/**
* Change the stop_codon_redefined_as_selenocysteine SO qualifier to the transl_except EMBL
* qualifier.
*
* @param qualifiers
* @param feature
*/
private void handleSelenocysteine(QualifierVector qualifiers, Feature feature) {
if (!feature.getKey().getKeyString().equals(DatabaseDocument.EXONMODEL)) return;
qualifiers.removeQualifierByName("stop_codon_redefined_as_selenocysteine");
uk.ac.sanger.artemis.Feature f = ((uk.ac.sanger.artemis.Feature) feature.getUserData());
int translatedBasePosion = 0;
String aa = f.getTranslation().toString();
for (int i = 0; i < aa.length(); i++) {
if (AminoAcidSequence.isStopCodon(aa.charAt(i))) {
translatedBasePosion = i * 3;
break;
}
}
FeatureSegmentVector segments = f.getSegments();
int nbases = 0;
int sequenceloc = 0;
for (int i = 0; i < segments.size(); i++) {
int seglen = segments.elementAt(i).getBases().length();
if (nbases + seglen > translatedBasePosion) {
Bases bases = f.getStrand().getBases();
sequenceloc =
segments.elementAt(i).getStart().getPosition() + (translatedBasePosion - nbases);
if (!f.isForwardFeature()) sequenceloc = bases.getComplementPosition(sequenceloc);
}
nbases += seglen;
}
String pos = "";
if (f.isForwardFeature()) pos = sequenceloc + ".." + (sequenceloc + 2);
else pos = "complement(" + (sequenceloc - 2) + ".." + sequenceloc + ")";
qualifiers.add(new Qualifier("transl_except", "(pos:" + pos + ",aa:Sec)"));
}
