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Model * | getModel () |
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SBMLDocument * | getSBMLDocument () |
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StringListContainer | getDerivedUnitDefinition (const std::string &sId) |
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StringListContainer | getListOfBoundarySpeciesIds () |
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StringListContainer | getListOfErrors () |
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StringListContainer | getListOfFloatingSpecies () |
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StringListContainer | getListOfFloatingSpeciesIds () |
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StringListContainer | getListOfParameters () |
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StringListContainer | getNthError (const int &nIndex) |
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StringListContainer | getNthEvent (const int &arg) |
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StringListContainer | getNthFunctionDefinition (const int &arg) |
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StringListContainer | getNthListOfModifiers (const int &nIndex) |
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StringListContainer | getNthListOfProducts (const int &nIndex) |
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StringListContainer | getNthListOfReactants (const int &nIndex) |
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ASTNode | replaceSymbol (ASTNode *node, const std::string &oldId, const std::string &newId) |
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bool | exists (const std::string &sId) |
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bool | getNthParameterHasValue (const int &nReactionIndex, const int &nParameterIndex) |
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bool | getNthUseValuesFromTriggerTime (const int &arg) |
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bool | hasInitialAmount (const std::string &sId) |
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bool | hasInitialConcentration (const std::string &sId) |
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bool | hasSBOTerm (const std::string &sId) |
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bool | hasValue (const std::string &sId) |
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bool | isBoundary (const std::string &sId) |
| Checks whether the element for the given SBML id is a boundary species. More...
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bool | isCompartment (const std::string &sId) |
| Checks whether the element for the given SBML id is a compartment. More...
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bool | isConstantImpl (const std::string &sId) |
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bool | isFloating (const std::string &sId) |
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bool | isReactionReversible (const int &nIndex) |
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bool | isSpecies (const std::string &sId) |
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bool | multiplyCompartment (const std::string &sbmlId, std::string &compartmentId) |
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bool | needEmptySetNode (Model model) |
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bool | needSinkNode (Model model) |
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bool | needSourceNode (Model model) |
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double | getNthParameterValue (const int &nReactionIndex, const int &nParameterIndex) |
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double | getNthProductStoichiometryDouble (const int &nIndex, const int &nProduct) |
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double | getNthReactantStoichiometryDouble (const int &nIndex, const int &nReactant) |
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double | getValue (const std::string &sId) |
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int | checkConsistency () |
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int | getNthProductStoichiometry (const int &nIndex, const int &nProduct) |
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int | getNthReactantStoichiometry (const int &nIndex, const int &nReactant) |
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int | getNumBoundarySpecies () |
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int | getNumCompartments () |
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int | getNumConstraints () |
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int | getNumErrors () |
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int | getNumEvents () |
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int | getNumFloatingSpecies () |
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int | getNumFunctionDefinitions () |
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int | getNumGlobalParameters () |
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int | getNumInitialAssignments () |
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int | getNumParameters (int reaction) |
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int | getNumProducts (const int &var0) |
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int | getNumReactants (const int &var0) |
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int | getNumReactions () |
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int | getNumRules () |
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int | getSBOTerm (const std::string &sId) |
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std::pair< std::string, std::string > | getNthInitialAssignmentPair (const int &nIndex) |
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SBase * | getElement (const std::string &sId) |
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std::string | addEmptySetNode (const std::string &sbml) |
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std::string | addEmptySetNodes (const std::string &sbml) |
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std::string | addMissingModifiers (const std::string &sModel) |
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std::string | addSourceSinkNodes (const std::string &sbml) |
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std::string | convertLevel1ToLevel2Impl (const std::string &sSBML) |
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std::string | convertLevel2ToLevel1Impl (const std::string &sSBML) |
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std::string | convertPowImpl (const std::string &sSBML) |
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std::string | convertSBML (const std::string &sModel, const int &nLevel, const int &nVersion) |
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std::string | convertSBML (const std::string &sModel, const int &nLevel, const int &nVersion, bool throwError) |
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std::string | convertTimeToCSymbol (const std::string &sArg, const std::string &sTimeSymbol) |
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std::string | fixCommonIssues (const std::string &sbml) |
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std::string | fixCommonIssues (const std::string &sbml, const std::string &programName, const std::string &programVersion) |
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std::string | fetAnnotatedModel (const std::string &targetSBML, const std::string &sourceSBML, bool checkModelId) |
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std::string | getAnnotation (const std::string &sId) |
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std::string | getCompartmentIdBySpeciesId (const std::string &sId) |
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std::string | getKineticLaw (const int &index) |
| gets the kinetic law math formula for the i'th reaction. More...
