void checkComp(CompSBMLDocumentPlugin* compdoc, set<string>& components, set<string>& tests, const map<string, vector<double> >& results)
{
SBMLDocument* doc = compdoc->getSBMLDocument();
List* allElements = doc->getAllElements();
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
ReplacedElement* re;
Submodel* submod;
switch(element->getTypeCode()) {
case SBML_COMP_SUBMODEL:
components.insert("comp:Submodel");
submod = static_cast<Submodel*>(element);
if (submod->isSetExtentConversionFactor()) {
tests.insert("comp:ExtentConversionFactor");
}
if (submod->isSetTimeConversionFactor()) {
tests.insert("comp:TimeConversionFactor");
}
break;
case SBML_COMP_MODELDEFINITION:
components.insert("comp:ModelDefinition");
break;
case SBML_COMP_EXTERNALMODELDEFINITION:
components.insert("comp:ExternalModelDefinition");
break;
case SBML_COMP_SBASEREF:
components.insert("comp:SBaseRef");
break;
case SBML_COMP_DELETION:
components.insert("comp:Deletion");
break;
case SBML_COMP_REPLACEDELEMENT:
components.insert("comp:ReplacedElement");
re = static_cast<ReplacedElement*>(element);
if (re->isSetConversionFactor()) {
tests.insert("comp:ConversionFactor");
}
break;
case SBML_COMP_REPLACEDBY:
components.insert("comp:ReplacedBy");
break;
case SBML_COMP_PORT:
components.insert("comp:Port");
break;
default:
break;
}
}
for (map<string, vector<double> >::const_iterator result=results.begin();
result != results.end(); result++) {
string id = result->first;
if (id.find("__") != string::npos) {
//It is probably a submodel element, renamed
tests.insert("comp:SubmodelOutput");
}
}
}
void
UnitReplacementCheck::checkReferencedElement(ReplacedElement& repE,
const Model& m)
{
// if the deletion attribute is set then it is not a true replacement
if (repE.isSetDeletion() == true)
{
return;
}
unsigned int numErrsB4 = repE.getSBMLDocument()->getNumErrors();
SBase* refElem = repE.getReferencedElement();
// if there is an issue with references the getReferencedElement
// will log errors and possibly fail
// we dont want to try any further
unsigned int numErrsAfter = repE.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repE.getParentSBMLObject()->getParentSBMLObject();
UnitDefinition *parentUnits = parent->getDerivedUnitDefinition();
UnitDefinition *refElemUnits = refElem->getDerivedUnitDefinition();
bool delrefelem = false;
bool cfPresent = false;
/* adjust the refElement units for conversion factor */
if (repE.isSetConversionFactor() == true && refElemUnits && refElemUnits->getNumUnits() > 0)
{
Parameter * p = const_cast<Model *>(&m)
->getParameter(repE.getConversionFactor());
UnitDefinition *ud = p->getDerivedUnitDefinition();
UnitDefinition *newRefElemUnits = UnitDefinition::combine(refElemUnits, ud);
refElemUnits = newRefElemUnits;
delrefelem = true;
cfPresent = true;
}
if (parentUnits == NULL)
{
if (delrefelem)
{
delete refElemUnits;
}
return;
}
if (refElemUnits == NULL)
{
return;
}
if (parent->containsUndeclaredUnits() == true ||
refElem->containsUndeclaredUnits() == true)
{
if (delrefelem)
{
delete refElemUnits;
}
return;
}
if (UnitDefinition::areIdentical(parentUnits, refElemUnits) == false)
{
logMismatchUnits(repE, refElem, parent, cfPresent);
}
else
{
// if we have Compartments that have spatialDimensions but no units
// we can check this
if (parent->getTypeCode() == SBML_COMPARTMENT
&& parentUnits->getNumUnits() == 0
&& refElem->getTypeCode() == SBML_COMPARTMENT
&& refElemUnits->getNumUnits() == 0)
{
if (static_cast<Compartment *>(parent)->isSetSpatialDimensions() == true
&& static_cast<Compartment *>(refElem)->isSetSpatialDimensions() == true)
{
if (util_isEqual(
static_cast<Compartment *>(parent)->getSpatialDimensionsAsDouble(),
static_cast<Compartment *>(refElem)->getSpatialDimensionsAsDouble())
== 0)
{
logMismatchSpatialDimensions(repE, refElem, parent);
}
}
}
}
if (delrefelem)
{
delete refElemUnits;
}
}