CMetab * CMetabNameInterface::getMetabolite(const CModel* model,
    const std::string & metabolite,
    const std::string & compartment)
{
  unsigned C_INT32 Index;

  if (compartment != "")
    {
      Index = model->getCompartments().getIndex(compartment);
      if (Index != C_INVALID_INDEX)
        {
          CCompartment *pCompartment = model->getCompartments()[Index];

          Index = pCompartment->getMetabolites().getIndex(metabolite);
          if (Index != C_INVALID_INDEX)
            return pCompartment->getMetabolites()[Index];
        }

      return NULL;
    }

  Index = model->findMetabByName(metabolite);

  if (Index != C_INVALID_INDEX)
    return model->getMetabolites()[Index];

  return NULL;
}
Example #2
0
void CModelExpansion::replaceInMetab(CMetab* pX, const ElementsMap & emap)
{
  replaceInModelEntity(pX, emap);

  //is the metab in a compartment that needs to be replaced?
  if (emap.exists(pX->getCompartment()))
    {
      //move the metab to the new compartment
      CCompartment* oldComp = const_cast<CCompartment*>(pX->getCompartment());
      CCompartment* newComp = dynamic_cast<CCompartment*>(emap.getDuplicatePtr(pX->getCompartment()));
      bool success = false;

      do
        {
          success = newComp->addMetabolite(pX);

          if (success)
            {
              oldComp->getMetabolites().remove(pX->getObjectName());
              mpModel->setCompileFlag();
              mpModel->initializeMetabolites();
            }
          else
            {
              //rename the metab so that it can be added to the new compartment
              pX->setObjectName(pX->getObjectName() + "_");
              //TODO: check if the renaming actually worked
            }
        }
      while (!success);
    }
}
Example #3
0
CMetab *
UndoSpeciesData::createObjectIn(CModel *pModel)
{
  if (pModel == NULL)
    return NULL;

  createDependentObjects(pModel);

  if (pModel->getCompartments().getIndex(mCompartment) == C_INVALID_INDEX)
    return NULL;

  CCompartment * pCompartment = &pModel->getCompartments()[getCompartment()];

  if (pCompartment == NULL)
    return NULL;

  if (pCompartment->getMetabolites().getIndex(getName()) != C_INVALID_INDEX)
    return NULL;

  CMetab *pSpecies =  pModel->createMetabolite(getName(), getCompartment(), getIConc(), getStatus());

  if (pSpecies == NULL)
    return NULL;

  mKey = pSpecies->getKey();

  return pSpecies;
}
Example #4
0
void CQEventWidget1::addEvent(UndoEventData *pSData)
{
  assert(CCopasiRootContainer::getDatamodelList()->size() > 0);
  CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
  assert(pDataModel != NULL);

  CModel * pModel = pDataModel->getModel();
  assert(pModel != NULL);

  //reinsert the Event
  CEvent *pEvent =  pModel->createEvent(pSData->getName());

  //set the expressions
  pEvent->setTriggerExpression(pSData->getTriggerExpression());
  pEvent->setDelayExpression(pSData->getDelayExpression());
  pEvent->setPriorityExpression(pSData->getPriorityExpression());

  QList <UndoEventAssignmentData *> *assignmentData = pSData->getEventAssignmentData();
  QList <UndoEventAssignmentData *>::const_iterator i;

  for (i = assignmentData->begin(); i != assignmentData->end(); ++i)
    {
      UndoEventAssignmentData * assignData = *i;

      CCopasiObject * pObject = NULL;
      bool speciesExist = false;
      size_t ci;

      for (ci = 0; ci < pModel->getCompartments().size(); ci++)
        {
          CCompartment * pCompartment = pModel->getCompartments()[ci];

          if (pCompartment->getMetabolites().getIndex(assignData->getName()) != C_INVALID_INDEX)
            speciesExist = true;
        }

      if (speciesExist)
        {
          size_t index = pModel->findMetabByName(assignData->getName());
          pObject =  pModel->getMetabolites()[index];
        }
      else if (pModel->getModelValues().getIndex(assignData->getName()) != C_INVALID_INDEX)
        {
          pObject = pModel->getModelValues()[assignData->getName()];
        }
      else if (pModel->getReactions().getIndex(assignData->getName()) != C_INVALID_INDEX)
        {
          pObject = pModel->getReactions()[assignData->getName()];
        }

      const CModelEntity * pEntity = dynamic_cast< const CModelEntity * >(pObject);
      CEventAssignment *eventAssign = new CEventAssignment(pObject->getKey(), pEvent->getObjectParent());
      eventAssign->setExpression(assignData->getExpression());
      eventAssign->getExpressionPtr()->compile();
      pEvent->getAssignments().add(eventAssign);
    }

  std::string key = pEvent->getKey();
  protectedNotify(ListViews::EVENT, ListViews::ADD, key);

  mpListView->switchToOtherWidget(C_INVALID_INDEX, key);
}