// virtual
CXMLHandler * ModelValueHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
const char * Name;
const char * simulationType;
CModelEntity::Status SimulationType;
bool AddNoise;
switch (mCurrentElement.first)
{
case ModelValue:
mKey = mpParser->getAttributeValue("key", papszAttrs);
Name = mpParser->getAttributeValue("name", papszAttrs);
simulationType = mpParser->getAttributeValue("simulationType", papszAttrs, false);
// We need to handle old files which used the attribute status.
if (!simulationType)
{
simulationType = mpParser->getAttributeValue("status", papszAttrs, false);
if (!simulationType) // status and simulationType are both missing
simulationType = mpParser->getAttributeValue("simulationType", papszAttrs);
}
SimulationType = toEnum(simulationType, CModelEntity::XMLStatus, CModelEntity::FIXED);
AddNoise = mpParser->toBool(mpParser->getAttributeValue("addNoise", papszAttrs, "false"));
mpMV = new CModelValue();
addFix(mKey, mpMV);
mpMV->setObjectName(Name);
mpMV->setStatus(SimulationType);
mpMV->setAddNoise(AddNoise);
mpData->pModel->getModelValues().add(mpMV, true);
break;
case MiriamAnnotation:
case Comment:
case Expression:
case MathML:
case InitialExpression:
case NoiseExpression:
case Unit:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
case ListOfUnsupportedAnnotations:
mpData->mUnsupportedAnnotations.clear();
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
// virtual
CXMLHandler * TaskHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
const char * Key;
const char * type;
CTaskEnum::Task Type;
bool Scheduled = false;
bool UpdateModel = false;
switch (mCurrentElement.first)
{
case Task:
mpData->pCurrentTask = NULL;
Key = mpParser->getAttributeValue("key", papszAttrs, false);
type = mpParser->getAttributeValue("type", papszAttrs);
Type = toEnum(type, CTaskEnum::TaskXML, CTaskEnum::UnsetTask);
Scheduled = mpParser->toBool(mpParser->getAttributeValue("scheduled", papszAttrs, "false"));
UpdateModel = mpParser->toBool(mpParser->getAttributeValue("updateModel", papszAttrs, "false"));
mpData->pCurrentTask = CTaskFactory::createTask(Type, mpData->pTaskList);
if (mpData->pCurrentTask != NULL)
{
mpData->pCurrentTask->setScheduled(Scheduled);
mpData->pCurrentTask->setUpdateModel(UpdateModel);
mpData->pCurrentTask->setMathContainer(&mpData->pModel->getMathContainer());
if (Key != NULL)
{
addFix(Key, mpData->pCurrentTask);
}
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCXML + 5, type, mpParser->getCurrentLineNumber());
pHandlerToCall = getHandler(UNKNOWN);
}
break;
case ReportTarget:
case Method:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
case Problem:
pHandlerToCall = getHandler(mCurrentElement.second);
static_cast< ParameterGroupHandler * >(pHandlerToCall)->setDerivedElement(pszName, mpData->pCurrentTask->getProblem());
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
// virtual
CXMLHandler * ReactionGlyphHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
switch (mCurrentElement.first)
{
case ReactionGlyph:
{
//workload
const char * key;
const char * name;
const char * reaction;
key = mpParser->getAttributeValue("key", papszAttrs);
name = mpParser->getAttributeValue("name", papszAttrs);
reaction = mpParser->getAttributeValue("reaction", papszAttrs, false);
mpData->pReactionGlyph = new CLReactionGlyph(name);
const char * objectRole = mpParser->getAttributeValue("objectRole", papszAttrs, false);
if (objectRole != NULL && objectRole[0] != 0)
{
mpData->pReactionGlyph->setObjectRole(objectRole);
}
if (reaction && reaction[0])
{
CReaction * pReaction = dynamic_cast< CReaction * >(mpData->mKeyMap.get(reaction));
if (!pReaction)
{
CCopasiMessage(CCopasiMessage::WARNING, MCXML + 19, "ReactionGlyph" , key);
}
else
{
mpData->pReactionGlyph->setModelObjectKey(pReaction->getKey());
}
}
mpData->pCurrentLayout->addReactionGlyph(mpData->pReactionGlyph);
addFix(key, mpData->pReactionGlyph);
}
break;
case BoundingBox:
case Curve:
case ListOfMetaboliteReferenceGlyphs:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
// virtual
CXMLHandler * ReportDefinitionHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
const char * Key;
const char * Name;
const char * Separator;
const char * Precision;
CTaskEnum::Task type;
switch (mCurrentElement.first)
{
case ReportDefinition:
Key = mpParser->getAttributeValue("key", papszAttrs);
Name = mpParser->getAttributeValue("name", papszAttrs);
type = CTaskEnum::TaskXML.toEnum(mpParser->getAttributeValue("taskType", papszAttrs), CTaskEnum::Task::UnsetTask);
Separator = mpParser->getAttributeValue("separator", papszAttrs, "\t");
Precision = mpParser->getAttributeValue("precision", papszAttrs, "6");
// create a new report
mpData->pReport = new CReportDefinition();
mpData->pReport->setTaskType(type);
mpData->pReport->setSeparator(Separator);
mpData->pReport->setPrecision(strToUnsignedInt(Precision));
{
// We need to make sure that the name is unique.
