bool CChemEq::addMetabolite(const std::string & key, const C_FLOAT64 multiplicity, const MetaboliteRole & role)
{
CChemEqElement element;
element.setMetabolite(key);
element.setMultiplicity(multiplicity);
switch (role)
{
case CChemEq::SUBSTRATE:
addElement(mSubstrates, element);
addElement(mBalances, element, CChemEq::SUBSTRATE);
break;
case CChemEq::PRODUCT:
addElement(mProducts, element);
addElement(mBalances, element);
break;
case CChemEq::MODIFIER:
addElement(mModifiers, element);
break;
default:
fatalError();
break;
}
return true;
}
void CModelExpansion::replaceInReaction(CReaction* pX, const ElementsMap & emap)
{
//replace in the chemical equation
size_t i;
for (i = 0; i < pX->getChemEq().getSubstrates().size(); ++i)
{
CChemEqElement * sourceElement = pX->getChemEq().getSubstrates()[i];
const CMetab* pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
if (pMetab)
{
sourceElement->setMetabolite(pMetab->getKey());
}
}
for (i = 0; i < pX->getChemEq().getProducts().size(); ++i)
{
CChemEqElement * sourceElement = pX->getChemEq().getProducts()[i];
const CMetab* pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
if (pMetab)
{
sourceElement->setMetabolite(pMetab->getKey());
}
}
for (i = 0; i < pX->getChemEq().getModifiers().size(); ++i)
{
CChemEqElement * sourceElement = pX->getChemEq().getModifiers()[i];
const CMetab* pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
if (pMetab)
{
sourceElement->setMetabolite(pMetab->getKey());
}
}
//mapping and local parameters
for (i = 0; i < pX->getFunctionParameters().size(); ++i)
{
switch (pX->getFunctionParameters()[i]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
case CFunctionParameter::VOLUME:
case CFunctionParameter::PARAMETER:
{
size_t k;
for (k = 0; k < pX->getParameterMappings()[i].size(); ++k)
{
std::string targetKey = emap.getDuplicateKey(pX->getParameterMappings()[i][k]);
if (targetKey != "")
pX->getParameterMappings()[i][k] = targetKey;
}
}
break;
case CFunctionParameter::TIME:
default:
break;
}
}
}
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;
}