std::string
SEDMLUtils::getXPathForObject(const CCopasiObject& object)
{
const std::string& type = object.getObjectName();
const CCopasiDataModel* dm = object.getObjectDataModel();
std::string yAxis = object.getObjectDisplayName();
std::string targetXPathString = getXPathAndName(yAxis, type,
dm->getModel(), *dm);
return targetXPathString;
}
/**
* Creates the data generators for SEDML.
*/
void CSEDMLExporter::createDataGenerators(CCopasiDataModel & dataModel,
std::string & taskId,
CCopasiTask* task)
{
const CModel* pModel = dataModel.getModel();
std::vector<std::string> stringsContainer; //split string container
if (pModel == NULL)
CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No model for this SED-ML document. An SBML model must exist for every SED-ML document.");
SedPlot2D* pPSedPlot;
SedCurve* pCurve; // = pPSedPlot->createCurve();
//create generator for special varibale time
const CCopasiObject* pTime = static_cast<const CCopasiObject *>(dataModel.getModel()->getObject(CCopasiObjectName("Reference=Time")));
SedDataGenerator *pTimeDGenp = this->mpSEDMLDocument->createDataGenerator();
pTimeDGenp->setId("time");
pTimeDGenp->setName(pTime->getObjectName());
SedVariable *pTimeVar = pTimeDGenp->createVariable();
pTimeVar->setId("var_time");
pTimeVar->setTaskReference(taskId);
pTimeVar->setSymbol(SEDML_TIME_URN);
pTimeDGenp->setMath(SBML_parseFormula(pTimeVar->getId().c_str()));
size_t i, imax = dataModel.getPlotDefinitionList()->size();
SedDataGenerator *pPDGen;
if (imax == 0 && (task == NULL || task->getReport().getTarget().empty()))
CCopasiMessage(CCopasiMessage::ERROR, "SED-ML: No plot/report definition for this SED-ML document.");
// export report
if (task != NULL && !task->getReport().getTarget().empty())
{
CReportDefinition* def = task->getReport().getReportDefinition();
if (def != NULL)
{
SedReport* pReport = mpSEDMLDocument->createReport();
std::string name = def->getObjectName();
SEDMLUtils::removeCharactersFromString(name, "[]");
//
pReport->setId(SEDMLUtils::getNextId("report", mpSEDMLDocument->getNumOutputs()));
pReport->setName(name);
std::vector<CRegisteredObjectName> header = *def->getHeaderAddr();
std::vector<CRegisteredObjectName> body =
def->isTable() ? *def->getTableAddr() :
*def->getBodyAddr();
int dsCount = 0;
for (size_t i = 0; i < body.size(); ++i)
{
CRegisteredObjectName& current = body[i];
if (current == def->getSeparator().getCN()) continue;
CCopasiObject *object = dataModel.getDataObject(current);
if (object == NULL) continue;
const std::string& typeX = object->getObjectName();
std::string xAxis = object->getObjectDisplayName();
std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
pModel, dataModel);
if (object->getCN() == pTime->getCN())
pPDGen = pTimeDGenp;
else
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
xAxis,
targetXPathStringX,
taskId,
i,
0
);
SedDataSet* pDS = pReport->createDataSet();
pDS->setId(SEDMLUtils::getNextId("ds", ++dsCount));
if (def->isTable())
{
CCopasiObject *headerObj = NULL;
if (header.size() > i)
headerObj = dataModel.getDataObject(header[i]);
else
headerObj = dataModel.getDataObject(body[i]);
if (headerObj != NULL)
pDS->setLabel(headerObj->getObjectDisplayName());
else
pDS->setLabel(xAxis);
}
else
pDS->setLabel(xAxis);
pDS->setDataReference(pPDGen->getId());
}
}
}
// export plots
for (i = 0; i < imax; i++)
{
pPSedPlot = this->mpSEDMLDocument->createPlot2D();
const CPlotSpecification* pPlot = (*dataModel.getPlotDefinitionList())[i];
std::string plotName = pPlot->getObjectName();
SEDMLUtils::removeCharactersFromString(plotName, "[]");
pPSedPlot->setId(SEDMLUtils::getNextId("plot", mpSEDMLDocument->getNumOutputs()));
pPSedPlot->setName(plotName);
size_t j, jmax = pPlot->getItems().size();
for (j = 0; j < jmax; j++)
{
const CPlotItem* pPlotItem = pPlot->getItems()[j];
CCopasiObject *objectX, *objectY;
if (pPlotItem->getChannels().size() >= 1)
{
objectX = dataModel.getDataObject(pPlotItem->getChannels()[0]);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s', as it has no data channel.", pPlotItem->getObjectName().c_str());
continue;
}
if (objectX == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as it cannot be resolved.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[0].c_str());
