public void handleEndElement(
      OtterContentHandler theContentHandler,
      String namespaceURI,
      String localName,
      String qualifiedName) {

    //
    // should pop the mode off the stack.
    super.handleEndElement(theContentHandler, namespaceURI, localName, qualifiedName);

    // grab the annotation off the stack, and set it into the
    // parent sequence_set.
    AssemblyFeature sequenceFragment = (AssemblyFeature) theContentHandler.popStackObject();
    ((AnnotatedFeatureI) theContentHandler.getCurrentObject()).addFeature(sequenceFragment);
  } // end handleTag
 public void handleEndElement(
     OtterContentHandler theContentHandler,
     String namespaceURI,
     String localName,
     String qualifiedName) {
   Transcript trans = (Transcript) theContentHandler.getStackObject();
   trans.addProperty(TagHandler.AUTHOR_EMAIL, getCharacters());
   super.handleEndElement(theContentHandler, namespaceURI, localName, qualifiedName);
 }
 public void handleEndElement(
     OtterContentHandler theContentHandler,
     String namespaceURI,
     String localName,
     String qualifiedName) {
   Transcript transcript = (Transcript) theContentHandler.getStackObject();
   DbXref dbx = new DbXref("OtterId", getCharacters(), "otter");
   transcript.addDbXref(dbx);
   super.handleEndElement(theContentHandler, namespaceURI, localName, qualifiedName);
 }
  public void handleEndElement(
      OtterContentHandler theContentHandler,
      String namespaceURI,
      String localName,
      String qualifiedName) {
    Exon exon = (Exon) theContentHandler.getStackObject();
    int strand = Integer.valueOf(getCharacters()).intValue();
    exon.setStrand(strand);

    super.handleEndElement(theContentHandler, namespaceURI, localName, qualifiedName);
  }
  public void handleEndElement(
      OtterContentHandler theContentHandler,
      String namespaceURI,
      String localName,
      String qualifiedName) {
    Transcript transcript = (Transcript) theContentHandler.getStackObject();
    Comment comment =
        new Comment(
            transcript.getId(),
            getCharacters(),
            "no author",
            0 // should be a long representing a timestamp.
            );
    transcript.addComment(comment);

    super.handleEndElement(theContentHandler, namespaceURI, localName, qualifiedName);
  }
  public void handleStartElement(
      OtterContentHandler theContentHandler,
      String namespaceURI,
      String localName,
      String qualifiedName,
      Attributes attributes) {
    //
    // should just push the mode - so subsequence tags know we're
    // dealing with a sequence fragment.
    super.handleStartElement(theContentHandler, namespaceURI, localName, qualifiedName, attributes);

    AssemblyFeature sequenceFragment = new AssemblyFeature();
    //
    // pushes annotation on the stack so subsequence tags can
    // modify it.
    theContentHandler.pushStackObject(sequenceFragment);
  } // end handleTag