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;
          }
      }
    }
}
Esempio n. 2
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/** @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();
  }
}
Esempio n. 3
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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;
}