- for (SequenceFeature sequenceFeature : features)
- {
- isnonpos = sequenceFeature.begin == 0
- && sequenceFeature.end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(sequenceFeature.type)))
- {
- // skip if feature is nonpos and we ignore them or if we only
- // output visible and it isn't non-pos and it's not visible
- continue;
- }
+ features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
+ false, group, types));
+ }
+ features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
+ true, group, types));