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