Merge branch 'bug/JAL-2687concurrentModification' into features/JAL-2608closeOverview

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7d82dd7..4b9d90f 100644 (file)
--- 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)