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; } }