X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationExporter.java;h=0d47e36bdd5c71d1dec26f62d42113a650ee363c;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=136a38e37a9e6ee6c16dae0bc5b0d644c869de8f;hpb=26ba864a6c290121fe6cf616794d2d0bea65fb7d;p=jalview.git

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 136a38e..0d47e36 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
@@ -155,19 +156,26 @@ public class AnnotationExporter extends JPanel
             .getString("label.no_features_on_alignment");
     if (features)
     {
+      Map<String, FeatureColourI> displayedFeatureColours = ap
+              .getFeatureRenderer().getDisplayedFeatureCols();
       FeaturesFile formatter = new FeaturesFile();
-      SequenceI[] sequences = ap.av.getAlignment().getDataset()
-              .getSequencesArray();
-      Map<String, Object> featureColours = ap.getFeatureRenderer()
+      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);
       }