LIBSBML_CPP_NAMESPACE_BEGIN
/*
* takes an annotation that has been read into the model
* identifies the RDF elements
* and creates a List of CVTerms from the annotation
*/
void
RDFAnnotationParser::parseRDFAnnotation(const XMLNode * annotation, List * CVTerms)
{
if (annotation == NULL) return;
const string& name = annotation->getName();
const XMLNode* RDFTop = NULL;
unsigned int n = 0;
CVTerm * term;
if (CVTerms == NULL)
CVTerms = new List();
// need to find the RDF desciption opening annotation
if (name == "annotation" && annotation->getNumChildren() > 0)
{
while (n < annotation->getNumChildren())
{
const string &name1 = annotation->getChild(n).getName();
if (name1 == "RDF")
{
if (annotation->getChild(n).getNumChildren() > 0)
{
if (annotation->getChild(n).getChild(0).getName() == "Description")
{
RDFTop = &(annotation->getChild(n).getChild(0));
break;
}
}
}
n++;
}
}
// find qualifier nodes and create CVTerms
n = 0;
if (RDFTop != NULL)
{
while (n < RDFTop->getNumChildren())
{
const string &name2 = RDFTop->getChild(n).getPrefix();
if (name2 == "bqbiol" || name2 == "bqmodel")
{
term = new CVTerm(RDFTop->getChild(n));
if (term->getResources()->getLength() > 0)
CVTerms->add((void *)term);
}
n++;
}
}
}
/*
* internal sub function that derives the cvterms from the annotation
*/
void
RDFAnnotationParser::deriveCVTermsFromAnnotation(
const XMLNode * annotation,
List * CVTerms)
{
if (annotation == NULL)
return;
// the annotation passed in may have a toplevel annotation tag BUT
// it may not be- so need to check
// if it isnt then it must be RDF or we do not have an rdf annotation
bool topLevelIsAnnotation = false;
if (annotation->getName() == "annotation")
{
topLevelIsAnnotation = true;
}
CVTerm * term;
if (CVTerms == NULL)
CVTerms = new List();
const XMLNode* RDFDesc = NULL;
if (topLevelIsAnnotation == true)
{
RDFDesc = &(annotation->getChild("RDF").getChild("Description"));
}
else
{
if (annotation->getName() == "RDF")
{
RDFDesc = &(annotation->getChild("Description"));
}
}
// find qualifier nodes and create CVTerms
unsigned int n = 0;
if (RDFDesc != NULL)
{
while (n < RDFDesc->getNumChildren())
{
const string &name2 = RDFDesc->getChild(n).getPrefix();
if (name2 == "bqbiol" || name2 == "bqmodel")
{
term = new CVTerm(RDFDesc->getChild(n));
if (term->getResources()->getLength() > 0)
CVTerms->add((void *)term);
}
n++;
}
}
// rest modified flags
for (n = 0; n < CVTerms->getSize(); n++)
{
static_cast<CVTerm*>(CVTerms->get(n))->resetModifiedFlags();
}
}
XMLNode *
RDFAnnotationParser::createCVTerms(const SBase * object)
{
if (object == NULL) return NULL;
/* create the basic triples */
XMLTriple li_triple = XMLTriple("li",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLTriple bag_triple = XMLTriple("Bag",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
/* attributes */
XMLAttributes blank_att = XMLAttributes();
/* tokens */
XMLToken bag_token = XMLToken(bag_triple, blank_att);
std::string prefix;
std::string name;
std::string uri;
XMLAttributes *resources;
XMLNode *description = createRDFDescription(object);
/* loop through the cv terms and add */
/* want to add these in blocks of same qualifier */
if (object->getCVTerms())
{
for (unsigned int n = 0; n < object->getCVTerms()->getSize(); n++)
{
CVTerm* current = static_cast <CVTerm *> (object->getCVTerms()->get(n));
if (current == NULL) continue;
if (current->getQualifierType() == MODEL_QUALIFIER)
{
prefix = "bqmodel";
uri = "http://biomodels.net/model-qualifiers/";
const char* term = ModelQualifierType_toString(
current->getModelQualifierType());
if (term == NULL) return NULL;
name = term;
}
else if (current
->getQualifierType() == BIOLOGICAL_QUALIFIER)
{
prefix = "bqbiol";
uri = "http://biomodels.net/biological-qualifiers/";
const char* term = BiolQualifierType_toString(
current->getBiologicalQualifierType());
if (term == NULL) return NULL;
name = term;
}
else
{
continue;
}
resources = current->getResources();
XMLNode bag(bag_token);
for (int r = 0; r < resources->getLength(); r++)
{
XMLAttributes att;
att.add(resources->getName(r), resources->getValue(r));
XMLToken li_token(li_triple, att);
li_token.setEnd();
XMLNode li(li_token);
bag.addChild(li);
}
XMLTriple type_triple(name, uri, prefix);
XMLToken type_token(type_triple, blank_att);
XMLNode type(type_token);
type.addChild(bag);
description->addChild(type);
}
}
return description;
}