continue;
}
bool xIsTime = objectX->getCN() == pTime->getCN();
if (pPlotItem->getChannels().size() >= 2)
{
objectY = dataModel.getDataObject(pPlotItem->getChannels()[1]);
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s', as it has only 1 data channel.", pPlotItem->getObjectName().c_str());
continue;
}
if (objectY == NULL)
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as it cannot be resolved.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[1].c_str());
continue;
}
const std::string& type = objectY->getObjectName();
std::string yAxis = objectY->getObjectDisplayName();
std::string sbmlId = yAxis;
std::string targetXPathString = SEDMLUtils::getXPathAndName(sbmlId, type,
pModel, dataModel);
if (targetXPathString.empty())
{
CCopasiMessage(CCopasiMessage::WARNING, "SED-ML: Can't export plotItem '%s' variable '%s', as no xpath expression for it could be generated.", pPlotItem->getObjectName().c_str(), pPlotItem->getChannels()[1].c_str());
continue;
}
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
sbmlId,
targetXPathString,
taskId,
i,
j
);
pPDGen->setName(yAxis);
pCurve = pPSedPlot->createCurve();
std::ostringstream idCurveStrStream;
idCurveStrStream << "p";
idCurveStrStream << i + 1;
idCurveStrStream << "_curve_";
idCurveStrStream << j + 1;
pCurve->setId(idCurveStrStream.str());
pCurve->setLogX(pPlot->isLogX());
pCurve->setLogY(pPlot->isLogY());
pCurve->setName(yAxis);
pCurve->setYDataReference(pPDGen->getId());
if (xIsTime)
{
pCurve->setXDataReference(pTimeDGenp->getId());
}
else
{
const std::string& typeX = objectX->getObjectName();
std::string xAxis = objectX->getObjectDisplayName();
std::string targetXPathStringX = SEDMLUtils::getXPathAndName(xAxis, typeX,
pModel, dataModel);
pPDGen = createDataGenerator(
this->mpSEDMLDocument,
xAxis,
targetXPathStringX,
taskId,
i,
j
);
pCurve->setXDataReference(pPDGen->getId());
}
}
}
}
void CMMLOutput::createParameterMapping(const CReaction* pReac,
std::vector<std::vector<std::string> > & params,
bool numbers)
{
assert(pReac);
assert(pReac->getFunction());
const CFunctionParameters & functionParams = pReac->getFunctionParameters();
size_t j, jmax;
size_t i, imax = functionParams.size();
params.resize(imax);
for (i = 0; i < imax; ++i)
{
params[i].resize(1);
std::string name;
//std::ostringstream number;
switch (functionParams[i]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
if (functionParams[i]->getType() == CFunctionParameter::FLOAT64)
{
CCopasiObject * pObject = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0]);
if (pObject != NULL)
{
name = pObject->getObjectDisplayName();
}
else
{
name = "unknown";
}
//params[i][0] = "<mi>"+ CMathMl::fixName(name)+"</mi>";
params[i][0] = "<mi>[" + CMathMl::fixName(name) + "]</mi>";
}
else if (functionParams[i]->getType() == CFunctionParameter::VFLOAT64)
{
jmax = pReac->getParameterMappings()[i].size();
params[i].resize(jmax);
for (j = 0; j < jmax; ++j)
{
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][j])->getObjectDisplayName();
//params[i][j] = "<mi>"+ CMathMl::fixName(name)+"</mi>";
params[i][j] = "<mi>[" + CMathMl::fixName(name) + "]</mi>";
}
}
else assert(false);
break;
case CFunctionParameter::PARAMETER:
if (pReac->isLocalParameter(i))
{
if (numbers)
{
std::ostringstream number;
number << pReac->getParameterValue(functionParams[i]->getObjectName());
params[i][0] = "<mn>" + number.str() + "</mn>";
}
else
{
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0])->getObjectName();
//params[i][0] = "<mi>" + CMathMl::fixName(name) + "</mi>";
params[i][0] = "<msub><mi>" + CMathMl::fixName(name) + "</mi><mi>("
+ CMathMl::fixName(pReac->getObjectName()) + ")</mi></msub>";
}
}
else
{
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0])->getObjectName();
params[i][0] = "<mi>" + CMathMl::fixName(name) + "</mi>";
//params[i][0] = "<mi>ggg</mi>";
}
break;
case CFunctionParameter::VOLUME:
name = CCopasiRootContainer::getKeyFactory()->get(pReac->getParameterMappings()[i][0])->getObjectName();
params[i][0] = "<msub><mi>V</mi><mi>" + CMathMl::fixName(name)
+ "</mi></msub>";
break;
case CFunctionParameter::TIME:
params[i][0] = "<mi>time</mi>";
break;
default:
break;
}
}
}