void
PackageIdReplacementCheck::checkReferencedElement(ReplacedElement& repE)
{
// if the deletion attribute is set then it does not point
// to another package element
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();
if (refElem->isSetId() == true && parent->isSetId() == false)
{
logMissingIdAttribute(repE, refElem, parent);
}
}
void
ClassReplacements::checkReferencedElement(ReplacedElement& repE)
{
// if the deletion attribute is set then we don't care what
// it points to
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();
if (refElem->getTypeCode() != parent->getTypeCode())
{
int parentTC = parent->getTypeCode();
// exception is anything with mathematical meaning
// may replace a parameter
if (refElem->getTypeCode() == SBML_PARAMETER)
{
if (parentTC == SBML_COMPARTMENT || parentTC == SBML_SPECIES ||
parentTC == SBML_SPECIES_REFERENCE || parentTC == SBML_REACTION
|| parentTC == SBML_LOCAL_PARAMETER)
{
return;
}
}
else if (refElem->getTypeCode() == SBML_LOCAL_PARAMETER)
{
if (parentTC == SBML_PARAMETER)
{
return;
}
}
logBadClassReplacement(repE, refElem, parent);
}
}
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;
}
}