LIBSBML_EXTERN
void
copySBaseAttributes(const SBase& source,SBase& target)
{
target.setMetaId(source.getMetaId());
// target.setId(source.getId());
// target.setName(source.getName());
target.setSBMLDocument(const_cast<SBMLDocument*>(source.getSBMLDocument()));
target.setSBOTerm(source.getSBOTerm());
if(source.isSetAnnotation())
{
target.setAnnotation(new XMLNode(*const_cast<SBase&>(source).getAnnotation()));
}
if(source.isSetNotes())
{
target.setNotes(new XMLNode(*const_cast<SBase&>(source).getNotes()));
}
if (source.getSBMLNamespaces())
{
target.setSBMLNamespaces(source.getSBMLNamespaces());
}
List* pCVTerms=target.getCVTerms();
// first delete all the old CVTerms
if(pCVTerms)
{
while(pCVTerms->getSize()>0)
{
CVTerm* object=static_cast<CVTerm*>(pCVTerms->remove(0));
delete object;
}
// add the cloned CVTerms from source
if(source.getCVTerms()!=NULL)
{
unsigned int i=0,iMax=source.getCVTerms()->getSize();
while(i<iMax)
{
target.addCVTerm(static_cast<CVTerm*>(static_cast<CVTerm*>(source.getCVTerms()->get(i))->clone()));
++i;
}
}
}
}
/** @cond doxygenLibsbmlInternal */
void CompModelPlugin::resetPorts()
{
for (unsigned int p=0; p<getNumPorts(); p++) {
Port* port = getPort(p);
SBase* referenced = port->getReferencedElement();
if (port->isSetSBaseRef()) {
port->unsetSBaseRef();
port->unsetIdRef();
port->unsetMetaIdRef();
port->unsetUnitRef();
int type = referenced->getTypeCode();
if (referenced->isSetId() &&
type != SBML_INITIAL_ASSIGNMENT &&
type != SBML_ASSIGNMENT_RULE &&
type != SBML_RATE_RULE &&
type != SBML_EVENT_ASSIGNMENT) {
if (type==SBML_UNIT_DEFINITION) {
port->setUnitRef(referenced->getId());
}
else {
port->setIdRef(referenced->getId());
}
}
else if (referenced->isSetMetaId()) {
port->setMetaIdRef(referenced->getMetaId());
}
else {
stringstream newname;
newname << "auto_port_" << p;
referenced->setMetaId(newname.str());
port->setMetaIdRef(newname.str());
}
}
port->clearReferencedElement();
}
}
int ReplacedBy::performReplacementAndCollect(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
//Find the various objects and plugin objects we need for this to work.
SBase* parent = getParentSBMLObject();
if (parent==NULL) {
if (doc) {
string error = "Unable to perform replacement in ReplacedBy::performReplacement: no parent object for this <replacedBy> could be found.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
SBase* ref = getReferencedElement();
if (ref==NULL) {
//getReferencedElement sets its own error messages.
return LIBSBML_INVALID_OBJECT;
}
//Update the IDs. (Will set its own error messages.)
int ret = updateIDs(ref, parent);
//ReplacedBy elements do get the name of the top-level element, assuming it has one:
if (parent->isSetId()) {
ref->setId(parent->getId());
}
if (parent->isSetMetaId()) {
ref->setMetaId(parent->getMetaId());
}
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
//And finally, get ready to delete the parent object.
if (toremove) {
toremove->insert(parent);
}
return LIBSBML_OPERATION_SUCCESS;
}