//static
CLayout * SBMLDocumentLoader::createLayout(const Layout & sbmlLayout,
const std::map<std::string, std::string> & modelmap,
std::map<std::string, std::string> & layoutmap
#ifdef USE_CRENDER_EXTENSION
, const std::map<std::string, std::string>& globalIdToKeyMap
//,const std::map<std::string,std::map<std::string,std::string> >& globalColorIdToKeyMapMap
//,const std::map<std::string,std::map<std::string,std::string> >& globalGradientIdToKeyMapMap
//,const std::map<std::string,std::map<std::string,std::string> >& globalLineEndingIdToKeyMapMap
#endif /* USE_CRENDER_EXTENSION */
, const CCopasiContainer * pParent
)
{
CLayout* layout = new CLayout(sbmlLayout, layoutmap, pParent);
//compartments
unsigned C_INT32 i, iMax = sbmlLayout.getListOfCompartmentGlyphs()->size();
for (i = 0; i < iMax; ++i)
{
const CompartmentGlyph* tmp
= dynamic_cast<const CompartmentGlyph*>(sbmlLayout.getListOfCompartmentGlyphs()->get(i));
if (tmp)
layout->addCompartmentGlyph(new CLCompartmentGlyph(*tmp, modelmap, layoutmap));
}
//species
iMax = sbmlLayout.getListOfSpeciesGlyphs()->size();
for (i = 0; i < iMax; ++i)
{
const SpeciesGlyph* tmp
= dynamic_cast<const SpeciesGlyph*>(sbmlLayout.getListOfSpeciesGlyphs()->get(i));
if (tmp)
layout->addMetaboliteGlyph(new CLMetabGlyph(*tmp, modelmap, layoutmap));
}
//reactions
iMax = sbmlLayout.getListOfReactionGlyphs()->size();
for (i = 0; i < iMax; ++i)
{
const ReactionGlyph* tmp
= dynamic_cast<const ReactionGlyph*>(sbmlLayout.getListOfReactionGlyphs()->get(i));
if (tmp)
layout->addReactionGlyph(new CLReactionGlyph(*tmp, modelmap, layoutmap));
}
//text
iMax = sbmlLayout.getListOfTextGlyphs()->size();
for (i = 0; i < iMax; ++i)
{
const TextGlyph* tmp
= dynamic_cast<const TextGlyph*>(sbmlLayout.getListOfTextGlyphs()->get(i));
if (tmp)
layout->addTextGlyph(new CLTextGlyph(*tmp, modelmap, layoutmap));
}
//additional
iMax = sbmlLayout.getListOfAdditionalGraphicalObjects()->size();
for (i = 0; i < iMax; ++i)
{
const GraphicalObject* graphical
= dynamic_cast<const GraphicalObject*>(sbmlLayout.getListOfAdditionalGraphicalObjects()->get(i));
if (graphical)
layout->addGeneralGlyph(new CLGeneralGlyph(*graphical, modelmap, layoutmap));
}
//second pass text (the text glyph can refer to other glyphs. These references can)
//only be resolved after all glyphs are created).
