X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=dfc236e23e6dca7c0946ca30eb2e25c9f0413b51;hb=3261dc1e0830659cf50d975f19177894af778ecd;hp=e6ed8f295dbfa9c5ee61026ca85cd2fb59c749c2;hpb=8b80cdbcd6ca4928049ec518a61d10ce90c21cab;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index e6ed8f2..dfc236e 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -639,11 +639,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   public void highlightSequence(SearchResults results)
   {
-    seqCanvas.highlightSearchResults(results);
     if (av.followHighlight)
     {
-      ap.scrollToPosition(results);
+      if (ap.scrollToPosition(results, false))
+      {
+        // ap.invalidate();
+      }
     }
+    seqCanvas.highlightSearchResults(results);
+
   }
 
   public void updateColours(SequenceI seq, int index)
@@ -1683,6 +1687,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
   }
+
   /**
    * modify current selection according to a received message.
    */
@@ -1693,9 +1698,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // handles selection messages...
     // TODO: extend config options to allow user to control if selections may be
     // shared between viewports.
-    if (av!=null && (av == source
-            || !av.followSelection
-            || (source instanceof AlignViewport && ((AlignViewport) source)
+    if (av != null
+            && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source)
                     .getSequenceSetId().equals(av.getSequenceSetId()))))
     {
       return;
@@ -1708,13 +1712,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.selectionGroup == null || !av.isSelectionGroupChanged())
     {
       SequenceGroup sgroup = null;
-      if (seqsel != null)
+      if (seqsel != null && seqsel.getSize()>0)
       {
         if (av.alignment == null)
         {
-          System.out.println("Selection message: alignviewport av SeqSetId="
-                  + av.getSequenceSetId() + " ViewId=" + av.getViewId()
-                  + " 's alignment is NULL! returning immediatly.");
+          System.out
+                  .println("Selection message: alignviewport av SeqSetId="
+                          + av.getSequenceSetId() + " ViewId="
+                          + av.getViewId()
+                          + " 's alignment is NULL! returning immediatly.");
           return;
         }
         sgroup = seqsel.intersect(av.alignment,
@@ -1768,9 +1774,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     if (repaint)
     {
-      // probably finessing with multiple redraws here
-      PaintRefresher.Refresh(this, av.getSequenceSetId());
-      // ap.paintAlignment(false);
+      ap.repaint();
+      //ap.paintAlignment(false);
     }
   }