JAL-882; VARNA crashed when non-standard gaps where in structure; the

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index a4808cf..82ce835 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -282,7 +282,7 @@ public class PopupMenu extends JPopupMenu
                  {
                          System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
                          //TODO: VARNA does'nt print gaps in the sequence
-                         new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName());
+                         new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName(),ap);
                  }
                        });       
                        viewStructureMenu.add(menuItem);