iMax = sbmlLayout.getListOfTextGlyphs()->size();
for (i = 0; i < iMax; ++i)
{
const TextGlyph* tmp
= dynamic_cast<const TextGlyph*>(sbmlLayout.getListOfTextGlyphs()->get(i));
if (tmp)
postprocessTextGlyph(*tmp, layoutmap);
}
#ifdef USE_CRENDER_EXTENSION
RenderLayoutPlugin* rlPlugin = (RenderLayoutPlugin*) sbmlLayout.getPlugin("render");
assert(rlPlugin != NULL);
// import the local render information
iMax = rlPlugin->getNumLocalRenderInformationObjects();
std::map<std::string, std::string> idToKeyMap;
CLLocalRenderInformation* pLRI = NULL;
//std::map<std::string,std::string> colorIdToKeyMap;
//std::map<std::string,std::string> gradientIdToKeyMap;
//std::map<std::string,std::string> lineEndingIdToKeyMap;
//std::map<std::string,std::map<std::string,std::string> > colorIdToKeyMapMap;
//std::map<std::string,std::map<std::string,std::string> > gradientIdToKeyMapMap;
//std::map<std::string,std::map<std::string,std::string> > lineEndingIdToKeyMapMap;
for (i = 0; i < iMax; ++i)
{
//colorIdToKeyMap.clear();
//gradientIdToKeyMap.clear();
//lineEndingIdToKeyMap.clear();
//pLRI=new CLLocalRenderInformation(*sbmlLayout.getRenderInformation(i),colorIdToKeyMap,gradientIdToKeyMap,lineEndingIdToKeyMap,layout);
pLRI = new CLLocalRenderInformation(*rlPlugin->getRenderInformation(i), layout);
if (rlPlugin->getRenderInformation(i)->isSetId())
idToKeyMap.insert(std::pair<std::string, std::string>(rlPlugin->getRenderInformation(i)->getId(), pLRI->getKey()));
else
idToKeyMap.insert(std::pair<std::string, std::string>(pLRI->getKey(), pLRI->getKey()));
//colorIdToKeyMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pLRI->getKey(),colorIdToKeyMap));
//gradientIdToKeyMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pLRI->getKey(),gradientIdToKeyMap));
//lineEndingIdToKeyMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pLRI->getKey(),lineEndingIdToKeyMap));
// fix the references to layout objects in id lists
size_t j, jMax = pLRI->getNumStyles();
for (j = 0; j < jMax; j++)
{
SBMLDocumentLoader::convertLayoutObjectIds(*(pLRI->getStyle(j)), layoutmap);
}
layout->addLocalRenderInformation(pLRI);
}
// fix the references
// we have to consider the global ids as well
// since all ids in these two map should be unique, we can just combine them
size_t count = idToKeyMap.size() + globalIdToKeyMap.size();
idToKeyMap.insert(globalIdToKeyMap.begin(), globalIdToKeyMap.end());
// make sure the ids were really unique
assert(idToKeyMap.size() == count);
SBMLDocumentLoader::convertRenderInformationReferencesIds<CLLocalRenderInformation>(layout->getListOfLocalRenderInformationObjects(), idToKeyMap);
// fix the color ids, gradient ids and line ending ids.
/*
std::map<std::string,std::map<std::string,std::string> >::const_iterator mapPos;
std::map<std::string,std::map<std::string,std::string> > expandedColorIdToKeyMapMap, expandedGradientIdToKeyMapMap, expandedLineEndingIdToKeyMapMap;
for(i=0;i < iMax; ++i)
{
pLRI=dynamic_cast<CLLocalRenderInformation*>(layout->getRenderInformation(i));
assert(pLRI != NULL);
std::set<std::string> chain;
SBMLDocumentLoader::expandIdToKeyMaps<CLLocalRenderInformation>(pLRI,
layout->getListOfLocalRenderInformationObjects(),
expandedColorIdToKeyMapMap,
expandedGradientIdToKeyMapMap,
expandedLineEndingIdToKeyMapMap,
