/**
* Handle UTR joins
*
* @param feature
* @param key
* @param qualifiers
* @return
*/
private Location joinUtrs(Feature feature, Key key, QualifierVector qualifiers) {
Location location = feature.getLocation();
if (key.getKeyString().equals("5'UTR") || key.getKeyString().equals("3'UTR")) {
ChadoCanonicalGene gene = ((GFFStreamFeature) feature).getChadoGene();
String utrName = GeneUtils.getUniqueName(feature);
String transcriptName = gene.getTranscriptFromName(utrName);
List<Feature> utrs;
if (key.getKeyString().equals("5'UTR")) utrs = gene.get5UtrOfTranscript(transcriptName);
else utrs = gene.get3UtrOfTranscript(transcriptName);
if (utrs.size() > 1) {
int start = Integer.MAX_VALUE;
RangeVector ranges = new RangeVector();
for (int i = 0; i < utrs.size(); i++) {
Feature utr = utrs.get(i);
Range range = utr.getLocation().getTotalRange();
if (start > range.getStart()) start = range.getStart();
ranges.add(range);
}
if (start != feature.getLocation().getTotalRange().getStart()) return null;
location = new Location(ranges, feature.getLocation().isComplement());
}
int ntranscripts = gene.getTranscripts().size();
if (ntranscripts == 1) transcriptName = gene.getGeneUniqueName();
qualifiers.setQualifier(new Qualifier("locus_tag", transcriptName));
qualifiers.removeQualifierByName("ID");
}
return location;
}
/**
* Routine to combine transcript qualifiers and for multiple transcripts create links to the other
* transcripts (other_transcript) and to use the transcript ID.
*
* @param qualifiers
* @param transcript
* @param ntranscripts
* @param chadoGene
*/
private int handleTranscripts(
QualifierVector qualifiers,
Feature transcript,
int ntranscripts,
ChadoCanonicalGene chadoGene) {
QualifierVector transcriptQualifiers = transcript.getQualifiers().copy();
combineQualifiers(qualifiers, transcriptQualifiers, false);
ntranscripts = chadoGene.getTranscripts().size();
if (ntranscripts > 1) {
addNewQualifier(qualifiers, transcriptQualifiers.getQualifierByName("ID"));
List<Feature> transcripts = chadoGene.getTranscripts();
for (int i = 0; i < ntranscripts; i++) {
Feature thisTranscript = (Feature) transcripts.get(i);
String thisTranscriptName = GeneUtils.getUniqueName(thisTranscript);
if (!thisTranscriptName.equals(GeneUtils.getUniqueName(transcript))) {
Qualifier qualifier = new Qualifier("other_transcript", thisTranscriptName);
addNewQualifier(qualifiers, qualifier);
}
}
}
return ntranscripts;
}
