void CLayout::exportToSBML(Layout * layout, const std::map<CCopasiObject*, SBase*> & copasimodelmap,
std::map<std::string, const SBase*>& sbmlIDs) const
{
if (!layout) return;
//Name and ID
std::string id = CSBMLExporter::createUniqueId(sbmlIDs, "layout_");
layout->setId(id);
sbmlIDs.insert(std::pair<const std::string, const SBase*>(id, layout));
//we do not check if the layout is already present in the libsbml data
//structures. This is no big deal since at the moment no software
//relies on persistent IDs for layout elements.
//Dimensions
Dimensions tmpDim = mDimensions.getSBMLDimensions();
layout->setDimensions(&tmpDim);
//some of the following code is not used at the moment: the COPASI model map
//does not contain glyphs. Since this may change in the future I leave the code
//below.
// create a map from COPASI layout object to SBML objects. We do not put
//the layout objects into the global map (copasimodelmap) but we need to have
//access to all objects in the current layout since speciesReferenceGlyph and
//textGlyph need to reference other graphical objects.
std::map<const CLBase*, const SBase*> layoutmap;
//Compartment glyphs
unsigned C_INT32 i, imax = mvCompartments.size();
for (i = 0; i < imax; ++i)
{
CLCompartmentGlyph * tmp = mvCompartments[i];
//check if the compartment glyph exists in the libsbml data
std::map<CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
CompartmentGlyph * pCG;
if (it == copasimodelmap.end()) //not found
{
pCG = new CompartmentGlyph;
layout->getListOfCompartmentGlyphs()->appendAndOwn(pCG);
}
else
{
pCG = dynamic_cast<CompartmentGlyph*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pCG));
tmp->exportToSBML(pCG, copasimodelmap, sbmlIDs);
}
//Species glyphs
imax = mvMetabs.size();
for (i = 0; i < imax; ++i)
{
CLMetabGlyph * tmp = mvMetabs[i];
//check if the glyph exists in the libsbml data
std::map<CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
SpeciesGlyph * pG;
if (it == copasimodelmap.end()) //not found
{
pG = new SpeciesGlyph;
layout->getListOfSpeciesGlyphs()->appendAndOwn(pG);
}
else
{
pG = dynamic_cast<SpeciesGlyph*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
tmp->exportToSBML(pG, copasimodelmap, sbmlIDs);
}
//Reaction glyphs
imax = mvReactions.size();
for (i = 0; i < imax; ++i)
{
CLReactionGlyph * tmp = mvReactions[i];
//check if the glyph exists in the libsbml data
std::map<CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
ReactionGlyph * pG;
if (it == copasimodelmap.end()) //not found
{
pG = new ReactionGlyph;
layout->getListOfReactionGlyphs()->appendAndOwn(pG);
}
else
{
pG = dynamic_cast<ReactionGlyph*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
//we need to pass the layoutmap here for 2 reasons:
//1. the metabreferenceglyphs need to be added
//2. the metabreferenceglyphs need to resolve the reference to the metabglyph
tmp->exportToSBML(pG, copasimodelmap, sbmlIDs, layoutmap);
}
//Text glyphs
imax = mvLabels.size();
for (i = 0; i < imax; ++i)
{
CLTextGlyph * tmp = mvLabels[i];
//check if the glyph exists in the libsbml data
std::map<CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
TextGlyph * pG;
if (it == copasimodelmap.end()) //not found
{
pG = new TextGlyph;
layout->getListOfTextGlyphs()->appendAndOwn(pG);
}
else
{
pG = dynamic_cast<TextGlyph*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
tmp->exportToSBML(pG, copasimodelmap, sbmlIDs);
}
//generic glyphs
imax = mvGraphicalObjects.size();
for (i = 0; i < imax; ++i)
{
CLGraphicalObject * tmp = mvGraphicalObjects[i];
//check if the glyph exists in the libsbml data
std::map<CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
GraphicalObject * pG;
if (it == copasimodelmap.end()) //not found
{
pG = new GraphicalObject;
layout->getListOfAdditionalGraphicalObjects()->appendAndOwn(pG);
}
else
{