colorIdToKeyMapMap,
gradientIdToKeyMapMap,
lineEndingIdToKeyMapMap,
chain,
globalColorIdToKeyMapMap,
globalGradientIdToKeyMapMap,
globalLineEndingIdToKeyMapMap
);
SBMLDocumentLoader::convertPropertyKeys<CLLocalRenderInformation>(pLRI,expandedColorIdToKeyMapMap[pLRI->getKey()],expandedGradientIdToKeyMapMap[pLRI->getKey()],expandedLineEndingIdToKeyMapMap[pLRI->getKey()]);
}
*/
#endif /* USE_CRENDER_EXTENSION */
return layout;
}
CLayout* CCopasiSpringLayout::createLayout(
CDataContainer *parent,
const std::set<const CCompartment*>& compartments,
const std::set<const CReaction*>& reactions,
const std::set<const CMetab*>& metabs,
const std::set<const CMetab*>& sideMetabs,
Parameters* mParams
)
{
CLayout *pResult = new CLayout("Layout", parent);
double fontSize = 16.0;
double fontHeight = fontSize * 1.5;
// create a species glyph for each species in metabs
std::map<const CCompartment*, CompartmentInfo> compInfo;
std::map<const CMetab*, CLMetabGlyph*> metabMap;
std::set<const CMetab*>::const_iterator metabIt;
for (metabIt = metabs.begin(); metabIt != metabs.end(); ++metabIt)
{
if (sideMetabs.find(*metabIt) != sideMetabs.end())
continue;
//estimate the size of the glyph
double width = (double)((*metabIt)->getObjectName().length() * fontSize);
double height = (double)fontHeight;
if (width < height)
{
width = height;
}
//create the glyph
CLMetabGlyph* pMetabGlyph = new CLMetabGlyph;
pMetabGlyph->setDimensions(CLDimensions(width + 4, height + 4));
pMetabGlyph->setModelObjectKey((*metabIt)->getKey());
pResult->addMetaboliteGlyph(pMetabGlyph);
metabMap[*metabIt] = pMetabGlyph;
//create the text glyph for the label
CLTextGlyph* pTextGlyph = new CLTextGlyph;
pTextGlyph->setDimensions(CLDimensions(width, height));
pTextGlyph->setGraphicalObjectKey(pMetabGlyph->getKey());
pTextGlyph->setModelObjectKey((*metabIt)->getKey());
pResult->addTextGlyph(pTextGlyph);
//add up the sizes for the compartment
const CCompartment* pComp = NULL;
if (compartments.find((*metabIt)->getCompartment()) != compartments.end())
pComp = (*metabIt)->getCompartment();
compInfo[pComp].add((width + 4) * (height + 4));
}
//now the reaction glyphs
std::set<const CReaction*>::const_iterator reactIt;
for (reactIt = reactions.begin(); reactIt != reactions.end(); ++reactIt)
{
CLReactionGlyph* pReactionGlyph = new CLReactionGlyph;
//pResult->setDimensions(CLDimensions(width, height));
pReactionGlyph->setModelObjectKey((*reactIt)->getKey());
//pReactionGlyph->getCurve().addCurveSegment(CLLineSegment(CLPoint(x, y),
// CLPoint(x + length, y)));
bool isReversible = (*reactIt)->isReversible();
pResult->addReactionGlyph(pReactionGlyph);
//now add the species reference glyphs.
//substrates
const CDataVector < CChemEqElement >& substrates = (*reactIt)->getChemEq().getSubstrates();
bool substrateExists = false;
CDataVector<CChemEqElement>::const_iterator elIt;
for (elIt = substrates.begin(); elIt != substrates.end(); ++elIt)
{
const CMetab* pMetab = elIt->getMetabolite();
if (!pMetab)
continue;
CLMetabGlyph* pMetabGlyph = NULL;
CLMetabReferenceGlyph::Role role; // = CLMetabReferenceGlyph::SUBSTRATE;
CLMetabReferenceGlyph::Role functionalRole;
//is it a side reactant? If yes, create a new metab glyph
if (sideMetabs.find(pMetab) != sideMetabs.end())
{
