X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=0848a4dc03f839bb35097849a227fbacad87441c;hb=e1aa3fdd1ca82abf5acc0cd3c2b86a5ca1083941;hp=ac72e936279e7cb8a8f1a321cab084b226ef0c46;hpb=4c1ab51e2c08f85ba8c38486adf4a6ce0b0f25c3;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index ac72e93..0848a4d 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -484,8 +484,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               errorsDuringUpdate = true;
               Cache.log.error("Exception synchronizing " + af.getTitle()
                       + " "
-                      + (af.getViewport().viewName == null ? ""
-                              : " view " + af.getViewport().viewName)
+                      + (af.getViewport().getViewName() == null ? ""
+                              : " view " + af.getViewport().getViewName())
                       + " to document.", e);
               stored = false;
             }
@@ -688,7 +688,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
   public void disableGui(boolean b)
   {
-    Desktop.instance.setVamsasUpdate(b);
+    // JAL-3311 TODO: remove this class!
+    // Desktop.instance.setVamsasUpdate(b);
   }
 
   Hashtable _backup_vobj2jv;
@@ -1076,7 +1077,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     Iterator<int[]> intervals = hidden
                             .getVisContigsIterator(seqsel.getStartRes(),
-                                    seqsel.getEndRes() + 1);
+                                    seqsel.getEndRes() + 1, false);
                     while (intervals.hasNext())
                     {
                       int[] region = intervals.next();