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 CReactionInterface::loadMappingAndValues(const CReaction & rea) { bool success = true; std::vector< std::vector<std::string> >::const_iterator it; std::vector< std::vector<std::string> >::const_iterator iEnd; std::vector<std::string>::const_iterator jt; std::vector<std::string>::const_iterator jEnd; size_t i; std::string metabName; const CModelEntity* pObj; std::vector<std::string> SubList; SubList.resize(1); SubList[0] = "unknown"; mNameMap.resize(size()); for (i = 0; i != size(); ++i) { mNameMap[i] = SubList; } mValues.resize(size(), 0.1); mIsLocal.resize(size(), false); it = rea.getParameterMappings().begin(); iEnd = rea.getParameterMappings().end(); for (i = 0; it != iEnd; ++it, ++i) { if (isVector(i)) { assert((getUsage(i) == CFunctionParameter::SUBSTRATE) || (getUsage(i) == CFunctionParameter::PRODUCT) || (getUsage(i) == CFunctionParameter::MODIFIER)); SubList.clear(); for (jt = it->begin(), jEnd = it->end(); jt != jEnd; ++jt) { metabName = CMetabNameInterface::getDisplayName(mpModel, *jt, true); assert(metabName != ""); SubList.push_back(metabName); } } else { assert(it->size() == 1); SubList.resize(1); SubList[0] = "unknown"; switch (getUsage(i)) { case CFunctionParameter::SUBSTRATE: case CFunctionParameter::PRODUCT: case CFunctionParameter::MODIFIER: metabName = CMetabNameInterface::getDisplayName(mpModel, *(it->begin()), true); // assert(metabName != ""); SubList[0] = metabName; //TODO: check if the metabolite is in the chemical equation with the correct rule break; case CFunctionParameter::VOLUME: pObj = dynamic_cast<const CCompartment*>(CCopasiRootContainer::getKeyFactory()->get(*(it->begin()))); assert(pObj); SubList[0] = pObj->getObjectName(); break; case CFunctionParameter::TIME: pObj = dynamic_cast<const CModel*>(CCopasiRootContainer::getKeyFactory()->get(*(it->begin()))); assert(pObj); SubList[0] = pObj->getObjectName(); break; case CFunctionParameter::PARAMETER: { const CCopasiParameter * pParameter = rea.getParameters().getParameter(getParameterName(i)); if (pParameter != NULL) { mValues[i] = * pParameter->getValue().pDOUBLE; } else { mValues[i] = std::numeric_limits< C_FLOAT64 >::quiet_NaN(); } mIsLocal[i] = rea.isLocalParameter(i); if (!mIsLocal[i]) { pObj = dynamic_cast<const CModelValue*>(CCopasiRootContainer::getKeyFactory()->get(*(it->begin()))); if (pObj) { SubList[0] = pObj->getObjectName(); mValues[i] = pObj->getInitialValue(); } } } break; default: break; } } mNameMap[i] = SubList; } return success; }
bool CModelAdd::addReactions(std::string name) { bool info = false; //create copies of the relevant reactions size_t i, imax = mmModel->getReactions().size(); size_t ic, icmax = mmModel->getCompartments().size(); for (ic = 0; ic < icmax; ++ic) { const CCompartment* sourceComp = &mmModel->getCompartments()[ic]; if (!sourceComp) return info; for (i = 0; i < imax; ++i) { CReaction * sourceReac = &mmModel->getReactions()[i]; if (reactionInvolvesCompartment(sourceReac, sourceComp)) { std::string newName = sourceReac->getObjectName() + "_" + name; CReaction* newReac = mpModel->createReaction(newName); if (!newReac) return info; //copy the chemical equation. If the involved metabs are among those that //were copied with the compartment, replace them. Otherwise keep the original metab newReac->setReversible(sourceReac->isReversible()); std::map<std::string, std::string>::const_iterator mapIt; std::string targetKey; size_t j, jmax = sourceReac->getChemEq().getSubstrates().size(); for (j = 0; j < jmax; ++j) { const CChemEqElement * sourceElement = &sourceReac->getChemEq().getSubstrates()[j]; //check if the metab is in the map. If yes, translate it, otherwise not. mapIt = keyMap.find(sourceElement->getMetaboliteKey()); if (mapIt == keyMap.end()) { targetKey = sourceElement->getMetaboliteKey(); } else targetKey = mapIt->second; newReac->addSubstrate(targetKey, sourceElement->getMultiplicity()); } jmax = sourceReac->getChemEq().getProducts().size(); for (j = 0; j < jmax; ++j) { const CChemEqElement * sourceElement = &sourceReac->getChemEq().getProducts()[j]; //check if the metab is in the map. If yes, translate it, otherwise not. mapIt = keyMap.find(sourceElement->getMetaboliteKey()); if (mapIt == keyMap.end()) { targetKey = sourceElement->getMetaboliteKey(); } else targetKey = mapIt->second; newReac->addProduct(targetKey, sourceElement->getMultiplicity()); } jmax = sourceReac->getChemEq().getModifiers().size(); for (j = 0; j < jmax; ++j) { const CChemEqElement * sourceElement = &sourceReac->getChemEq().getModifiers()[j]; //check if the metab is in the map. If yes, translate it, otherwise not. mapIt = keyMap.find(sourceElement->getMetaboliteKey()); if (mapIt == keyMap.end()) { targetKey = sourceElement->getMetaboliteKey(); } else targetKey = mapIt->second; newReac->addModifier(targetKey); } //set the kinetic function newReac->setFunction(const_cast<CFunction*>(sourceReac->getFunction())); //mapping and local parameters for (j = 0; j < newReac->getFunctionParameters().size(); ++j) { switch (newReac->getFunctionParameters()[j]->getUsage()) { case CFunctionParameter::SUBSTRATE: case CFunctionParameter::PRODUCT: case CFunctionParameter::MODIFIER: //translate the metab keys { bool isVector = (newReac->getFunctionParameters()[j]->getType() == CFunctionParameter::VFLOAT64); //we assume that only SUBSTRATE, PRODUCT, MODIFIER can be vectors if (isVector) newReac->clearParameterMapping(j); size_t k; for (k = 0; k < sourceReac->getParameterMappings()[j].size(); ++k) { mapIt = keyMap.find(sourceReac->getParameterMappings()[j][k]); if (mapIt == keyMap.end()) { targetKey = sourceReac->getParameterMappings()[j][k]; } else targetKey = mapIt->second; if (isVector) newReac->addParameterMapping(j, targetKey); else newReac->setParameterMapping(j, targetKey); } } break; case CFunctionParameter::TIME: //just copy the key { mapIt = keyMap.find(sourceReac->getParameterMappings()[j][0]); if (mapIt == keyMap.end()) { targetKey = sourceReac->getParameterMappings()[j][0]; } else targetKey = mapIt->second; newReac->setParameterMapping(j, targetKey); } break; case CFunctionParameter::VOLUME: //translate the compartment key if necessary if (sourceReac->getParameterMappings()[j][0] == sourceComp->getKey()) newReac->setParameterMapping(j, keyMap[sourceComp->getKey()]); else { mapIt = keyMap.find(sourceReac->getParameterMappings()[j][0]); if (mapIt == keyMap.end()) { targetKey = sourceReac->getParameterMappings()[j][0]; } else targetKey = mapIt->second; newReac->setParameterMapping(j, targetKey); } //TODO: this needs to be adapted when sets of compartments will be copied break; case CFunctionParameter::PARAMETER: if (sourceReac->isLocalParameter(j)) newReac->setParameterValue(newReac->getFunctionParameters()[j]->getObjectName(), sourceReac->getParameterValue(newReac->getFunctionParameters()[j]->getObjectName())); else { mapIt = keyMap.find(sourceReac->getParameterMappings()[j][0]); if (mapIt == keyMap.end()) { targetKey = sourceReac->getParameterMappings()[j][0]; } else targetKey = mapIt->second; newReac->setParameterMapping(j, targetKey); } break; default: return info; break; } } } } } return true; }