/**
* Gets all the annotations in a particular feature set
*
* @param featureSet
* @return
*/
public static Set<SeqFeatureI> getAnnotations(SeqFeatureI featureSet) {
HashSet<SeqFeatureI> result = new HashSet<SeqFeatureI>();
if (featureSet.isTranscript()) {
if (featureSet.isContainedByRefSeq())
// only add if its fully in range
result.add(featureSet);
} else if (featureSet.isAnnotTop() && !featureSet.hasKids()) {
// only add if its fully in range
if (featureSet.isContainedByRefSeq()) result.add(featureSet);
} else {
for (int i = 0, size = featureSet.getFeatures().size(); i < size; i++) {
SeqFeatureI feature = featureSet.getFeatureAt(i);
if (feature.canHaveChildren()) {
result.addAll(getAnnotations(feature));
}
}
}
return result;
}