pG = dynamic_cast<GraphicalObject*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
tmp->exportToSBML(pG, copasimodelmap, sbmlIDs);
}
//now that we have all graphical objects in the layoutmap we can resolve the references
//in the text glyphs
imax = mvLabels.size();
for (i = 0; i < imax; ++i)
{
const CLTextGlyph * tmp = mvLabels[i];
//find the corresponding SBML object
std::map<const CLBase*, const SBase*>::const_iterator it = layoutmap.find(tmp);
if (it != layoutmap.end() && it->second && dynamic_cast<const TextGlyph*>(it->second))
{
tmp->exportReferenceToSBML(const_cast<TextGlyph*>(dynamic_cast<const TextGlyph*>(it->second)), layoutmap);
}
}
}
void CLGeneralGlyph::exportToSBML(GraphicalObject * g, //TODO
const std::map<const CCopasiObject*, SBase*> & copasimodelmap,
std::map<std::string, const SBase*>& sbmlIDs,
std::map<const CLBase*, const SBase*> & layoutmap) const
{
if (!g) return;
//call the coresponding method of the base class
CLGraphicalObject::exportToSBML(g, copasimodelmap, sbmlIDs);
#if LIBSBML_VERSION >= 50800
GeneralGlyph *general = dynamic_cast<GeneralGlyph *>(g);
if (!general) return;
//reference to model objects
CCopasiObject* tmp = getModelObject();
if (tmp)
{
std::map<const CCopasiObject*, SBase*>::const_iterator it = copasimodelmap.find(tmp);
if (it != copasimodelmap.end())
{
if (it->second)
general->setReferenceId(it->second->getId());
}
const CLBase* base = dynamic_cast<const CLBase*>(tmp);
if (base)
{
std::map<const CLBase*, const SBase*>::const_iterator it2 = layoutmap.find(base);
if (it2 != layoutmap.end())
{
if (it2->second)
general->setReferenceId(it2->second->getId());
}
}
}
//curve
mCurve.exportToSBML(general->getCurve(), copasimodelmap);
//reference glyphs
size_t i, imax = mvReferences.size();
for (i = 0; i < imax; ++i)
{
CLReferenceGlyph * tmp = mvReferences[i];
//check if the glyph exists in the libsbml data
std::map<const CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
ReferenceGlyph * pG;
if (it == copasimodelmap.end()) //not found
{
pG = general->createReferenceGlyph();
}
else
{
pG = dynamic_cast<ReferenceGlyph*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
tmp->exportToSBML(pG, copasimodelmap, sbmlIDs, layoutmap);
}
imax = mvSubglyphs.size();
for (i = 0; i < imax; ++i)
{
CLGraphicalObject * tmp = mvSubglyphs[i];
CLMetabGlyph * metab = dynamic_cast<CLMetabGlyph*>(tmp);
CLCompartmentGlyph* comp = dynamic_cast<CLCompartmentGlyph*>(tmp);
CLGeneralGlyph* gg = dynamic_cast<CLGeneralGlyph*>(tmp);
CLTextGlyph* text = dynamic_cast<CLTextGlyph*>(tmp);
//check if the glyph exists in the libsbml data
std::map<const CCopasiObject*, SBase*>::const_iterator it;
it = copasimodelmap.find(tmp);
GraphicalObject * pG;
if (it == copasimodelmap.end()) //not found
{
if (metab)
pG = ((Layout*)g->getParentSBMLObject()->getParentSBMLObject())->createSpeciesGlyph();
else if (comp)
pG = ((Layout*)g->getParentSBMLObject()->getParentSBMLObject())->createCompartmentGlyph();
else if (gg)
pG = ((Layout*)g->getParentSBMLObject()->getParentSBMLObject())->createGeneralGlyph();
else if (text)
pG = ((Layout*)g->getParentSBMLObject()->getParentSBMLObject())->createTextGlyph();
else
pG = ((Layout*)g->getParentSBMLObject()->getParentSBMLObject())->createAdditionalGraphicalObject();
}
else
{
pG = dynamic_cast<GraphicalObject*>(it->second);
}
layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
if (metab)
metab->exportToSBML(static_cast<SpeciesGlyph*>(pG), copasimodelmap, sbmlIDs);
else if (comp)
comp->exportToSBML(static_cast<CompartmentGlyph*>(pG), copasimodelmap, sbmlIDs);
else if (text)
text->exportToSBML(static_cast<TextGlyph*>(pG), copasimodelmap, sbmlIDs);
else if (gg)
gg->exportToSBML(pG, copasimodelmap, sbmlIDs, layoutmap);
else
tmp->exportToSBML(pG, copasimodelmap, sbmlIDs);
}
#endif // LIBSBML_VERSION >= 50800
}