/* * The functions determins wether the given UnitDefinition contains only * units from the list given as the second argument. * @param const UnitDefinition& uDef * @param const ListOf& unitList * @return bool containsOnlyGivenUnits */ LIBSBML_EXTERN bool UnitConversionFactory::containsOnlyGivenUnits(const UnitDefinition& uDef, const ListOf& unitList) { bool result = true; UnitDefinition* pTmpUdef = UnitConversionFactory::convertToSI(uDef); if (pTmpUdef) { unsigned int i; unsigned int maxUnits = pTmpUdef->getNumUnits(); for (i = 0; i < maxUnits; ++i) { Unit* pU = pTmpUdef->getUnit(i); UnitKind_t kind = pU->getKind(); unsigned int j; unsigned int maxUnits2 = unitList.size(); bool found = false; for (j = 0; j < maxUnits2; ++j) { const Unit* pU2 = dynamic_cast<const Unit*>(unitList.get(j)); if (!pU2) break; if (pU2->getKind() == kind) { found = true; break; } } if (!found) { result = false; break; } } delete pTmpUdef; } else { result = false; } return result; }
//static void SBMLDocumentLoader::readListOfLayouts(CListOfLayouts & lol, const ListOf & sbmlList, const std::map<CCopasiObject*, SBase*> & copasimodelmap) { unsigned C_INT32 i, iMax; #ifdef USE_CRENDER_EXTENSION // read the global render information const ListOfLayouts* pLoL = dynamic_cast<const ListOfLayouts*>(&sbmlList); assert(pLoL != NULL); RenderListOfLayoutsPlugin* rlolPlugin = (RenderListOfLayoutsPlugin*) pLoL ->getPlugin("render"); if (rlolPlugin == NULL) { const_cast<SBMLDocument *>(pLoL->getSBMLDocument())->enablePackage(RenderExtension::getXmlnsL3V1V1(), "render", true); rlolPlugin = (RenderListOfLayoutsPlugin*) pLoL ->getPlugin("render"); } iMax = rlolPlugin->getNumGlobalRenderInformationObjects(); std::map<std::string, std::string> idToKeyMap; CLGlobalRenderInformation* pGRI = NULL; /* std::map<std::string,std::string> colorIdToKeyMap; std::map<std::string,std::string> gradientIdToKeyMap; std::map<std::string,std::string> lineEndingIdToKeyMap; std::map<std::string,std::map<std::string,std::string> > colorIdToKeyMapMap; std::map<std::string,std::map<std::string,std::string> > gradientIdToKeyMapMap; std::map<std::string,std::map<std::string,std::string> > lineEndingIdToKeyMapMap; */ for (i = 0; i < iMax; ++i) { //colorIdToKeyMap.clear(); //gradientIdToKeyMap.clear(); //lineEndingIdToKeyMap.clear(); //pGRI=new CLGlobalRenderInformation(*pLoL->getRenderInformation(i),colorIdToKeyMap,gradientIdToKeyMap,lineEndingIdToKeyMap,&lol); pGRI = new CLGlobalRenderInformation(*rlolPlugin->getRenderInformation(i), &lol); if (rlolPlugin->getRenderInformation(i)->isSetId()) idToKeyMap.insert(std::pair<std::string, std::string>(rlolPlugin->getRenderInformation(i)->getId(), pGRI->getKey())); else idToKeyMap.insert(std::pair<std::string, std::string>(pGRI->getKey(), pGRI->getKey())); //colorIdToKeyMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pGRI->getKey(),colorIdToKeyMap)); //gradientIdToKeyMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pGRI->getKey(),gradientIdToKeyMap)); //lineEndingIdToKeyMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pGRI->getKey(),lineEndingIdToKeyMap)); lol.addGlobalRenderInformation(pGRI); } // fix the references SBMLDocumentLoader::convertRenderInformationReferencesIds<CLGlobalRenderInformation>(lol.getListOfGlobalRenderInformationObjects(), idToKeyMap); // fix the color ids, gradient ids and line ending ids. /* std::map<std::string,std::map<std::string,std::string> >::const_iterator mapPos; std::map<std::string,std::map<std::string,std::string> > expandedColorIdToKeyMapMap, expandedGradientIdToKeyMapMap, expandedLineEndingIdToKeyMapMap; std::map<std::string,std::map<std::string,std::string> > tmpMap1,tmpMap2,tmpMap3; for(i=0;i < iMax; ++i) { pGRI=dynamic_cast<CLGlobalRenderInformation*>(lol.getRenderInformation(i)); assert(pGRI != NULL); std::set<std::string> chain; SBMLDocumentLoader::expandIdToKeyMaps<CLGlobalRenderInformation>(pGRI, lol.getListOfGlobalRenderInformationObjects(), expandedColorIdToKeyMapMap, expandedGradientIdToKeyMapMap, expandedLineEndingIdToKeyMapMap, colorIdToKeyMapMap, gradientIdToKeyMapMap, lineEndingIdToKeyMapMap, chain, tmpMap1, tmpMap2, tmpMap3 ); SBMLDocumentLoader::convertPropertyKeys<CLGlobalRenderInformation>(pGRI,expandedColorIdToKeyMapMap[pGRI->getKey()],expandedGradientIdToKeyMapMap[pGRI->getKey()],expandedLineEndingIdToKeyMapMap[pGRI->getKey()]); } */ #endif /* USE_CRENDER_EXTENSION */ //convert the map as used by the CLxxx constructors std::map<std::string, std::string> modelmap; std::string s1, s2; std::map<CCopasiObject*, SBase*>::const_iterator it; std::map<CCopasiObject*, SBase*>::const_iterator itEnd = copasimodelmap.end(); for (it = copasimodelmap.begin(); it != itEnd; ++it) { s1 = SBMLUtils::getIdFromSBase(it->second); if (it->first) s2 = it->first->getKey(); else s2 = ""; if ((s1 != "") && (s2 != "")) modelmap[s1] = s2; } //iterate through list of layouts iMax = sbmlList.size(); for (i = 0; i < iMax; ++i) { std::map<std::string, std::string> layoutmap; const Layout* tmp = dynamic_cast<const Layout*>(sbmlList.get(i)); if (tmp) { #ifdef USE_CRENDER_EXTENSION //CLayout * pLayout = createLayout(*tmp, modelmap, layoutmap,idToKeyMap,expandedColorIdToKeyMapMap,expandedGradientIdToKeyMapMap,expandedLineEndingIdToKeyMapMap); CLayout * pLayout = createLayout(*tmp, modelmap, layoutmap, idToKeyMap); #else CLayout * pLayout = createLayout(*tmp, modelmap, layoutmap); #endif /* USE_CRENDER_EXTENSION */ lol.addLayout(pLayout, layoutmap); } } //TODO: the layout object should be added to the copasimodelmap. However, //if this is done, the object also need to be removed if necessary in the //sbml exporter (see comment in CListOfLayouts::exportToSBML()). }
//static void SBMLUtils::collectIds(Model* pModel, std::map<std::string, const SBase*>& ids, std::map<std::string, const SBase*>& metaIds) { if (pModel != NULL) { // the model itself SBase* pSBase = NULL; std::string id; if (pModel->isSetId()) { id = pModel->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pModel->isSetMetaId()) { id = pModel->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // ListOfFunctionDefinitions pSBase = pModel->getListOfFunctionDefinitions(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // all FunctionDefinitions unsigned int i, iMax = pModel->getListOfFunctionDefinitions()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getListOfFunctionDefinitions()->get(i); if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfUnitDefinition pSBase = pModel->getListOfUnitDefinitions(); if (pSBase != NULL) { if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // all UnitDefinitions // for each UnitDefinition: ListOfUnits, each Unit in ListOfUnits unsigned int i, iMax = pModel->getListOfUnitDefinitions()->size(); for (i = 0; i < iMax; ++i) { /* UnitDefinitions have their ids in a different namespace so we only consider meta ids. */ UnitDefinition* pUDef = pModel->getUnitDefinition(i); assert(pUDef != NULL); if (pUDef->isSetMetaId()) { id = pUDef->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pUDef)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } ListOf* pList = pUDef->getListOfUnits(); if (pList != NULL) { if (pList->isSetMetaId()) { id = pList->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pList)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } unsigned j, jMax = pList->size(); for (j = 0; j < jMax; ++j) { pSBase = pList->get(j); assert(pSBase != NULL); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } } } // ListOfCompartmentTypes pSBase = pModel->getListOfCompartmentTypes(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each compartment type unsigned int i, iMax = pModel->getListOfCompartmentTypes()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getCompartmentType(i); assert(pSBase != NULL); if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfSpeciesTypes pSBase = pModel->getListOfSpeciesTypes(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each species type unsigned int i, iMax = pModel->getListOfSpeciesTypes()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getSpeciesType(i); assert(pSBase != NULL); if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfCompartments pSBase = pModel->getListOfCompartments(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // all compartments unsigned int i, iMax = pModel->getListOfCompartments()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getCompartment(i); assert(pSBase != NULL); if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfSpecies pSBase = pModel->getListOfSpecies(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // all species unsigned int i, iMax = pModel->getListOfSpecies()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getSpecies(i); assert(pSBase != NULL); if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfParameters pSBase = pModel->getListOfParameters(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each parameter unsigned int i, iMax = pModel->getListOfParameters()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getParameter(i); assert(pSBase != NULL); if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfInitialAssignments pSBase = pModel->getListOfInitialAssignments(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each initial assignment unsigned int i, iMax = pModel->getListOfInitialAssignments()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getInitialAssignment(i); assert(pSBase != NULL); // initial assignments have no ids if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfRules pSBase = pModel->getListOfRules(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each