Example #1
0
void CModelExpansion::replaceInEvent(CEvent* pX, const ElementsMap & emap)
{
  replaceInExpression(pX->getTriggerExpressionPtr(), emap);
  replaceInExpression(pX->getDelayExpressionPtr(), emap);

  //now the event assignments...
  size_t i;

  for (i = 0; i < pX->getAssignments().size(); ++i)
    {
      CEventAssignment* pAssignment = pX->getAssignments()[i];
      replaceInExpression(pAssignment->getExpressionPtr(), emap);

      std::string replacekey = emap.getDuplicateKey(pAssignment->getTargetKey());

      if (replacekey != "")
        pAssignment->setTargetKey(replacekey);
    }
}
Example #2
0
bool CModelMerging::mergeMetabolites(std::string toKey, std::string  key)
{

  bool info = false;

  //merge in  the relevant reactions

  size_t i, imax = mpModel->getReactions().size();
  size_t j, jmax;

  for (i = 0; i < imax; ++i)
    {
      CReaction * reac = &mpModel->getReactions()[i];

      jmax = reac->getChemEq().getSubstrates().size();

      for (j = 0; j < jmax; ++j)
        {
          CChemEqElement * subst = const_cast< CChemEqElement * >(&reac->getChemEq().getSubstrates()[j]);

          if (subst->getMetabolite()->getKey() == key)
            subst->setMetabolite(toKey);
        }

      jmax = reac->getChemEq().getProducts().size();

      for (j = 0; j < jmax; ++j)
        {
          CChemEqElement * prod = const_cast< CChemEqElement * >(&reac->getChemEq().getProducts()[j]);

          if (prod->getMetabolite()->getKey() == key)
            prod->setMetabolite(toKey);
        }

      jmax = reac->getChemEq().getModifiers().size();

      for (j = 0; j < jmax; ++j)
        {
          CChemEqElement * modif = const_cast< CChemEqElement * >(&reac->getChemEq().getModifiers()[j]);

          if (modif->getMetabolite()->getKey() == key)
            modif->setMetabolite(toKey);
        }

      //change parameters of  the kinetic function

      for (j = 0; j < reac->getFunctionParameters().size(); ++j)
        {
          switch (reac->getFunctionParameters()[j]->getUsage())
            {
              case CFunctionParameter::SUBSTRATE:
              case CFunctionParameter::PRODUCT:
              case CFunctionParameter::MODIFIER:
                //translate the metab keys
              {

                //we assume that only SUBSTRATE, PRODUCT, MODIFIER can be vectors

                size_t k, kmax = reac->getParameterMappings()[j].size();

                for (k = 0; k < kmax; ++k)
                  if (reac->getParameterMappings()[j][k] == key)
                    reac->getParameterMappings()[j][k] = toKey;
              }
              break;

              case CFunctionParameter::TIME:
                break;

              case CFunctionParameter::VOLUME:
                // ??? TODO : have to ask
                break;

              case CFunctionParameter::PARAMETER:
                break;

              default:
                return info;
                break;
            }
        }
    }

  imax = mpModel->getEvents().size();

  for (i = 0; i < imax; ++i)
    {
      CEvent * event = &mpModel->getEvents()[i];

      if (!event) return info;

      /* merge in  trigger expressions */
      CExpression* pExpression = event->getTriggerExpressionPtr();

      if (pExpression == NULL) return info;

      if (!mergeInExpression(toKey, key, pExpression))  return info;

      pExpression = event->getDelayExpressionPtr();

      if (pExpression)
        if (!mergeInExpression(toKey, key, pExpression))
          return info;

      jmax = event->getAssignments().size();

      for (j = 0; j < jmax; ++j)
        {
          CEventAssignment* assignment = &event->getAssignments()[j];

          if (!assignment) return info;

          std::string assignmentKey = assignment->getTargetKey();

          if (assignmentKey == key) assignment->setTargetKey(toKey);

          pExpression = assignment->getExpressionPtr();

          if (pExpression == NULL) return info;

          if (!mergeInExpression(toKey, key, pExpression))    return info;
        }
    }

  imax = mpModel->getMetabolites().size();

  for (i = 0; i < imax; ++i)
    {
      CMetab* metab = &mpModel->getMetabolites()[i];

      if (!metab) return info;

