bool CCopasiSpringLayout::initFromLayout(CLayout* layout, Parameters* ppp)
{
mpLayout = layout;
mpPar = ppp;
if (!mpLayout) return false;
if (!ppp) return false;
mCompartmentMap.clear();
//store the compartment glyph for each species glyph (if it exists)
unsigned int i;
for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size() ; ++i)
{
CMetab* metab = dynamic_cast<CMetab*>(mpLayout->getListOfMetaboliteGlyphs()[i].getModelObject());
CLCompartmentGlyph* tmp = NULL;
if (metab)
{
unsigned int j;
for (j = 0; j < mpLayout->getListOfCompartmentGlyphs().size(); ++j)
if (mpLayout->getListOfCompartmentGlyphs()[j].getModelObjectKey() == metab->getCompartment()->getKey())
{
tmp = &mpLayout->getListOfCompartmentGlyphs()[j];
break;
}
}
mCompartmentMap[&mpLayout->getListOfMetaboliteGlyphs()[i]] = tmp;
}
//store the compartment glyph for each reaction glyph (if it exists)
for (i = 0; i < mpLayout->getListOfReactionGlyphs().size() ; ++i)
{
mCompartmentMap[&mpLayout->getListOfReactionGlyphs()[i]] = findCompartmentForReactionNode(mpLayout->getListOfReactionGlyphs()[i]);
}
//create the list of constant positional relations
//we assume that text glyphs are always moved with the glyph they refer to.
//(i.e. the are not layed out independently)
mFixedRelations.clear();
for (i = 0; i < mpLayout->getListOfTextGlyphs().size(); ++i)
{
CoordinateRelation tmp;
tmp.target = &mpLayout->getListOfTextGlyphs()[i];
tmp.source = mpLayout->getListOfTextGlyphs()[i].getGraphicalObject();
if (tmp.source)
{
tmp.diff = tmp.target->getPosition() - tmp.source->getPosition();
mFixedRelations.push_back(tmp);
}
}
return true;
}
bool
CMetabNameInterface::doesExist(const CModel* model,
const std::string & metabolite,
const std::string & compartment)
{
if (model == NULL)
return false;
CDataContainer::objectMap::range Range = model->getMetabolites().getObjects().equal_range(metabolite);
CMetab * pSpecies = NULL;
for (; Range.first != Range.second; ++Range.first)
if ((pSpecies = dynamic_cast< CMetab * >(*Range.first)) != NULL)
{
if (compartment.empty() ||
pSpecies->getCompartment()->getObjectName() == compartment) return true;
}
return false;
}
std::string
CMetabNameInterface::createUniqueDisplayName(const CMetab & metab, const bool & quoted)
{
return createUniqueDisplayName(metab.getObjectName(), metab.getCompartment()->getObjectName(), quoted);
}
std::string
CMetabNameInterface::getDisplayName(const CModel* model, const CMetab & metab, const bool & quoted)
{
return getDisplayName(model, metab.getObjectName(), metab.getCompartment()->getObjectName(), quoted);
}
void CChemEqInterface::completeCompartments()
{
std::string DefaultCompartment;
if (mpModel->getCompartments().size() == 0)
DefaultCompartment = "compartment";
else
DefaultCompartment = mpModel->getCompartments()[0]->getObjectName();
// We try to find a reaction compartment. Note, it is not possible to use
// getCompartment as writeToChemEq may fail;
std::string ReactionCompartment = "";
bool first = true;
bool HaveReactionCompartment = true;
std::vector< std::string >::iterator itCompartment, endCompartment;
itCompartment = mSubstrateCompartments.begin();
endCompartment = mSubstrateCompartments.end();
for (; itCompartment != endCompartment && HaveReactionCompartment; ++itCompartment)
{
if (*itCompartment == "") continue;
if (first)
{
ReactionCompartment = *itCompartment;
first = false;
}
else if (ReactionCompartment != *itCompartment)
HaveReactionCompartment = false;
}
itCompartment = mProductCompartments.begin();
endCompartment = mProductCompartments.end();
for (; itCompartment != endCompartment && HaveReactionCompartment; ++itCompartment)
{
if (*itCompartment == "") continue;
if (first)
{
ReactionCompartment = *itCompartment;
first = false;
}
else if (ReactionCompartment != *itCompartment)
HaveReactionCompartment = false;
}
itCompartment = mModifierCompartments.begin();
endCompartment = mModifierCompartments.end();
for (; itCompartment != endCompartment && HaveReactionCompartment; ++itCompartment)
{
if (*itCompartment == "") continue;
if (first)
{
ReactionCompartment = *itCompartment;
first = false;
}
else if (ReactionCompartment != *itCompartment)
HaveReactionCompartment = false;
}
if (first)
ReactionCompartment = DefaultCompartment;
CMetab * pMetab;
std::vector< std::string >::iterator itMetab;
itMetab = mSubstrateNames.begin();
itCompartment = mSubstrateCompartments.begin();
endCompartment = mSubstrateCompartments.end();
for (; itCompartment != endCompartment; ++itCompartment, ++itMetab)
if (*itCompartment == "")
{
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, "");
if (pMetab == NULL)
*itCompartment = ReactionCompartment;
else if (CMetabNameInterface::isUnique(mpModel, *itMetab))
*itCompartment = pMetab->getCompartment()->getObjectName();
else // Multiple metabolites with the given name exist.
{
// 1. Metabolite in the reaction compartment
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, ReactionCompartment);
// 2. Metabolite in the default compartment if different from reaction compartment
if (pMetab == NULL && ReactionCompartment != DefaultCompartment)
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, DefaultCompartment);
// 3. The first metabolite found
if (pMetab == NULL)
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, "");
*itCompartment = pMetab->getCompartment()->getObjectName();
}
}
itMetab = mProductNames.begin();
itCompartment = mProductCompartments.begin();
endCompartment = mProductCompartments.end();
for (; itCompartment != endCompartment; ++itCompartment, ++itMetab)
if (*itCompartment == "")
{
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, "");
if (pMetab == NULL)
*itCompartment = ReactionCompartment;
else if (CMetabNameInterface::isUnique(mpModel, *itMetab))
*itCompartment = pMetab->getCompartment()->getObjectName();
else // Multiple metabolites with the given name exist.
{
// 1. Metabolite in the reaction compartment
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, ReactionCompartment);
// 2. Metabolite in the default compartment if different from reaction compartment
if (pMetab == NULL && ReactionCompartment != DefaultCompartment)
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, DefaultCompartment);
// 3. The first metabolite found
if (pMetab == NULL)
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, "");
*itCompartment = pMetab->getCompartment()->getObjectName();
}
}
itMetab = mModifierNames.begin();
itCompartment = mModifierCompartments.begin();
endCompartment = mModifierCompartments.end();
for (; itCompartment != endCompartment; ++itCompartment, ++itMetab)
if (*itCompartment == "")
{
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, "");
if (pMetab == NULL)
*itCompartment = ReactionCompartment;
else if (CMetabNameInterface::isUnique(mpModel, *itMetab))
*itCompartment = pMetab->getCompartment()->getObjectName();
else // Multiple metabolites with the given name exist.
{
// 1. Metabolite in the reaction compartment
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, ReactionCompartment);
// 2. Metabolite in the default compartment if different from reaction compartment
if (pMetab == NULL && ReactionCompartment != DefaultCompartment)
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, DefaultCompartment);
// 3. The first metabolite found
if (pMetab == NULL)
pMetab = CMetabNameInterface::getMetabolite(mpModel, *itMetab, "");
*itCompartment = pMetab->getCompartment()->getObjectName();
}
}
}