rule unsigned int i, iMax = pModel->getListOfRules()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getRule(i); assert(pSBase != NULL); // rules don't have ids if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfConstraints pSBase = pModel->getListOfConstraints(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each constraint unsigned int i, iMax = pModel->getListOfConstraints()->size(); for (i = 0; i < iMax; ++i) { pSBase = pModel->getConstraint(i); assert(pSBase != NULL); // constraints don't have ids if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } // ListOfReactions pSBase = pModel->getListOfReactions(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // all reactions unsigned int i, iMax = pModel->getListOfReactions()->size(); for (i = 0; i < iMax; ++i) { Reaction* pReaction = pModel->getReaction(i); assert(pReaction != NULL); if (pReaction->isSetId()) { id = pReaction->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pReaction)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pReaction->isSetMetaId()) { id = pReaction->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pReaction)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // for each reaction: ListOfSubstrates, each substrate, ListOfProducts, each // Product, ListOfModifieres, each modifier, KineticLaw, ListOfparameters, // each parameter if (pReaction->getListOfReactants() != NULL) { pSBase = pReaction->getListOfReactants(); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } unsigned int j, jMax = pReaction->getListOfReactants()->size(); for (j = 0; j < jMax; ++j) { pSBase = pReaction->getReactant(j); assert(pSBase != NULL); // since L2V2 species references can have ids if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } if (pReaction->getListOfProducts() != NULL) { pSBase = pReaction->getListOfProducts(); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } unsigned int j, jMax = pReaction->getListOfProducts()->size(); for (j = 0; j < jMax; ++j) { pSBase = pReaction->getProduct(j); assert(pSBase != NULL); // since L2V2 species references can have ids if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } if (pReaction->getListOfModifiers() != NULL) { pSBase = pReaction->getListOfModifiers(); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } unsigned int j, jMax = pReaction->getListOfModifiers()->size(); for (j = 0; j < jMax; ++j) { pSBase = pReaction->getModifier(j); assert(pSBase != NULL); // since L2V2 species references can have ids if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } KineticLaw* pKLaw = pReaction->getKineticLaw(); if (pKLaw != NULL) { if (pKLaw->isSetMetaId()) { id = pKLaw->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pKLaw)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } pSBase = pKLaw->getListOfParameters(); if (pSBase != NULL) { if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } unsigned int j, jMax = pKLaw->getListOfParameters()->size(); for (j = 0; j < jMax; ++j) { pSBase = pKLaw->getParameter(j); assert(pSBase != NULL); // local parameters have their ids in a // different namespace if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } } } } // ListOfEvents pSBase = pModel->getListOfEvents(); if (pSBase != NULL) { if (pSBase->isSetId()) { id = pSBase->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // each event unsigned int i, iMax = pModel->getListOfEvents()->size(); for (i = 0; i < iMax; ++i) { Event* pEvent = pModel->getEvent(i); assert(pEvent != NULL); if (pEvent->isSetId()) { id = pEvent->getId(); if (ids.find(id) == ids.end()) { ids.insert(std::pair<const std::string, const SBase*>(id, pEvent)); } else { CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str()); } } if (pEvent->isSetMetaId()) { id = pEvent->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pEvent)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } // in each event Trigger,Delay,ListOfEventAssignments, each event assignment if (pEvent->isSetTrigger()) { pSBase = pEvent->getTrigger(); assert(pSBase != NULL); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } if (pEvent->isSetDelay()) { pSBase = pEvent->getDelay(); assert(pSBase != NULL); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } if (pEvent->getListOfEventAssignments() != NULL) { pSBase = pEvent->getListOfEventAssignments(); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } unsigned int j, jMax = pEvent->getListOfEventAssignments()->size(); for (j = 0; j < jMax; ++j) { pSBase = pEvent->getEventAssignment(j); assert(pSBase != NULL); if (pSBase->isSetMetaId()) { id = pSBase->getMetaId(); if (metaIds.find(id) == metaIds.end()) { metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase)); } else { CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str()); } } } } } } } }