//estimate the size of the glyph
double width = (double)((pMetab)->getObjectName().length() * fontSize);
double height = (double)fontHeight;
if (width < height)
{
width = height;
}
//create the glyph
pMetabGlyph = new CLMetabGlyph;
pMetabGlyph->setDimensions(CLDimensions(width + 4, height + 4));
pMetabGlyph->setModelObjectKey(pMetab->getKey());
//TODO: mark as duplicate
pResult->addMetaboliteGlyph(pMetabGlyph);
//create the text glyph for the label
CLTextGlyph* pTextGlyph = new CLTextGlyph;
pTextGlyph->setDimensions(CLDimensions(width, height));
pTextGlyph->setGraphicalObjectKey(pMetabGlyph->getKey());
pTextGlyph->setModelObjectKey(pMetab->getKey());
pResult->addTextGlyph(pTextGlyph);
//add up the sizes for the compartment
const CCompartment* pComp = NULL;
if (compartments.find(pMetab->getCompartment()) != compartments.end())
pComp = pMetab->getCompartment();
compInfo[pComp].add((width + 4) * (height + 4));
role = isReversible
? CLMetabReferenceGlyph::SIDEPRODUCT
: CLMetabReferenceGlyph::SIDESUBSTRATE;
functionalRole = CLMetabReferenceGlyph::SIDESUBSTRATE;
}
else
{
//find the existing metab glyph
std::map<const CMetab*, CLMetabGlyph*>::const_iterator mmIt;
mmIt = metabMap.find(pMetab);
if (mmIt != metabMap.end())
pMetabGlyph = mmIt->second;
role = isReversible
? CLMetabReferenceGlyph::PRODUCT
: CLMetabReferenceGlyph::SUBSTRATE;
functionalRole = CLMetabReferenceGlyph::SUBSTRATE;
}
if (!pMetabGlyph)
continue;
CLMetabReferenceGlyph* pRefGlyph = new CLMetabReferenceGlyph;
//pResult->setModelObjectKey(modelobjectkey);
pRefGlyph->setMetabGlyphKey(pMetabGlyph->getKey());
pRefGlyph->setRole(role);
pRefGlyph->setFunctionalRole(functionalRole);
pReactionGlyph->addMetabReferenceGlyph(pRefGlyph);
substrateExists = true;
} //substrates
// if we have no substrates, add a dummy / invisible node for now
if (!substrateExists)
{
CLMetabGlyph* pMetabGlyph = new CLMetabGlyph;
pMetabGlyph->setDimensions(CLDimensions(1, 1));
pMetabGlyph->setObjectRole("invisible");
pResult->addMetaboliteGlyph(pMetabGlyph);
CLMetabReferenceGlyph* pRefGlyph = new CLMetabReferenceGlyph;
//pResult->setModelObjectKey(modelobjectkey);
pRefGlyph->setMetabGlyphKey(pMetabGlyph->getKey());
pRefGlyph->setRole(CLMetabReferenceGlyph::SUBSTRATE); //TODO side substr?
pRefGlyph->setFunctionalRole(CLMetabReferenceGlyph::SUBSTRATE);
pReactionGlyph->addMetabReferenceGlyph(pRefGlyph);
}
//products
const CDataVector < CChemEqElement >& products = (*reactIt)->getChemEq().getProducts();
bool productExists = false;
for (elIt = products.begin(); elIt != products.end(); ++elIt)
{
const CMetab* pMetab = elIt->getMetabolite();
if (!pMetab)
continue;
CLMetabGlyph* pMetabGlyph = NULL;
CLMetabReferenceGlyph::Role role; // = CLMetabReferenceGlyph::SUBSTRATE;
CLMetabReferenceGlyph::Role functionalRole;
//is it a side reactant? If yes, create a new metab glyph
if (sideMetabs.find(pMetab) != sideMetabs.end())
{
//estimate the size of the glyph
double width = (double)((pMetab)->getObjectName().length() * fontSize);
double height = (double)fontHeight;
if (width < height)
{
width = height;
}
//create the glyph
pMetabGlyph = new CLMetabGlyph;
pMetabGlyph->setDimensions(CLDimensions(width + 4, height + 4));
pMetabGlyph->setModelObjectKey(pMetab->getKey());
//TODO: mark as duplicate
