virtual bool visit(const SBase &x)
{
if (&x == NULL || x.getPackageName() != "arrays")
{
return SBMLVisitor::visit(x);
}
int code = x.getTypeCode();
const ListOf* list = dynamic_cast<const ListOf*>(&x);
if (list != NULL)
{
return SBMLVisitor::visit(x);
}
else
{
if (code == SBML_ARRAYS_DIMENSION)
{
return visit((const Dimension&)x);
}
else if (code == SBML_ARRAYS_INDEX)
{
return visit((const Index&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
}
virtual bool visit(const SBase &x)
{
if (&x == NULL || x.getPackageName() != "req")
{
return SBMLVisitor::visit(x);
}
int code = x.getTypeCode();
const ListOf* list = dynamic_cast<const ListOf*>(&x);
if (list != NULL)
{
return SBMLVisitor::visit(x);
}
else
{
if (code == SBML_REQ_CHANGED_MATH)
{
return visit((const ChangedMath&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
}
virtual bool visit(const SBase &x)
{
if (&x == NULL || x.getPackageName() != "groups")
{
return SBMLVisitor::visit(x);
}
int code = x.getTypeCode();
const ListOf* list = dynamic_cast<const ListOf*>(&x);
if (list != NULL)
{
return SBMLVisitor::visit(x);
}
else
{
if (code == SBML_GROUPS_MEMBER)
{
return visit((const Member&)x);
}
else if (code == SBML_GROUPS_MEMBER_CONSTRAINT)
{
return visit((const MemberConstraint&)x);
}
else if (code == SBML_GROUPS_GROUP)
{
return visit((const Group&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
}
virtual bool visit(const SBase &x)
{
if (&x == NULL || x.getPackageName() != "distrib")
{
return SBMLVisitor::visit(x);
}
int code = x.getTypeCode();
const ListOf* list = dynamic_cast<const ListOf*>(&x);
if (list != NULL)
{
return SBMLVisitor::visit(x);
}
else
{
if (code == SBML_DISTRIB_DRAW_FROM_DISTRIBUTION)
{
return visit((const DrawFromDistribution&)x);
}
else if (code == SBML_DISTRIB_INPUT)
{
return visit((const DistribInput&)x);
}
else if (code == SBML_DISTRIB_UNCERTAINTY)
{
return visit((const Uncertainty&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
}
virtual bool visit (const SBase &x)
{
if(&x == NULL || x.getPackageName() != "qual")
{
return SBMLVisitor::visit(x);
}
int code = x.getTypeCode();
const ListOf* list = dynamic_cast<const ListOf*>(&x);
if (list != NULL)
{
code = list->getItemTypeCode();
if (code == SBML_QUAL_FUNCTION_TERM)
{
return visit((const ListOfFunctionTerms&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
else
{
if (code == SBML_QUAL_QUALITATIVE_SPECIES)
{
return visit((const QualitativeSpecies&)x);
}
else if (code == SBML_QUAL_TRANSITION)
{
return visit((const Transition&)x);
}
else if (code == SBML_QUAL_INPUT)
{
return visit((const Input&)x);
}
else if (code == SBML_QUAL_OUTPUT)
{
return visit((const Output&)x);
}
else if (code == SBML_QUAL_FUNCTION_TERM)
{
return visit((const FunctionTerm&)x);
}
else if (code == SBML_QUAL_DEFAULT_TERM)
{
return visit((const DefaultTerm&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
}
/*
* Logs a constraint failure to the validator for the given SBML object.
* The parameter message is used instead of the constraint's member
* variable msg.
