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;
}
private Collection<String> populateFromFeatureCvTerms(String cvNamePrefix) {
List<String> ret = new ArrayList<String>();
for (FeatureCvTerm fct : getFeatureCvTermsFilteredByCvNameStartsWith(cvNamePrefix)) {
ret.add(
String.format(
"%s %s", fct.getCvTerm().getName(), fct.getCvTerm().getDbXRef().getAccession()));
}
return ret;
}
@Transient
public List<String> getProducts() {
List<String> products = new ArrayList<String>();
for (FeatureCvTerm featureCvTerm : this.getFeatureCvTerms()) {
if (featureCvTerm.getType().getCv().getName().equals("genedb_products")) {
products.add(featureCvTerm.getType().getName());
}
}
return products;
}