std::string
SEDMLUtils::translateTargetXpathInSBMLId(const std::string &xpath, std::string& SBMLType)
{
std::vector<std::string> xpathStrings;
std::string id, nextString;
splitStrings(xpath, ':', xpathStrings);
nextString = xpathStrings[xpathStrings.size() - 1];
splitStrings(nextString, '[', xpathStrings);
SBMLType = xpathStrings[0];
nextString = xpathStrings[xpathStrings.size() - 1];
splitStrings(nextString, '=', xpathStrings);
nextString = xpathStrings[xpathStrings.size() - 1];
splitStrings(nextString, ']', xpathStrings);
id = xpathStrings[0];
//remove the remaining unwanted characters
removeCharactersFromString(id, "\"']");
return id;
}
GraphSize OperationDrawer::drawClass(DiagramDrawer &drawer, const OperationClass &node,
const OperationDrawOptions & /*options*/, bool draw)
{
GraphPoint startpos = node.getPosition();
const ModelType *type = node.getType();
OovStringRef const typeName = type->getName();
int rectx = 0;
int recty = 0;
const ModelClassifier *classifier = type->getClass();
if(classifier)
{
if(draw)
{
drawer.groupText(true, false);
}
OovStringVec strs;
std::vector<GraphPoint> positions;
strs.push_back(typeName);
splitStrings(strs, 30, 40);
for(auto const &str : strs)
{
recty += mCharHeight + (mPad * 2);
positions.push_back(GraphPoint(startpos.x+mPad, startpos.y + recty - mPad));
int curx = static_cast<int>(drawer.getTextExtentWidth(str)) + mPad*2;
if(curx > rectx)
rectx = curx;
}
if(draw)
{
drawer.groupShapes(true, Color(0,0,0), Color(245,245,255));
drawer.drawRect(GraphRect(startpos.x, startpos.y, rectx, recty));
drawer.groupShapes(false, Color(0,0,0), Color(245,245,255));
for(size_t i=0; i<strs.size(); i++)
{
drawer.drawText(positions[i], strs[i]);
}
drawer.groupText(false, false);
}
}
return GraphSize(rectx, recty);
}
std::string
SEDMLUtils::getXPathAndName(std::string& sbmlId,
const std::string &type,
const CModel *pModel,
const CCopasiDataModel& dataModel)
{
std::vector<std::string> stringsContainer;
std::string targetXPathString;
const std::map<CCopasiObject*, SBase*>& copasi2sbmlmap =
const_cast<CCopasiDataModel&>(dataModel).getCopasi2SBMLMap();
std::string displayName = sbmlId;
if (copasi2sbmlmap.size() == 0)
{
// this should not be happening, as this is used to verify the element.
return "";
}
std::map<CCopasiObject*, SBase*>::const_iterator pos;
if (type == "Concentration" || type == "InitialConcentration")
{
targetXPathString = "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=\'";
//remove unwanted characters from the plot item object name
removeCharactersFromString(displayName, "[]");
if (type == "InitialConcentration")
{
displayName = displayName.substr(0, displayName.length() - 2);
}
sbmlId = findIdByNameAndType(copasi2sbmlmap, SBML_SPECIES, displayName);
if (!sbmlId.empty())
{
return targetXPathString + sbmlId + "\']";
}
else
return "";
}
else if (type == "Flux")
{
targetXPathString = "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id=\'";
splitStrings(displayName, ')', stringsContainer);
displayName = stringsContainer[0];
removeCharactersFromString(displayName, "(");
sbmlId = findIdByNameAndType(copasi2sbmlmap, SBML_REACTION, displayName);
if (!sbmlId.empty())
{
return targetXPathString + sbmlId + "\']";
}
else
return "";
}
else if (type == "Value" || type == "InitialValue")
{
if (type == "InitialValue")
{
displayName = displayName.substr(0, displayName.find(".InitialValue"));
}
targetXPathString = "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id=\'";
splitStrings(displayName, '[', stringsContainer);
if (stringsContainer.size() == 1)
{
// not found ... might be a local parameter
removeCharactersFromString(displayName, "()");
splitStrings(displayName, '.', stringsContainer);
if (stringsContainer.size() == 2)
{
sbmlId = stringsContainer[0] + "_" + stringsContainer[1];
std::stringstream xpath;
xpath << "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id=\'";
xpath << stringsContainer[0];
xpath << "\']/sbml:kineticLaw/sbml:listOfParameters/sbml:parameter[@id=\'";
xpath << stringsContainer[1];
xpath << "\']";
return xpath.str();
}
}
displayName = stringsContainer[1];
removeCharactersFromString(displayName, "]");
sbmlId = findIdByNameAndType(copasi2sbmlmap, SBML_PARAMETER , displayName);
if (sbmlId.empty())
sbmlId = findIdByNameAndType(copasi2sbmlmap, SBML_LOCAL_PARAMETER , displayName);
if (!sbmlId.empty())
{
return targetXPathString + sbmlId + "\']";
}
else
return "";
}
else if (type == "Volume" || type == "InitialVolume")
{
targetXPathString = "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id=\'";
splitStrings(displayName, '[', stringsContainer);
displayName = stringsContainer[1];
if (type == "InitialVolume")
{
displayName = displayName.substr(0, displayName.find(".InitialVolume"));
}
if (type == "Volume")
{
displayName = displayName.substr(0, displayName.find(".Volume"));
}
removeCharactersFromString(displayName, "]");
sbmlId = findIdByNameAndType(copasi2sbmlmap, SBML_COMPARTMENT, displayName);
if (!sbmlId.empty())
{
return targetXPathString + sbmlId + "\']";
}
else
return "";
}
else if (type == "Time" || type == "Initial Time")
return SEDML_TIME_URN;
sbmlId = "";
return targetXPathString;
}