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std::string | getMetaId (const std::string &sId) |
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std::string | getModelId () |
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std::string | getModelName () const |
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std::string | getNotes (const std::string &sId) |
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std::string | getNthBoundarySpeciesId (const int &nIndex) |
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std::string | getNthBoundarySpeciesName (const int &nIndex) |
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std::string | getNthCompartmentId (const int &nIndex) |
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std::string | getNthCompartmentName (const int &nIndex) |
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std::string | getNthConstraint (const int &nIndex, std::string &sMessage) |
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std::string | getNthFloatingSpeciesId (const int &nIndex) |
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std::string | getNthFloatingSpeciesName (const int &nIndex) |
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std::string | getNthGlobalParameterId (const int &nIndex) |
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std::string | getNthGlobalParameterName (const int &nIndex) |
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std::string | getNthInitialAssignment (const int &nIndex) |
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std::string | getNthParameterId (const int &nReactionIndex, const int &nParameterIndex) |
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std::string | getNthParameterName (const int &nReactionIndex, const int &nParameterIndex) |
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std::string | getNthProductName (const int &nIndex, const int &nProduct) |
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std::string | getNthReactantName (const int &nIndex, const int &nReactant) |
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std::string | getNthReactionId (const int &nIndex) |
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std::string | getNthReactionName (const int &nIndex) |
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std::string | getNthRule (const int &nIndex) |
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std::string | getNthRuleType (const int &arg) |
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std::string | getOutsideCompartment (const std::string &var0) |
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std::string | getSBML () |
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std::string | getSBOCapableSBML (const std::string &sModel) |
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std::string | removeJD1Layout (const std::string &sSBML) |
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std::string | removeJD2Layout (const std::string &sSBML) |
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std::string | removeLayoutInformation (const std::string &sSBML) |
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std::string | validateSBML (const std::string &sModel) |
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std::string | validateWithConsistency (const std::string &sModel) |
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std::vector< std::string > | getBuiltinFunctionInfo (const std::string &var0) |
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std::vector< std::string > | getBuiltinFunctions () |
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void | changeConstantForRules (Model *model) |
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void | loadFromFile (const std::string &fileName) |
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void | loadParameterPromotedSBML (const std::string &var0, const std::string &sTimeSymbol) |
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void | loadSBML (const std::string &var0) |
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void | loadSBML (const std::string &var0, const std::string &sTimeSymbol) |
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void | setAnnotation (const std::string &sId, const std::string &sAnnotation) |
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void | setModelId (const std::string &sId) |
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void | setNotes (const std::string &sId, const std::string &sNotes) |
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void | setSBOTerm (const std::string &sId, const int &nSBOTerm) |
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void | setValue (const std::string &sId, const double &dValue) |
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void | setValue (Model *model, const std::string &id, const double &value, const bool &throwIfNotFound) |
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void | testASTTime () |
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std::string | getNthBoundarySpeciesCompartmentName (const int &nIndex) |
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std::string | getNthFloatingSpeciesCompartmentName (int index) |
| gets the compartment name of the i'th species with boundary condition's compartment name. More...
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StringListContainer | getListOfBoundarySpecies () |
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stack< std::string > | getMatchForSymbol (const std::string &sbmlId) |
| This should return an initialization for the given sbmlId that is sideeffect free.
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Methods to query various information from an SBML document.
This class provides a set of static method to query various items from sbml objects.