#include <SBMLDocumentLoader.h>

Static Public Member Functions
static void	combineMaps (const std::map< std::string, std::string > &sourceMap, std::map< std::string, std::string > &destMap)

static void	convertLayoutObjectIds (CLLocalStyle &style, const std::map< std::string, std::string > &idToKeyMap)

static void	convertLayoutObjectKeys (LocalStyle &style, const std::map< std::string, std::string > &keyToIdMap)

static void	convertPropertyIds (CLTransformation2D *pObject, const std::map< std::string, std::string > &colorIdToKeyMap, const std::map< std::string, std::string > &gradientIdToKeyMap, const std::map< std::string, std::string > &lineEndingIdToKeyMap)

template<typename RENDER_INFORMATION >
static void	convertRenderInformationReferencesIds (CDataVector< RENDER_INFORMATION > &list, const std::map< std::string, std::string > &idToKeyMap)

template<typename RENDER_INFORMATION >
static void	convertRenderInformationReferencesKeys (ListOf &list, const std::map< std::string, std::string > &keyToIdMap)

static CLayout *	createLayout (const Layout &sbmlLayout, const std::map< std::string, std::string > &modelmap, std::map< std::string, std::string > &layoutmap, const std::map< std::string, std::string > &globalIdToKeyMap, const CDataContainer *pParent=NO_PARENT)

static void	readListOfLayouts (CListOfLayouts &lol, const ListOf &sbmlList, const std::map< const CDataObject , SBase > &copasimodelmap)

Static Protected Member Functions
static void	postprocessTextGlyph (const TextGlyph &sbml, const std::map< std::string, std::string > &layoutmap)

Member Function Documentation

◆ combineMaps()

void SBMLDocumentLoader::combineMaps	(	const std::map< std::string, std::string > &	sourceMap,
		std::map< std::string, std::string > &	destMap
	)

static

converts references to color keys, gradient keys and/or line ending keys in graphical primitives to references to the corresponding Ids. template<typename RENDER_INFORMATION> static void convertPropertyKeys(RENDER_INFORMATION* pObject, const std::map<std::string,std::string>& colorKeyToIdMap, const std::map<std::string,std::string>& gradientKeyToIdMap, const std::map<std::string,std::string>& lineEndingKeyToIdMap); converts references to color keys, gradient keys and/or line ending keys in graphical primitives to references to the corresponding Ids. static void convertPropertyKeys(Transformation2D* pObject, const std::map<std::string,std::string>& colorKeyToIdMap, const std::map<std::string,std::string>& gradientKeyToIdMap, const std::map<std::string,std::string>& lineEndingKeyToIdMap); converts references to color ids in gradient stops to references to the corresponding keys. static void convertColorKeys(GradientBase& gradient, const std::map<std::string,std::string>& colorKeyToIdMap); Adds all elements of the source map into the dest map if an element with the same key does not already exist in the dest map.

converts references to color keys, gradient keys and/or line ending keys in graphical primitives to references to the corresponding Ids. void SBMLDocumentLoader::convertPropertyKeys(Transformation2D* pObject, const std::map<std::string,std::string>& colorKeyToIdMap, const std::map<std::string,std::string>& gradientKeyToIdMap, const std::map<std::string,std::string>& lineEndingKeyToIdMap) { GraphicalPrimitive1D* pGP1=dynamic_cast<GraphicalPrimitive1D*>(pObject); if(pGP1 != NULL) { std::map<std::string,std::string>::const_iterator pos; fix the stroke color std::string s=pGP1->getStroke(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none" && s[0] != '#') { pos=colorKeyToIdMap.find(s); check if we found the color, else it must be a gradient if(pos==colorKeyToIdMap.end()) { pos=gradientKeyToIdMap.find(s); assert(pos != gradientKeyToIdMap.end()); pGP1->setStroke(pos->second); } else { pGP1->setStroke(pos->second); } } GraphicalPrimitive2D* pGP2=dynamic_cast<GraphicalPrimitive2D*>(pObject); if(pGP2 != NULL) { fix the fill color std::string s=pGP2->getFillColor(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none" && s[0] != '#') { pos=colorKeyToIdMap.find(s); check if we found the color, else it must be a gradient if(pos==colorKeyToIdMap.end()) { pos=gradientKeyToIdMap.find(s); assert(pos != gradientKeyToIdMap.end()); pGP2->setFillColor(pos->second); } else { pGP2->setFillColor(pos->second); } } Group* pG=dynamic_cast<Group*>(pObject); if(pG != NULL) { fix the line endings s=pG->getStartHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingKeyToIdMap.find(s); assert(pos != lineEndingKeyToIdMap.end()); pG->setStartHead(pos->second); } s=pG->getEndHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingKeyToIdMap.find(s); assert(pos != lineEndingKeyToIdMap.end()); pG->setEndHead(pos->second); } call this method for all children size_t i,iMax=pG->getNumElements(); for(i=0; i < iMax; ++i) { SBMLDocumentLoader::convertPropertyKeys(dynamic_cast<Transformation2D*>(pG->getElement(i)),colorKeyToIdMap,gradientKeyToIdMap,lineEndingKeyToIdMap); } } } else { RenderCurve* pC=dynamic_cast<RenderCurve*>(pObject); if(pC != NULL) { fix the line endings s=pC->getStartHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingKeyToIdMap.find(s); assert(pos != lineEndingKeyToIdMap.end()); pC->setStartHead(pos->second); } s=pC->getEndHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingKeyToIdMap.find(s); assert(pos != lineEndingKeyToIdMap.end()); pC->setEndHead(pos->second); } } } } } converts references to color ids in gradient stops to references to the corresponding keys. void SBMLDocumentLoader::convertColorKeys(GradientBase& gradient, const std::map<std::string,std::string>& colorKeyToIdMap) { size_t i,iMax=gradient.getNumGradientStops(); GradientStop* pStop=NULL; std::map<std::string,std::string>::const_iterator pos; for(i=0; i < iMax; ++i) { pStop=gradient.getGradientStop(i); std::string color=pStop->getStopColor(); if(color.find_first_not_of(" \t\n\r") != std::string::npos && color != "none" && color[0] != '#') { pos=colorKeyToIdMap.find(color); assert(pos!=colorKeyToIdMap.end()); pStop->setStopColor(pos->second); } } } Adds all elements of the source map into the dest map if an element with the same key does not already exist in the dest map.

