C++ (Cpp) CChemEqElement::getMultiplicity Examples

Example #1

File: CChemEq.cpp Project: mgaldzic/copasi_api

void CChemEq::addElement(CCopasiVector < CChemEqElement > & structure,
                         const CChemEqElement & element,
                         CChemEq::MetaboliteRole role)
{
  unsigned C_INT32 i;

  std::string key = element.getMetaboliteKey();

  if (key == "")
    return; // don�t add empty element

  for (i = 0; i < structure.size(); i++)
    if (key == structure[i]->getMetaboliteKey())
      break;

  if (i >= structure.size())
    {
      CChemEqElement * Element = new CChemEqElement(element);

      if (role == CChemEq::SUBSTRATE)
        Element->setMultiplicity(- Element->getMultiplicity());

      structure.add(Element, true);
    }
  else if (role == CChemEq::SUBSTRATE)
    structure[i]->addToMultiplicity(- element.getMultiplicity());
  else
    structure[i]->addToMultiplicity(element.getMultiplicity());
}

Example #2

File: CODEExporterC.cpp Project: sachiinb/COPASI

std::string CODEExporterC::KineticFunction2ODEmember(const CReaction *reac)
{
  std::ostringstream equation;

  if (reac->getFunction()->getType() != CEvaluationTree::MassAction)
    {
      const CFunctionParameters & params = reac->getFunctionParameters();
      size_t k, params_size = params.size();
      const std::vector<std::vector<std::string> > & keyMap = reac->getParameterMappings();
      std::string name;
      equation << NameMap[reac->getFunction()->getKey()] << "(";

      for (k = 0; k < params_size; ++k)
        {

          CFunctionParameter::Role role = params[k]->getUsage();

          CCopasiObject * obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[k][0]);

          if ((role == CFunctionParameter::SUBSTRATE)
              || (role == CFunctionParameter::PRODUCT)
              || (role == CFunctionParameter::MODIFIER))
            {
              if (obj)
                name = NameMap[obj->getKey()];
              else
                name = "unknown";
            }

          if (role == CFunctionParameter::PARAMETER)
            {
              if (!(reac->isLocalParameter(k)))
                {
                  CModelValue* modval;
                  modval = dynamic_cast< CModelValue * >(obj);
                  name = NameMap[modval->getKey()];
                }
              else
                {
                  CCopasiParameter* param;
                  param = dynamic_cast< CCopasiParameter * >(obj);
                  name = NameMap[param->getKey()];
                }
            }

          if (role == CFunctionParameter::VOLUME)
            {
              CCompartment* comp;
              comp = dynamic_cast< CCompartment * >(obj);
              name = NameMap[comp->getKey()];
            }

          if (role == CFunctionParameter::TIME)
            {
              name = "T";
            }

          if (name.empty())
            {
              std::string message = "Could not export C code, since one of the arguments could not be resolved. Please consider filing a bug with the COPASI tracker: http://www.copasi.org/tracker";
              CCopasiMessage(CCopasiMessage::EXCEPTION, message.c_str());
            }

          equation << name;

          if (k != params_size - 1)
            equation << ", ";
        }

      equation << ")";
    }
  else
    {
      const CCopasiVector<CChemEqElement> & substrs = reac->getChemEq().getSubstrates();
      const CCopasiVector<CChemEqElement> & prods = reac->getChemEq().getProducts();
      const std::vector<std::vector<std::string> > & keyMap = reac->getParameterMappings();
      CCopasiObject * obj;

      size_t substrs_size = substrs.size(), prods_size = prods.size();
      size_t k, m, mult;

      CChemEqElement* substr;
      CChemEqElement* prod;

      const CMassAction cMassAction = *static_cast<const CMassAction*>(reac->getFunction());

      equation << "(";

      obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[0][0]);

      if (!(reac->isLocalParameter(0)))
        {
          CModelValue* modval;
          modval = dynamic_cast< CModelValue * >(obj);

          equation << NameMap[modval->getKey()];
        }
      else
        {
          CCopasiParameter* param;
          param = dynamic_cast< CCopasiParameter * >(obj);

          equation << NameMap[param->getKey()];
        }

      for (k = 0; k < substrs_size; ++k)
        {
          substr = substrs[k];
          mult = (size_t) substr->getMultiplicity();

          assert(substr->getMetabolite());
          equation << " * " << NameMap[substr->getMetabolite()->getKey()];

          if (mult > 1)
            for (m = 1; m < mult; ++m)
              equation << " * " << NameMap[substr->getMetabolite()->getKey()];
        }

      if (cMassAction.isReversible() == TriTrue)
        {
          equation << " - ";

          obj = CCopasiRootContainer::getKeyFactory()->get(keyMap[2][0]);

          if (!(reac->isLocalParameter(2)))
            {
              CModelValue* modval;
              modval = dynamic_cast< CModelValue * >(obj);

              equation << NameMap[modval->getKey()];
            }
          else
            {
              CCopasiParameter* param;
              param = dynamic_cast< CCopasiParameter * >(obj);

              equation << NameMap[param->getKey()];
            }

          for (k = 0; k < prods_size; ++k)
            {
              prod = prods[k];
              mult = (size_t) prod->getMultiplicity();

              assert(prod->getMetabolite());
              equation << " * " << NameMap[prod->getMetabolite()->getKey()];

              if (mult > 1)
                for (m = 1; m < mult; ++m)
                  equation << " * " << NameMap[prod->getMetabolite()->getKey()];
            }
        }

      equation << ") ";
    }

  return equation.str();
}