pResult->addMetaboliteGlyph(pMetabGlyph);
//create the text glyph for the label
CLTextGlyph* pTextGlyph = new CLTextGlyph;
pTextGlyph->setDimensions(CLDimensions(width, height));
pTextGlyph->setGraphicalObjectKey(pMetabGlyph->getKey());
pTextGlyph->setModelObjectKey(pMetab->getKey());
pResult->addTextGlyph(pTextGlyph);
//add up the sizes for the compartment
const CCompartment* pComp = NULL;
if (compartments.find(pMetab->getCompartment()) != compartments.end())
pComp = pMetab->getCompartment();
compInfo[pComp].add((width + 4) * (height + 4));
role = CLMetabReferenceGlyph::SIDEPRODUCT;
functionalRole = CLMetabReferenceGlyph::SIDEPRODUCT;
}
else
{
//find the existing metab glyph
std::map<const CMetab*, CLMetabGlyph*>::const_iterator mmIt;
mmIt = metabMap.find(pMetab);
if (mmIt != metabMap.end())
pMetabGlyph = mmIt->second;
role = CLMetabReferenceGlyph::PRODUCT;
functionalRole = CLMetabReferenceGlyph::PRODUCT;
}
if (!pMetabGlyph)
continue;
CLMetabReferenceGlyph* pRefGlyph = new CLMetabReferenceGlyph;
//pResult->setModelObjectKey(modelobjectkey);
pRefGlyph->setMetabGlyphKey(pMetabGlyph->getKey());
pRefGlyph->setRole(role);
pRefGlyph->setFunctionalRole(functionalRole);
pReactionGlyph->addMetabReferenceGlyph(pRefGlyph);
productExists = true;
} //products
// if we have no substrates, add a dummy / invisible node for now
if (!productExists)
{
CLMetabGlyph* pMetabGlyph = new CLMetabGlyph;
pMetabGlyph->setDimensions(CLDimensions(1, 1));
pMetabGlyph->setObjectRole("invisible");
pResult->addMetaboliteGlyph(pMetabGlyph);
CLMetabReferenceGlyph* pRefGlyph = new CLMetabReferenceGlyph;
//pResult->setModelObjectKey(modelobjectkey);
pRefGlyph->setMetabGlyphKey(pMetabGlyph->getKey());
pRefGlyph->setRole(CLMetabReferenceGlyph::PRODUCT); //TODO side substr?
pReactionGlyph->addMetabReferenceGlyph(pRefGlyph);
}
//modifiers
const CDataVector < CChemEqElement >& modifiers = (*reactIt)->getChemEq().getModifiers();
for (elIt = modifiers.begin(); elIt != modifiers.end(); ++elIt)
{
const CMetab* pMetab = elIt->getMetabolite();
if (!pMetab)
continue;
CLMetabGlyph* pMetabGlyph = NULL;
CLMetabReferenceGlyph::Role role; // = CLMetabReferenceGlyph::SUBSTRATE;
//is it a side reactant? If yes, create a new metab glyph
if (sideMetabs.find(pMetab) != sideMetabs.end())
{
//estimate the size of the glyph
double width = (double)((pMetab)->getObjectName().length() * fontSize);
double height = (double)fontHeight;
if (width < height)
{
width = height;
}
//create the glyph
pMetabGlyph = new CLMetabGlyph;
pMetabGlyph->setDimensions(CLDimensions(width + 4, height + 4));
pMetabGlyph->setModelObjectKey(pMetab->getKey());
//TODO: mark as duplicate
pResult->addMetaboliteGlyph(pMetabGlyph);
//create the text glyph for the label
CLTextGlyph* pTextGlyph = new CLTextGlyph;
pTextGlyph->setDimensions(CLDimensions(width, height));
pTextGlyph->setGraphicalObjectKey(pMetabGlyph->getKey());
pTextGlyph->setModelObjectKey(pMetab->getKey());
pResult->addTextGlyph(pTextGlyph);
//add up the sizes for the compartment
const CCompartment* pComp = NULL;
if (compartments.find(pMetab->getCompartment()) != compartments.end())
pComp = pMetab->getCompartment();
compInfo[pComp].add((width + 4) * (height + 4));
role = CLMetabReferenceGlyph::MODIFIER; //TODO SIDEMODIFIER???
