//static void SBMLDocumentLoader::postprocessTextGlyph(const TextGlyph & sbml, const std::map<std::string, std::string> & layoutmap) { //the corresponding CLTextGlyph should already exist. Let's find it... CLTextGlyph * pTg = NULL; if (sbml.getId() != "") { std::map<std::string, std::string>::const_iterator it = layoutmap.find(sbml.getId()); if (it != layoutmap.end()) pTg = dynamic_cast<CLTextGlyph *>(CCopasiRootContainer::getKeyFactory()->get(it->second)); if (!pTg) { //error? return; } } else { //error? return; } //resolve the graphical object reference assert(pTg); if (sbml.getGraphicalObjectId() != "") { std::map<std::string, std::string>::const_iterator it = layoutmap.find(sbml.getGraphicalObjectId()); if (it != layoutmap.end()) pTg->setGraphicalObjectKey(it->second); } }
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; }