X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1c7be464b88154657ea2c65f1fb8c33ec8061cc7;hb=03496bf88fc1bec3ce628ac79ce69440ce244007;hp=3da449446b684cf6df1a02e032bbf56083f1b9e4;hpb=c46ac1bbccd595dfeb504220b465023d38815223;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3da4494..1c7be46 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1875,7 +1875,6 @@ public class PopupMenu extends JPopupMenu
      * Add annotations at the top of the annotation, in the same order as their
      * related sequences.
      */
-    int insertPosition = 0;
     for (SequenceI seq : candidates.keySet())
     {
       for (AlignmentAnnotation ann : candidates.get(seq))
@@ -1896,7 +1895,7 @@ public class PopupMenu extends JPopupMenu
         // adjust for gaps
         copyAnn.adjustForAlignment();
         // add to the alignment and set visible
-        this.ap.getAlignment().addAnnotation(copyAnn, insertPosition++);
+        this.ap.getAlignment().addAnnotation(copyAnn);
         copyAnn.visible = true;
       }
     }
@@ -2567,7 +2566,8 @@ public class PopupMenu extends JPopupMenu
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, sequence, true);
+              jalview.io.AppletFormatAdapter.FILE, sequence, true,
+              Desktop.instance);
     }
 
   }