synchronized Iterator<Mutation> getFeatures(String trackKey, String chr, int start, int end)
throws IOException {
if (currentRange == null || !currentRange.contains(chr, start, end)) {
Iterator<Feature> features = tribbleFeatureSource.getFeatures(chr, start, end);
while (features.hasNext()) {
Mutation feat = (Mutation) features.next();
String thisKey = feat.getSampleId();
List<Mutation> keyFeatures = featureMap.get(thisKey);
if (keyFeatures == null) {
keyFeatures = new ArrayList<Mutation>();
featureMap.put(thisKey, keyFeatures);
}
keyFeatures.add(feat);
currentRange = new Range(chr, start, end);
}
}
List<Mutation> featureList = featureMap.get(trackKey);
return featureList == null ? Collections.EMPTY_LIST.iterator() : featureList.iterator();
}
public boolean overlaps(Range range) {
return this.overlaps(range.getChr(), range.getStart(), range.getEnd());
}