◆ convertLayoutObjectIds()

void SBMLDocumentLoader::convertLayoutObjectIds	(	CLLocalStyle &	style,
		const std::map< std::string, std::string > &	idToKeyMap
	)

static

Converts references to ids of layout objects to the corresponding key.

References CLLocalStyle::getKeyList(), and CLLocalStyle::setKeyList().

Referenced by createLayout().

◆ convertLayoutObjectKeys()

void SBMLDocumentLoader::convertLayoutObjectKeys	(	LocalStyle &	style,
		const std::map< std::string, std::string > &	keyToIdMap
	)

static

Converts references to keys of layout objects to the corresponding id.

converts references to color ids, gradient ids and/or line ending ids in graphical primitives to references to the corresponding keys. void SBMLDocumentLoader::convertPropertyIds(CLTransformation2D* pObject, const std::map<std::string,std::string>& colorIdToKeyMap, const std::map<std::string,std::string>& gradientIdToKeyMap, const std::map<std::string,std::string>& lineEndingIdToKeyMap) { CLGraphicalPrimitive1D* pGP1=dynamic_cast<CLGraphicalPrimitive1D*>(pObject); if(pGP1 != NULL) { std::map<std::string,std::string>::const_iterator pos; fix the stroke color std::string s=pGP1->getStroke(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none" && s[0] != '#') { pos=colorIdToKeyMap.find(s); check if we found the color, else it must be a gradient if(pos==colorIdToKeyMap.end()) { pos=gradientIdToKeyMap.find(s); assert(pos != gradientIdToKeyMap.end()); pGP1->setStroke(pos->second); } else { pGP1->setStroke(pos->second); } } CLGraphicalPrimitive2D* pGP2=dynamic_cast<CLGraphicalPrimitive2D*>(pObject); if(pGP2 != NULL) { fix the fill color std::string s=pGP2->getFillColor(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none" && s[0] != '#') { pos=colorIdToKeyMap.find(s); check if we found the color, else it must be a gradient if(pos==colorIdToKeyMap.end()) { pos=gradientIdToKeyMap.find(s); assert(pos != gradientIdToKeyMap.end()); pGP2->setFillColor(pos->second); } else { pGP2->setFillColor(pos->second); } } CLGroup* pG=dynamic_cast<CLGroup*>(pObject); if(pG != NULL) { fix the line endings s=pG->getStartHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingIdToKeyMap.find(s); assert(pos != lineEndingIdToKeyMap.end()); pG->setStartHead(pos->second); } s=pG->getEndHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingIdToKeyMap.find(s); assert(pos != lineEndingIdToKeyMap.end()); pG->setEndHead(pos->second); } call this method for all children size_t i,iMax=pG->getNumElements(); for(i=0; i < iMax; ++i) { SBMLDocumentLoader::convertPropertyIds(dynamic_cast<CLTransformation2D*>(pG->getElement(i)),colorIdToKeyMap,gradientIdToKeyMap,lineEndingIdToKeyMap); } } } else { CLRenderCurve* pC=dynamic_cast<CLRenderCurve*>(pObject); if(pC != NULL) { fix the line endings s=pC->getStartHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingIdToKeyMap.find(s); assert(pos != lineEndingIdToKeyMap.end()); pC->setStartHead(pos->second); } s=pC->getEndHead(); if(s.find_first_not_of(" \t\n\r") != std::string::npos && s != "none") { pos=lineEndingIdToKeyMap.find(s); assert(pos != lineEndingIdToKeyMap.end()); pC->setEndHead(pos->second); } } } } } converts references to color ids in gradient stops to references to the corresponding keys. void SBMLDocumentLoader::convertColorIds(CLGradientBase& gradient, const std::map<std::string,std::string>& colorIdToKeyMap) { size_t i,iMax=gradient.getNumGradientStops(); CLGradientStop* pStop=NULL; std::map<std::string,std::string>::const_iterator pos; for(i=0; i < iMax; ++i) { pStop=gradient.getGradientStop(i); std::string color=pStop->getStopColor(); if(color.find_first_not_of(" \t\n\r") != std::string::npos && color != "none" && color[0] != '#') { pos=colorIdToKeyMap.find(color); assert(pos!=colorIdToKeyMap.end()); pStop->setStopColor(pos->second); } } } Converts references to keys of layout objects to the corresponding id.

