if (features)
{
FeaturesFile formatter = new FeaturesFile();
- SequenceI[] sequences = ap.av.getAlignment().getDataset()
- .getSequencesArray();
+ SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
Map<String, Object> featureColours = ap.getFeatureRenderer()
.getDisplayedFeatureCols();
boolean includeNonPositional = ap.av.isShowNPFeats();