From b482f8156c38c7b5ea498eec33f312375441c352 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 8 Jun 2010 14:30:37 +0000
Subject: [PATCH 1/1] better test for when to update column selection when
 receiving a selection message * JAL-574

---
 src/jalview/gui/SeqPanel.java |   13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index f3502a6..640b7e4 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1883,7 +1883,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     // do we want to thread this ? (contention with seqsel and colsel locks, I
     // suspect)
-    boolean repaint = false;
+    // rules are: colsel is copied if there is a real intersection between sequence selection
+    boolean repaint = false,copycolsel=true;
     if (av.selectionGroup == null || !av.isSelectionGroupChanged())
     {
       SequenceGroup sgroup = null;
@@ -1898,6 +1899,11 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         sgroup = seqsel.intersect(av.alignment,
                 (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+        if ((sgroup==null || sgroup.getSize()==0) && (colsel==null || colsel.size()==0))
+        {
+          // don't copy columns if the region didn't intersect.
+          copycolsel=false;
+        }
       }
       if (sgroup != null && sgroup.getSize() > 0)
       {
@@ -1909,7 +1915,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       repaint = av.isSelectionGroupChanged();
     }
-    if (av.colSel == null || !av.isColSelChanged())
+    if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
@@ -1922,6 +1928,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       else
       {
+        // TODO: shift colSel according to the intersecting sequences
         if (av.colSel == null)
         {
           av.colSel = new ColumnSelection(colsel);
@@ -1933,7 +1940,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       repaint |= av.isColSelChanged();
     }
-    if (av.hasHiddenColumns
+    if (copycolsel && av.hasHiddenColumns
             && (av.colSel == null || av.colSel.getHiddenColumns() == null))
     {
       System.err.println("Bad things");
-- 
1.7.10.2