*/
void
VConstraint::logFailure (const SBase& object, const std::string& message)
{
std::string pkg = object.getPackageName();
unsigned int pkgVersion = object.getPackageVersion();
if (mId > 99999 && pkg == "core")
{
// we are dealing with a core object that is logging errors
// relating to a package
// need to work out which pkg
unsigned int offset = (unsigned int)(floor((double)mId/100000.0)) * 100000;
if (offset == 9900000)
{
// we are dealing with the strict units validator
mId = mId - offset;
}
else
{
// it is possible that the object does not have a direct plugin
// it may the child of an object that does
// so lets cut straight to the parent document
const SBMLDocument * doc = object.getSBMLDocument();
if (doc != NULL)
{
for (unsigned int i = 0; i < doc->getNumPlugins(); i++)
{
const SBMLExtension * ext = doc->getPlugin(i)->getSBMLExtension();
if (ext->getErrorIdOffset() == offset)
{
pkg = doc->getPlugin(i)->getPackageName();
pkgVersion = doc->getPlugin(i)->getPackageVersion();
break;
}
}
}
}
}
SBMLError error = SBMLError( mId, object.getLevel(), object.getVersion(),
message, object.getLine(), object.getColumn(),
LIBSBML_SEV_ERROR, LIBSBML_CAT_SBML, pkg, pkgVersion);
if (error.getSeverity() != LIBSBML_SEV_NOT_APPLICABLE)
mValidator.logFailure(error);
/* ( SBMLError( mId, object.getLevel(), object.getVersion(),
message, object.getLine(), object.getColumn(),
LIBSBML_SEV_ERROR, LIBSBML_CAT_SBML ));*/
}
void
ReportEmptyListOf::logEmptyList(const ListOf* list, const SBase& parent)
{
msg = "The ListOf";
msg += SBMLTypeCode_toString( list->getItemTypeCode(), list->getPackageName().c_str());
msg += "s in the ";
msg += SBMLTypeCode_toString(parent.getTypeCode(), parent.getPackageName().c_str());
msg += " with id '";
msg += parent.getId();
msg += "' has no child ";
msg += SBMLTypeCode_toString( list->getItemTypeCode(), list->getPackageName().c_str());
msg += " elements.";
logFailure(*list);
}
/*
* Logs a message about dupliacte top level annotations.
*/
void
DuplicateTopLevelAnnotation::logDuplicate (std::string name, const SBase& object )
{
msg = "The namespaces '";
msg += name;
msg += "' is duplicated within the annotation of the ";
msg += SBMLTypeCode_toString( object.getTypeCode(), object.getPackageName().c_str() );
msg += " with id '";
msg += object.getId();
msg += "'.";
logFailure(object);
}
virtual bool visit(const SBase &x)
{
if (&x == NULL || x.getPackageName() != "multi")
{
return SBMLVisitor::visit(x);
}
int code = x.getTypeCode();
const ListOf* list = dynamic_cast<const ListOf*>(&x);
if (list != NULL)
{
return SBMLVisitor::visit(x);
}
else
{
if (code == SBML_MULTI_POSSIBLE_SPECIES_FEATURE_VALUE)
{
return visit((const PossibleSpeciesFeatureValue&)x);
}
else if (code == SBML_MULTI_SPECIES_FEATURE_VALUE)
{
return visit((const SpeciesFeatureValue&)x);
}
else if (code == SBML_MULTI_COMPARTMENT_REFERENCE)
{
return visit((const CompartmentReference&)x);
}
else if (code == SBML_MULTI_SPECIES_TYPE_INSTANCE)
{
return visit((const SpeciesTypeInstance&)x);
}
else if (code == SBML_MULTI_IN_SPECIES_TYPE_BOND)
{
return visit((const InSpeciesTypeBond&)x);
}
else if (code == SBML_MULTI_DENOTED_SPECIES_TYPE_COMPONENT_INDEX)
{
return visit((const DenotedSpeciesTypeComponentIndex&)x);
}
else if (code == SBML_MULTI_OUTWARD_BINDING_SITE)
{
return visit((const OutwardBindingSite&)x);
}
else if (code == SBML_MULTI_SPECIES_FEATURE_CHANGE)
{
return visit((const SpeciesFeatureChange&)x);
}
else if (code == SBML_MULTI_SPECIES_FEATURE_TYPE)
{
return visit((const SpeciesFeatureType&)x);
}
else if (code == SBML_MULTI_SPECIES_TYPE_COMPONENT_INDEX)
{
return visit((const SpeciesTypeComponentIndex&)x);
}
else if (code == SBML_MULTI_SPECIES_FEATURE)
{
return visit((const SpeciesFeature&)x);
}
else if (code == SBML_MULTI_SPECIES_TYPE_COMPONENT_MAP_IN_PRODUCT)
{
return visit((const SpeciesTypeComponentMapInProduct&)x);
}
else if (code == SBML_MULTI_SPECIES_TYPE)
{
return visit((const MultiSpeciesType&)x);
}
else
{
return SBMLVisitor::visit(x);
}
}
}