X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=e40e936d3f89ade69afaf71f6ea6e96407a1a00c;hb=9ccf8e858d98d9bc0cca84504fecb566ee5afdca;hp=360cf6badfe7975af812227f380585a4ccec5ba8;hpb=68405aa972a7fc07ff21b35c7b2272d1d4ecb1b7;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 360cf6b..e40e936 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2370,7 +2370,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * If the cut affects all sequences, warn, remove highlighted columns
      */
-    if (sg.getSize() == viewport.getAlignment().getHeight())
+
+    boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+            .getAlignment().getWidth()) ? true : false;
+    if (sg.getSize() == viewport.getAlignment().getHeight()
+            && isEntireAlignWidth)
     {
       int confirm = JOptionPane.showConfirmDialog(this,
               MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
@@ -2397,6 +2401,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setSelectionGroup(null);
     viewport.sendSelection();
     viewport.getAlignment().deleteGroup(sg);
+    viewport.getColumnSelection().clear();
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
@@ -2411,6 +2416,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+
   /**
    * DOCUMENT ME!
    *