/**
* AssemblyFeature is the only GAI at the moment that has no relation to // a transcript. Dont
* think they can end up in ede (??). // Would be nice to have an interface that was solely for
* the exon // trans gene heirarchy? Should we actively make sure AssemblyFeatures dont // get
* into ede? (filter in AnnotationMenu?) returns null if no transcript can be found.
*/
private AnnotatedFeatureI getTransOrOneLevelAnn(AnnotatedFeatureI af) {
if (af != null) {
if (af.isTranscript()) return af;
if (af.isExon()) return af.getRefFeature().getAnnotatedFeature();
if (af.isAnnotTop()) {
if (af.hasKids()) return af.getFeatureAt(0).getAnnotatedFeature(); // transcript
else // 1 level annot
return af;
}
}
return null;
}
