+ if (datasetSequence == null)
+ {
+ sequenceFeatures = features;
+ }
+ else
+ {
+ if (datasetSequence.getSequenceFeatures() != features
+ && datasetSequence.getSequenceFeatures() != null
+ && datasetSequence.getSequenceFeatures().length > 0)
+ {
+ System.err
+ .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+ }
+ datasetSequence.setSequenceFeatures(features);
+ }