std::string ValidName(Name);
size_t Index = 1;
while (mpData->pReportList->getIndex(ValidName) != C_INVALID_INDEX)
{
std::ostringstream ValidNameStream;
ValidNameStream << Name << " " << Index++;
ValidName = ValidNameStream.str();
}
mpData->pReport->setObjectName(ValidName);
}
/* We have a new report and add it to the list */
mpData->pReportList->add(mpData->pReport, true);
addFix(Key, mpData->pReport);
break;
case Comment:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
case Header:
case Body:
case Footer:
mpData->pReport->setIsTable(false);
pHandlerToCall = getHandler(mCurrentElement.second);
break;
case Table:
mpData->pReport->setIsTable(true);
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}
// virtual
CXMLHandler * MetaboliteHandler::processStart(const XML_Char * pszName,
const XML_Char ** papszAttrs)
{
CXMLHandler * pHandlerToCall = NULL;
CCompartment * pCompartment = NULL;
const char * Name;
const char * simulationType;
CModelEntity::Status SimulationType;
const char reactions[] = "reactions";
const char * Compartment;
bool AddNoise;
switch (mCurrentElement.first)
{
case Metabolite:
mKey = mpParser->getAttributeValue("key", papszAttrs);
Name = mpParser->getAttributeValue("name", papszAttrs);
simulationType = mpParser->getAttributeValue("simulationType", papszAttrs, false);
// We need to handle old files which used the attribute status.
if (!simulationType)
{
simulationType = mpParser->getAttributeValue("status", papszAttrs, false);
if (!simulationType) // status and simulationType are both missing
simulationType = mpParser->getAttributeValue("simulationType", papszAttrs);
else if (!strcmp(simulationType, "variable")) // reactions was named variable
simulationType = reactions;
}
SimulationType = toEnum(simulationType, CModelEntity::XMLStatus, CModelEntity::REACTIONS);
Compartment = mpParser->getAttributeValue("compartment", papszAttrs);
AddNoise = mpParser->toBool(mpParser->getAttributeValue("addNoise", papszAttrs, "false"));
mpMetabolite = new CMetab();
addFix(mKey, mpMetabolite);
mpMetabolite->setObjectName(Name);
mpMetabolite->setStatus(SimulationType);
mpMetabolite->setAddNoise(AddNoise);
pCompartment =
dynamic_cast< CCompartment* >(mpData->mKeyMap.get(Compartment));
if (!pCompartment) fatalError();
pCompartment->addMetabolite(mpMetabolite);
mpData->pModel->getMetabolites().add(mpMetabolite, false);
break;;
case MiriamAnnotation:
case Comment:
case Expression:
case InitialExpression:
case NoiseExpression:
pHandlerToCall = getHandler(mCurrentElement.second);
break;
case ListOfUnsupportedAnnotations:
mpData->mUnsupportedAnnotations.clear();
pHandlerToCall = getHandler(mCurrentElement.second);
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return pHandlerToCall;
}