      switch (metab->getStatus())
        {
          case CModelEntity::FIXED:
          case CModelEntity::REACTIONS:

            break;

          case CModelEntity::ASSIGNMENT:

            if (!mergeInExpression(toKey, key, metab->getExpressionPtr())) return info;

            break;

          case CModelEntity::ODE:

            if (!mergeInExpression(toKey, key, metab->getExpressionPtr())) return info;

            if (metab->getInitialExpression() != "")
              if (!mergeInExpression(toKey, key, metab->getInitialExpressionPtr())) return info;

            break;

          default:
            return info;
            break;
        }
    }

  imax = mpModel->getCompartments().size();

  for (i = 0; i < imax; ++i)
    {
      CCompartment* comp = &mpModel->getCompartments()[i];

      if (!comp) return info;

      switch (comp ->getStatus())
        {
          case CModelEntity::FIXED:

            break;

          case CModelEntity::ASSIGNMENT:

            if (!mergeInExpression(toKey, key, comp->getExpressionPtr())) return info;

            break;

          case CModelEntity::ODE:

            if (!mergeInExpression(toKey, key, comp->getExpressionPtr())) return info;

            if (comp->getInitialExpression() != "")
              if (!mergeInExpression(toKey, key, comp->getInitialExpressionPtr())) return info;

            break;

          default:
            return info;
            break;
        }
    }

  imax = mpModel->getModelValues().size();

  for (i = 0; i < imax; ++i)
    {
      CModelValue* modval = &mpModel->getModelValues()[i];

      if (!modval) return info;

      switch (modval ->getStatus())
        {
          case CModelEntity::FIXED:

            break;

          case CModelEntity::ASSIGNMENT:

            if (!mergeInExpression(toKey, key, modval->getExpressionPtr())) return info;

            break;

          case CModelEntity::ODE:

            if (!mergeInExpression(toKey, key, modval->getExpressionPtr())) return info;

            if (modval->getInitialExpression() != "")
              if (!mergeInExpression(toKey, key, modval->getInitialExpressionPtr())) return info;

            break;

          default:
            return info;
            break;
        }
    }

  return true;
}
Example #3
0
bool CModelAdd::addEvents(std::string name)
{

  bool info = false;

  size_t i, imax = mmModel->getEvents().size();

  for (i = 0; i < imax; ++i)
    {
      const CEvent* sourceEvent = &mmModel->getEvents()[i];

      if (!sourceEvent) return info;

      //create new event

      std::string eventName;

      eventName = sourceEvent->getObjectName();

      std::string appendix = "";
#if 0
      unsigned int counter = 2;
      std::ostringstream numberStream;

      while (mpModel->getEvents().getIndex(eventName + appendix) != C_INVALID_INDEX)
        {
          numberStream.str("");
          numberStream << "_" << counter;
          counter++;
          appendix = numberStream.str();
        }

#else
      appendix = "_" + name;
#endif

      CEvent* newEvent = mpModel->createEvent(eventName + appendix);

      if (newEvent == NULL) return info;

      /* copy trigger expression */

      if (sourceEvent->getTriggerExpressionPtr() != NULL)
        {
          if (!copyTriggerExpression(sourceEvent, newEvent))
            return info;
        }
      else
        {
          return info;
        }

      /* set whether the calculation or the assignment shall be delayed */

      newEvent->setDelayAssignment(sourceEvent->getDelayAssignment());

      /* copy the delay expression */

      if (sourceEvent->getDelayExpressionPtr() != NULL)
        if (!copyDelayExpression(sourceEvent, newEvent)) return info;

      /* copy the assignments */

      size_t j, jmax = sourceEvent->getAssignments().size();

      for (j = 0; j < jmax; ++j)
        {
          const CEventAssignment* sourceAssignment = &sourceEvent->getAssignments()[j];

          if (!sourceAssignment) return info;

          std::string key = sourceAssignment->getTargetKey();

          CEventAssignment* newAssignment = new CEventAssignment;

          newEvent->getAssignments().add(newAssignment, true);

          newAssignment->setTargetKey(keyMap[key]);

          if (sourceAssignment->getExpressionPtr() != NULL)
            {
              if (!copyEventAssignmentExpression(sourceAssignment, newAssignment))
                return info;
            }
          else
            {
              return info;
            }
        }
    }

  return true;
}