/**
* If the given feature can be added directly to this Entry, then return it, otherwise create and
* return a new feature of the appropriate type.
*
* @param copy if true then always new a new copy of the Feature.
*/
protected Object makeNativeFeature(final Feature feature, final boolean copy) {
if (!copy
&& (feature instanceof EmblStreamFeature && this instanceof EmblDocumentEntry
|| feature instanceof GenbankStreamFeature && this instanceof GenbankDocumentEntry)) {
return (PublicDBStreamFeature) feature;
} else {
try {
if (feature instanceof GFFStreamFeature) return mapGffToNativeFeature(feature);
else if (this instanceof EmblDocumentEntry) return new EmblStreamFeature(feature);
else return new GenbankStreamFeature(feature);
} catch (NullPointerException npe) {
System.err.println(((uk.ac.sanger.artemis.Feature) feature.getUserData()).getIDString());
throw npe;
}
}
}
/**
* 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)"));
}