- FeaturesFile formatter = new FeaturesFile();
- SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
- Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
- .getDisplayedFeatureCols();
- List<String> featureGroups = ap.getFeatureRenderer()
- .getDisplayedFeatureGroups();
- boolean includeNonPositional = ap.av.isShowNPFeats();
- if (GFFFormat.isSelected())
- {
- text = formatter.printGffFormat(sequences, featureColours,
- featureGroups, includeNonPositional);
- }
- else
- {
- text = formatter.printJalviewFormat(sequences, featureColours,
- featureGroups, includeNonPositional);
- }