SBMLImporter	protectedstatic
sbmlId2CopasiCN(ASTNode *pNode, std::map< const CDataObject *, SBase * > &copasi2sbmlmap, CCopasiParameterGroup &pParamGroup, SBase *pParentObject=NULL)	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 *pProcessReport)	SBMLImporter
setInitialValues(CModel *pModel, const std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	SBMLImporter	protected
setLevelAndVersion(int level, int version)	SBMLUnitSupport
speciesMap	SBMLImporter	protected
unitKindToString(UnitKind_t kind)	SBMLUnitSupport	static
UnitType enum name	SBMLUnitSupport
updateSBMLSpeciesReferenceIds(Model *pModel, std::map< std::string, double > &ids)	SBMLImporter	static
validateUnit(SUnitInfo &unitInfo, const std::string &constraint) const	SBMLUnitSupport
variables2objects(const CEvaluationNode *pOrigNode, const std::map< std::string, std::string > &replacementMap)	SBMLImporter	protected
~SBMLImporter()	SBMLImporter
~SBMLUnitSupport()	SBMLUnitSupport