void CModelExpansion::createDiffusionReaction(const std::string & name,
const std::string & metabkey1, const std::string & metabkey2,
const std::string & parameterkey)
{
//try creating the object until we find a name that is not yet used
CReaction* newObj;
std::ostringstream name_;
name_ << name;
do
{
newObj = mpModel->createReaction(name_.str());
name_ << "_";
}
while (!newObj);
newObj->setReversible(true);
newObj->addSubstrate(metabkey1, 1);
newObj->addProduct(metabkey2, 1);
newObj->setFunction("Mass action (reversible)");
newObj->addParameterMapping("substrate", metabkey1);
newObj->addParameterMapping("product", metabkey2);
newObj->setParameterMapping(0, parameterkey);
newObj->setParameterMapping(2, parameterkey);
}
void CModelExpansion::duplicateReaction(const CReaction* source, const std::string & index, const SetOfModelElements & sourceSet, ElementsMap & emap)
{
//if the source object has already been duplicated: do nothing
if (emap.exists(source))
return;
//try creating the object until we find a name that is not yet used
CReaction* newObj;
std::ostringstream infix;
do
{
std::ostringstream name;
name << source->getObjectName() << infix.str() << index;
newObj = mpModel->createReaction(name.str());
infix << "_";
}
while (!newObj);
//add duplicated object to the map
emap.add(source, newObj);
//now copy the chemical equation
size_t i;
for (i = 0; i < source->getChemEq().getSubstrates().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getSubstrates()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addSubstrate(pMetab->getKey(), sourceElement->getMultiplicity());
}
for (i = 0; i < source->getChemEq().getProducts().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getProducts()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addProduct(pMetab->getKey(), sourceElement->getMultiplicity());
}
for (i = 0; i < source->getChemEq().getModifiers().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getModifiers()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addModifier(pMetab->getKey());
}
newObj->setReversible(source->isReversible());
//set the kinetic function
newObj->setFunction(const_cast<CFunction*>(source->getFunction()));
//mapping and local parameters
for (i = 0; i < newObj->getFunctionParameters().size(); ++i)
{
switch (newObj->getFunctionParameters()[i]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
{
bool isVector = (newObj->getFunctionParameters()[i]->getType() == CFunctionParameter::VFLOAT64);
if (isVector)
newObj->clearParameterMapping(i);
size_t k;
for (k = 0; k < source->getParameterMappings()[i].size(); ++k)
{
//we assume that by now the metab was copied if necessary.
//therefore we only need to check the map.
std::string targetKey;
if (emap.exists(source->getParameterMappings()[i][k]))
targetKey = emap.getDuplicateKey(source->getParameterMappings()[i][k]);
else
targetKey = source->getParameterMappings()[i][k];
if (isVector)
newObj->addParameterMapping(i, targetKey);
else
newObj->setParameterMapping(i, targetKey);
}
}
break;
case CFunctionParameter::TIME:
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
break;
case CFunctionParameter::VOLUME:
if (sourceSet.contains(source->getParameterMappings()[i][0]))
{
if (!emap.exists(source->getParameterMappings()[i][0]))
{
const CCompartment* pSource = dynamic_cast<const CCompartment*>(
(CCopasiRootContainer::getKeyFactory()->get(source->getParameterMappings()[i][0])));
duplicateCompartment(pSource, index, sourceSet, emap);
}
newObj->setParameterMapping(i, emap.getDuplicateKey(source->getParameterMappings()[i][0]));
}
else //add the original metab
{
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
}
break;
case CFunctionParameter::PARAMETER:
if (newObj->isLocalParameter(i))
{
//just copy the value
newObj->setParameterValue(newObj->getFunctionParameters()[i]->getObjectName(),
source->getParameterValue(newObj->getFunctionParameters()[i]->getObjectName()));
}
else
{
if (sourceSet.contains(source->getParameterMappings()[i][0]))
{
if (!emap.exists(source->getParameterMappings()[i][0]))
{
const CModelValue* pSource = dynamic_cast<const CModelValue*>(
(CCopasiRootContainer::getKeyFactory()->get(source->getParameterMappings()[i][0])));
duplicateGlobalQuantity(pSource, index, sourceSet, emap);
}
newObj->setParameterMapping(i, emap.getDuplicateKey(source->getParameterMappings()[i][0]));
}
else //add the original global quantity
{
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
}
}
break;
default:
break;
}
}
newObj->setNotes(source->getNotes());
newObj->setMiriamAnnotation(source->getMiriamAnnotation(), newObj->getKey(), source->getKey());
}
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;
}
