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