Referenced by CLayout::exportToSBML().

◆ convertPropertyIds()

static void SBMLDocumentLoader::convertPropertyIds	(	CLTransformation2D *	pObject,
		const std::map< std::string, std::string > &	colorIdToKeyMap,
		const std::map< std::string, std::string > &	gradientIdToKeyMap,
		const std::map< std::string, std::string > &	lineEndingIdToKeyMap
	)

static

converts references to color ids, gradient ids and/or line ending ids in graphical primitives to references to the corresponding keys.

◆ convertRenderInformationReferencesIds()

template<typename RENDER_INFORMATION >

static void SBMLDocumentLoader::convertRenderInformationReferencesIds	(	CDataVector< RENDER_INFORMATION > &	list,
		const std::map< std::string, std::string > &	idToKeyMap
	)

inlinestatic

converts the sbml id for render render information objects into the corresponding copasi key where they are used in a reference. This is used for the import from SBML.

References CDataVector< CType >::size().

◆ convertRenderInformationReferencesKeys()

template<typename RENDER_INFORMATION >

static void SBMLDocumentLoader::convertRenderInformationReferencesKeys	(	ListOf &	list,
		const std::map< std::string, std::string > &	keyToIdMap
	)

inlinestatic

converts references to color ids in gradient stops to references to the corresponding keys. static void convertColorIds(CLGradientBase& gradient, const std::map<std::string,std::string>& colorIdToKeyMap); converts the copasi key for global render information objects into the corresponding sbml id where they are used in a reference. This is used for the SBML export.

◆ createLayout()

CLayout * SBMLDocumentLoader::createLayout	(	const Layout &	sbmlLayout,
		const std::map< std::string, std::string > &	modelmap,
		std::map< std::string, std::string > &	layoutmap,
		const std::map< std::string, std::string > &	globalIdToKeyMap,
		const CDataContainer *	pParent = `NO_PARENT`
	)

static

References CLayout::addCompartmentGlyph(), CLayout::addGeneralGlyph(), CLayout::addLocalRenderInformation(), CLayout::addMetaboliteGlyph(), CLayout::addReactionGlyph(), CLayout::addTextGlyph(), C_INT32, convertLayoutObjectIds(), CLRenderInformationBase::getKey(), CLayout::getListOfLocalRenderInformationObjects(), CLLocalRenderInformation::getNumStyles(), CLLocalRenderInformation::getStyle(), and postprocessTextGlyph().

Referenced by readListOfLayouts().

◆ postprocessTextGlyph()

void SBMLDocumentLoader::postprocessTextGlyph	(	const TextGlyph &	sbml,
		const std::map< std::string, std::string > &	layoutmap
	)

staticprotected

resolves the graphical object reference of the text glyph

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and CLTextGlyph::setGraphicalObjectKey().

Referenced by createLayout().

◆ readListOfLayouts()

void SBMLDocumentLoader::readListOfLayouts	(	CListOfLayouts &	lol,
		const ListOf &	sbmlList,
		const std::map< const CDataObject , SBase > &	copasimodelmap
	)

static

References CListOfLayouts::addGlobalRenderInformation(), CListOfLayouts::addLayout(), C_INT32, createLayout(), SBMLUtils::getIdFromSBase(), CLRenderInformationBase::getKey(), and CListOfLayouts::getListOfGlobalRenderInformationObjects().

Referenced by SBMLImporter::parseSBML().

The documentation for this class was generated from the following files:

Static Public Member Functions

Static Protected Member Functions

Member Function Documentation

◆ combineMaps()

◆ convertLayoutObjectIds()

◆ convertLayoutObjectKeys()

◆ convertPropertyIds()

◆ convertRenderInformationReferencesIds()

◆ convertRenderInformationReferencesKeys()

◆ createLayout()

◆ postprocessTextGlyph()

◆ readListOfLayouts()