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;
}
/**
* Returns the featurelocs of amino acid features located on the polypeptide.
*
* @param <T> the type of feature, must be a subclass of amino acid feature For example <code>
* ModifiedAminoAcidFeature.class</code>.
* @return a sorted set of featurelocs
*/
@Transient
public <T extends AminoAcid> List<FeatureLoc> getAminoAcidFeatureLocs(Class<T> type) {
List<FeatureLoc> aminoAcidFeatureLocs = new ArrayList<FeatureLoc>();
for (FeatureLoc domainLoc : this.getFeatureLocsForSrcFeatureId()) {
Feature domain = domainLoc.getFeature();
if (type.isAssignableFrom(domain.getClass())) {
aminoAcidFeatureLocs.add(domainLoc);
}
}
return aminoAcidFeatureLocs;
}
/**
* Get all the polypeptide regions of the specified type.
*
* @param <T> the type of region. Must be a subclass of <code>PolypeptideRegion</code>
* @param type a class object representing the region type. For example, <code>
* PolypeptideDomain.class</code>
* @return a sorted set of those regions of the requested type
*/
@Transient
public <T extends PolypeptideRegion> SortedSet<T> getRegions(Class<T> type) {
SortedSet<T> domains = new TreeSet<T>();
for (FeatureLoc domainLoc : this.getFeatureLocsForSrcFeatureId()) {
Feature domain = domainLoc.getFeature();
if (type.isAssignableFrom(domain.getClass())) {
domains.add(type.cast(domain));
}
}
return domains;
}
/**
* Get a collection of the ProteinMatch features that represent similarities between this
* polypeptide and another (as defined by a /similarity qualifier in a PSU EMBL file).
*
* @return a collection of the ProteinMatch features that represent similarities between this
* polypeptide and another.
*/
@Transient
public Collection<ProteinMatch> getSimilarityMatches() {
List<ProteinMatch> proteinMatches = new ArrayList<ProteinMatch>();
for (FeatureLoc featureLoc : this.getFeatureLocsForSrcFeatureId()) {
if (featureLoc.getRank() != 0) {
continue;
}
Feature feature = featureLoc.getFeature();
if (feature instanceof ProteinMatch) {
proteinMatches.add((ProteinMatch) feature);
} else {
logger.debug(
String.format(
"getSimilarityMatches: %s is '%s', not ProteinMatch", feature, feature.getClass()));
}
}
return proteinMatches;
}
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());
}