private static Transcript makeTranscript(Feature feature) {
Transcript transcript = new Transcript();
transcript.setFmin(feature.getRankZeroFeatureLoc().getFmin());
transcript.setFmax(feature.getRankZeroFeatureLoc().getFmax());
transcript.setUniqueName(feature.getDisplayName());
Set<TranscriptComponent> exons = new HashSet<TranscriptComponent>();
for (FeatureRelationship fr : feature.getFeatureRelationshipsForObjectId()) {
Feature relatedFeature = fr.getSubjectFeature();
String relatedFeatureName = relatedFeature.getType().getName();
if (relatedFeatureName.equals("polypeptide")) {
transcript.setProtein(relatedFeature);
} else if (relatedFeatureName.equals("exon")) {
FeatureLoc otherFeatLoc = relatedFeature.getRankZeroFeatureLoc();
exons.add(new Exon(otherFeatLoc.getFmin(), otherFeatLoc.getFmax()));
}
}
transcript.setComponents(exons);
Feature protein = transcript.getProtein();
if (protein != null) {
List<String> products = new ArrayList<String>();
for (FeatureCvTerm fcvt : protein.getFeatureCvTerms()) {
CvTerm featCvTerm = fcvt.getType();
if (featCvTerm.getCv().getName().equals("genedb_products")) {
products.add(featCvTerm.getName());
}
}
transcript.setProducts(products);
}
return transcript;
}
protected BasicGene geneFromFeature(Feature feat) {
BasicGene ret = new Gene();
ret.setUniqueName(feat.getUniqueName());
ret.setFeatureId(feat.getFeatureId());
List<String> synonyms = new ArrayList<String>();
for (FeatureSynonym fs : feat.getFeatureSynonyms()) {
String type = fs.getSynonym().getType().getName();
if (type.equals("synonym")) {
synonyms.add(fs.getSynonym().getName());
}
}
ret.setSynonyms(synonyms);
if (StringUtils.hasText(feat.getName())) {
ret.setName(feat.getName());
}
for (FeatureRelationship fr : feat.getFeatureRelationshipsForObjectId()) {
Feature otherFeat = fr.getSubjectFeature();
if (otherFeat instanceof org.gmod.schema.feature.Transcript) {
ret.addTranscript(makeTranscript(otherFeat));
}
}
ret.setOrganism(feat.getOrganism().getCommonName());
FeatureLoc loc = feat.getRankZeroFeatureLoc();
Feature chromosomeFeature = loc.getSourceFeature();
Chromosome chromosome =
new Chromosome(
chromosomeFeature.getDisplayName(),
chromosomeFeature.getFeatureId(),
chromosomeFeature.getSeqLen());
ret.setChromosome(chromosome);
ret.setStrand(loc.getStrand());
ret.setFmin(loc.getFmin());
ret.setFmax(loc.getFmax());
return ret;
}
protected Gap gapFromFeature(Feature feat) {
FeatureLoc loc = feat.getRankZeroFeatureLoc();
return new Gap(feat.getUniqueName(), loc.getFmin(), loc.getFmax());
}