}
else
{
//find the existing metab glyph
std::map<const CMetab*, CLMetabGlyph*>::const_iterator mmIt;
mmIt = metabMap.find(pMetab);
if (mmIt != metabMap.end())
pMetabGlyph = mmIt->second;
role = CLMetabReferenceGlyph::MODIFIER;
}
if (!pMetabGlyph)
continue;
CLMetabReferenceGlyph* pRefGlyph = new CLMetabReferenceGlyph;
//pResult->setModelObjectKey(modelobjectkey);
pRefGlyph->setMetabGlyphKey(pMetabGlyph->getKey());
pRefGlyph->setRole(role);
pReactionGlyph->addMetabReferenceGlyph(pRefGlyph);
} //modifiers
} //reactions
//rules
size_t i;
for (i = 0; i < pResult->getListOfMetaboliteGlyphs().size(); ++i)
{
const CLMetabGlyph* pMetabGlyph = &pResult->getListOfMetaboliteGlyphs()[i];
const CMetab* pMetab = dynamic_cast<const CMetab*>(pMetabGlyph->getModelObject());
if (!pMetab)
continue;
if (pMetab->getStatus() == CModelEntity::Status::ODE || pMetab->getStatus() == CModelEntity::Status::ASSIGNMENT)
{
CLGeneralGlyph* pGG = new CLGeneralGlyph;
pGG->setDimensions(CLDimensions(10, 10));
pGG->setObjectRole("rule");
pResult->addGeneralGlyph(pGG);
CLReferenceGlyph* pRefGlyph = new CLReferenceGlyph;
pRefGlyph->setDimensions(CLDimensions(10, 10));
pRefGlyph->setTargetGlyphKey(pMetabGlyph->getKey());
pRefGlyph->setRole("rule connection");
pGG->addReferenceGlyph(pRefGlyph);
}
}
//after all other glyphs are created, create the compartment glyphs
double xxx = 0;
std::set<const CCompartment*>::const_iterator compIt;
for (compIt = compartments.begin(); compIt != compartments.end(); ++compIt)
{
double compSize = 10000;
std::map<const CCompartment*, CompartmentInfo>::const_iterator ccIt;
ccIt = compInfo.find(*compIt);
if (ccIt != compInfo.end())
{
//some glyphs are placed inside this compartment glyph
compSize = ccIt->second.mAreaSum * 40;
}
//create the glyph
CLCompartmentGlyph* pCompGlyph = new CLCompartmentGlyph;
pCompGlyph->setModelObjectKey((*compIt)->getKey());
pCompGlyph->setDimensions(CLDimensions(CLDimensions(sqrt(compSize), sqrt(compSize))));
pCompGlyph->setPosition(CLPoint(xxx, 5));
xxx += sqrt(compSize) + 10;
pResult->addCompartmentGlyph(pCompGlyph);
}
//
// double sss = sqrt(compInfo[NULL].mAreaSum * 40);
//
// // determine and set the layout dimensions
// CLBoundingBox box = pResult->calculateBoundingBox();
// if (box.getDimensions().getWidth() < sss)
// box.getDimensions().setWidth(sss);
//
// if (box.getDimensions().getHeight() < sss)
// box.getDimensions().setHeight(sss);
//
// pResult->setDimensions(CLDimensions(box.getDimensions().getWidth() + 30.0, box.getDimensions().getHeight() + 30.0));
// randomize
CCopasiSpringLayout l(pResult, mParams);
l.randomize();
// determine and set the layout dimensions
CLBoundingBox box = pResult->calculateBoundingBox();
pResult->setDimensions(CLDimensions(box.getDimensions().getWidth() + 30.0, box.getDimensions().getHeight() + 30.0));
return pResult;
}