X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=88752880345bdce8a48b339f1eb053a962b2fe7e;hb=refs%2Fheads%2Fbug%2FJAL-4290_headless_alignment_figure_with_sse;hp=57a2fa0b2c69dde70b18834565bfeed00077fcba;hpb=ce014a26884efee8ab5b0cd06863c499fd7855d7;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 57a2fa0..8875288 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1735,10 +1735,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   protected void addReferenceAnnotations_actionPerformed(
           Map<SequenceI, List<AlignmentAnnotation>> candidates)
   {
-    final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
     final AlignmentI alignment = this.ap.getAlignment();
-    AlignmentUtils.addReferenceAnnotations(candidates, alignment,
-            selectionGroup);
+    AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
     refresh();
   }
 
@@ -2192,7 +2190,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     String[] omitHidden = null;
 
-    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+    jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a
+                                                        // prompt happens
     // or we simply trust the user wants
     // wysiwig behaviour