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;
}
@Transient
@Field(index = Index.TOKENIZED, store = Store.NO)
public String getEcNums() {
List<String> ecNums = new ArrayList<String>();
for (FeatureProp fp : getFeatureProps()) {
CvTerm type = fp.getType();
if (type.getName().equals("EC_number") && type.getCv().getName().equals("genedb_misc")) {
ecNums.add(fp.getValue());
}
}
return StringUtils.collectionToDelimitedString(ecNums, " ");
}
@Transient
@Field(index = Index.TOKENIZED, store = Store.YES)
public String getAllCuration() {
List<String> curation = new ArrayList<String>();
for (FeatureProp fp : getFeatureProps()) {
CvTerm type = fp.getType();
if (type.getCv().getName().equals("genedb_misc") && type.getName().equals("curation")) {
curation.add(fp.getValue());
}
if (type.getCv().getName().equals("feature_property") && type.getName().equals("comment")) {
curation.add(fp.getValue());
}
}
// we add terms from the CC_genedb_controlledcuration featurecvterm here
curation.addAll(populateFromFeatureCvTerms("CC_genedb_controlledcuration"));
return StringUtils.collectionToDelimitedString(curation, " ");
}