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;
}
