X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=640b7e4b53c6dda68c4623ac366377df35a11227;hb=b482f8156c38c7b5ea498eec33f312375441c352;hp=f3502a6993fe6e789a714ee2f6055cee6649bae6;hpb=6ef8b014737c1dac4f2e566e27cf4b34b68af9c0;p=jalview.git

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");