void
PackageIdReplacementCheck::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.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 = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
if (parent->isSetId() == true && refElem->isSetId() == false)
{
logMissingIdAttribute(repBy, refElem, parent);
}
}
void
ClassReplacements::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.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 = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
if (refElem->getTypeCode() != parent->getTypeCode())
{
int refElemTC = refElem->getTypeCode();
// exception is anything with mathematical meaning
// may replace a parameter
if (parent->getTypeCode() == SBML_PARAMETER)
{
if (refElemTC == SBML_COMPARTMENT || refElemTC == SBML_SPECIES ||
refElemTC == SBML_SPECIES_REFERENCE || refElemTC == SBML_REACTION
|| refElemTC == SBML_LOCAL_PARAMETER)
{
return;
}
}
else if (parent->getTypeCode() == SBML_LOCAL_PARAMETER)
{
if (refElemTC == SBML_PARAMETER)
{
return;
}
}
logBadClassReplacement(repBy, refElem, parent);
}
}
void
UnitReplacementCheck::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.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 = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
UnitDefinition *parentUnits = parent->getDerivedUnitDefinition();
//bool delparunit = parent->getTypeCode()==SBML_PARAMETER;
UnitDefinition *refElemUnits = refElem->getDerivedUnitDefinition();
//bool delrefunit = refElem->getTypeCode()==SBML_PARAMETER;
if (parentUnits == NULL || refElemUnits == NULL)
{
//if (delparunit)
//{
// delete parentUnits;
//}
//if (delrefunit)
//{
// delete refElemUnits;
//}
return;
}
if (parent->containsUndeclaredUnits() == true ||
refElem->containsUndeclaredUnits() == true)
{
//if (delparunit)
//{
// delete parentUnits;
//}
//if (delrefunit)
//{
// delete refElemUnits;
//}
return;
}
if (UnitDefinition::areIdentical(parentUnits, refElemUnits) == false)
{
logMismatchUnits(repBy, refElem, parent);
}
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(repBy, refElem, parent);
}
}
}
}
//if (delparunit)
//{
// delete parentUnits;
//}
//if (delrefunit)
//{
// delete refElemUnits;
//}
}
