X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=0848a4dc03f839bb35097849a227fbacad87441c;hb=45922d35b5dc6c73b3d0c55ef2ab884079723782;hp=3bf7c24b5a8a38ea981c2041a426bcc1af25ead0;hpb=e2c3b3602486cee3f85dd8dfc7856a5ce6701669;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 3bf7c24..0848a4d 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -42,7 +42,6 @@ import java.io.IOException;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
-import java.util.List;
 
 import javax.swing.JInternalFrame;
 
@@ -485,8 +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;
             }
@@ -689,7 +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;
@@ -1075,15 +1075,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   }
                   else
                   {
-                    // int[] intervals = colsel.getVisibleContigs(
-                    // seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    List<int[]> intervals = hidden.getVisibleContigs(
-                            seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    for (int[] region : intervals)
+                    Iterator<int[]> intervals = hidden
+                            .getVisContigsIterator(seqsel.getStartRes(),
+                                    seqsel.getEndRes() + 1, false);
+                    while (intervals.hasNext())
                     {
+                      int[] region = intervals.next();
                       Seg s = new Seg();
-                      s.setStart(region[0] + 1); // vamsas indices begin at
-                      // 1, not zero.
+                      s.setStart(region[0] + 1); // vamsas indices begin at 1,
+                                                 // not zero.
                       s.setEnd(region[1] + 1);
                       s.setInclusive(true);
                       range.addSeg(s);