Example #1
0
//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());
                            }
                        }
                    }
                }
            }
        }
    }
}
Example #2
0
void
CompIdBase::checkId (const Reaction& x)
{
  if (x.isSetId()) doCheckId(x.getId(), x);
}
Example #3
0
void SbmlReader::createReaction(const map< string, Id > &molSidcmptMIdMap ) {
    Reaction* reac;

    map< string,double > rctMap;
    map< string,double >::iterator rctMap_iter;
    map< string,double >prdMap;
    map< string,double >::iterator prdMap_iter;
    map< string,EnzymeInfo >enzInfoMap;

    for ( unsigned int r = 0; r < model_->getNumReactions(); r++ ) {
        Id reaction_;
        reac = model_->getReaction( r );
        noOfsub_ = 0;
        noOfprd_ = 0;
        std:: string id; //=reac->getId();
        if ( reac->isSetId() )
            id = reac->getId();

        std::string name;
        if ( reac->isSetName() ) {
            name = reac->getName();
            name = nameString(name);
        }
        if (name.empty()) {
            if (id.empty())
                assert("Reaction id and name is empty");
            else
                name = id;
        }
        string grpname = getAnnotation( reac,enzInfoMap );
        if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) ) {
            setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap,name);
        }
        //if (grpname != "")
        // {
        //cout << "\n enz matic reaction " << enzInfoMap[grpname].stage;
        //setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap);
        //}

        else if ( grpname == "" ) {
            if (reac->getNumModifiers() > 0)
                setupMMEnzymeReaction( reac,id,name ,molSidcmptMIdMap);
            else {
                bool rev=reac->getReversible();
                bool fast=reac->getFast();
                if ( fast ) {
                    cout<<"warning: for now fast attribute is not handled"<<endl;
                    errorFlag_ = true;
                }
                int numRcts = reac->getNumReactants();
                int numPdts = reac->getNumProducts();
                if ( numRcts == 0 && numPdts != 0 ) {
                    cout << "Reaction with zero Substrate is not possible but exist in this model";
                    const SpeciesReference* pdt = reac->getProduct( 0 );
                    std::string spName = pdt->getSpecies();
                    Id parent = molSidcmptMIdMap.find( spName )->second; //gives compartment of spName
                    cout << " \n \t ################################# Sub = 0 and prd != 0 need to the reac ############### ";
                    const SpeciesReference* rect=reac->getReactant(0);
                    std::string sp=rect->getSpecies();
                    Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
                    Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
                    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
                    reaction_ = shell->doCreate("Reac", meshEntry, name, 1);
                    //shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
                    //Get Substrate
                    addSubPrd(reac,reaction_,"prd");
                } //if numRcts == 0
                else {
                    const SpeciesReference* rect=reac->getReactant(0);
                    std::string sp=rect->getSpecies();
                    Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
                    Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
                    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );

                    reaction_ = shell->doCreate("Reac", comptRef, name, 1);
                    //shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
                    //Get Substrate
                    addSubPrd(reac,reaction_,"sub");

                    //Get Product
                    addSubPrd(reac,reaction_,"prd");
                }
                if ( reac->isSetKineticLaw() ) {
                    KineticLaw * klaw=reac->getKineticLaw();

                    //vector< double > rate = getKLaw( klaw,rev );
                    vector< double > rate;
                    rate.clear();
                    getKLaw( klaw,rev,rate );
                    if ( errorFlag_ )
                        return;
                    else if ( !errorFlag_ ) {
                        //cout << " Reaction name " << name << " kf " << rate[0] << " kb " << rate[1]<<endl;

                        Field < double > :: set( reaction_, "Kf", rate[0] );
                        Field < double > :: set( reaction_, "Kb", rate[1] );
                        /*if (numRcts > 1)
                        rate[0] = rate[0]*pow(1e3,1.0);
                             cout << "Reaction " << id << " " << name << " " << rate[0] << "  " << rate[1]<<endl;
                             Field < double > :: set( reaction_, "Kf", rate[0] );
                             Field < double > :: set( reaction_, "Kb", rate[1] );
                             */
                    }
                } //issetKineticLaw

            } //else
        } // else grpname == ""
    }//for unsigned
} //reaction