+
+ /**
+ * Returns the text contents for output of features in either GFF or Jalview
+ * format
+ *
+ * @return
+ */
+ private String getFeaturesText()
+ {
+ String text;
+ SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
+ Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
+ .getDisplayedFeatureCols();
+ Map<String, FeatureMatcherSetI> featureFilters = ap.getFeatureRenderer()
+ .getFeatureFilters();
+ List<String> featureGroups = ap.getFeatureRenderer()
+ .getDisplayedFeatureGroups();
+ boolean includeNonPositional = ap.av.isShowNPFeats();
+
+ FeaturesFile formatter = new FeaturesFile();
+ if (GFFFormat.isSelected())
+ {
+ text = formatter.printGffFormat(sequences, featureColours,
+ featureGroups, includeNonPositional);
+ }
+ else
+ {
+ text = formatter.printJalviewFormat(sequences, featureColours,
+ featureFilters, featureGroups, includeNonPositional);
+ }
+ return text;
+ }
+
+ private void toTextbox_actionPerformed()