Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2eed311..24f882e 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1438,6 +1438,17 @@ 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;
@@ -1445,12 +1456,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (format.equalsIgnoreCase("Jalview"))
     {
       features = formatter.printJalviewFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols());
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
     else
     {
       features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols());
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
 
     if (displayTextbox)