X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4b9d90fb031875ebdbae9f84eb403976b6aab312;hb=be2991221f61799469e24b163d28ff58851d935f;hp=7d82dd7cbaf436a0e5d8006c6f5f01b240444533;hpb=eac3f8019fe37f2c84784adef3a7db56598c5cb8;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7d82dd7..4b9d90f 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1426,21 +1426,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return null;
   }
 
+  private List<String> getDisplayedFeatureGroups()
+  {
+    if (alignPanel.getFeatureRenderer() != null
+            && viewport.getFeaturesDisplayed() != null)
+    {
+      return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+    }
+    return null;
+  }
+
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printJalviewFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
     else
     {
-      features = formatter.printGffFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printGffFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
 
     if (displayTextbox)