private DasAnnotatedSegment getSegment(Collection<DasAnnotatedSegment> segments, String segmentId)
throws DataSourceException {
for (DasAnnotatedSegment segment : segments)
if (segment.getSegmentId().equals(segmentId)) return segment;
Integer length = this.getSegmentLength(segmentId);
DasAnnotatedSegment newSegment =
new DasAnnotatedSegment(
segmentId, 1, length, "FROM_DATABASE", segmentId, new ArrayList<DasFeature>());
segments.add(newSegment);
return newSegment;
}
private DasComponentFeature getGene(
String geneID, int startI, int stopI, DasAnnotatedSegment segment)
throws DataSourceException {
for (DasFeature feature : segment.getFeatures())
if (feature.getFeatureId().equals(geneID)) return (DasComponentFeature) feature;
return segment
.getSelfComponentFeature()
.addSubComponent(
geneID, startI, stopI, startI, stopI, geneID, geneType, geneID, geneID, method, null,
null, null, null, null);
}