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); } }
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; }
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; }