From 1bd5b4d3aba2805e8c6b9ad5054ce317c6aa1d31 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 8 May 2007 16:49:47 +0000
Subject: [PATCH] sort by score

---
 help/html/calculations/sorting.html |    7 ++++++-
 help/html/menus/alwcalculate.html   |    3 ++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index 47522ee..1c15890 100755
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -34,8 +34,13 @@ alignments by some measure of sequence identity.<br>
 If the current alignment has been generated by one of Jalview's
 alignment web services, the alignment ordering can be recovered by
 its corresponding entry in the Sort menu.
-</p><p>
+</p>
 </li>
+<li><p><strong>Sort by Score</strong></p>
+<p>This menu appears if the alignment contains any <a href="../features/annotationsFormat.html">sequence associated
+alignment annotation</a> with associated score values. Each entry is the
+label for a distinct group of sequence associated annotation
+scores which can be used for sorting.</p>
 </ul>
 <p><strong>Reversing the Order</strong></p>
 <p>Selecting any item from the Sort menu will sort sequences in an
diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 9d40868..6ee7ed8 100755
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -18,7 +18,8 @@
         identity to the consensus sequence. The most similar sequence is put at 
         the top. </em></li>
       <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have 
-        some additional options if you have just done a multiple alignment calculation, 
+        some additional options if the alignment has any associated
+	score annotation, or you have just done a multiple alignment calculation
         or opened a tree viewer window.</em><br>
       </li>
     </ul>
-- 
1.7.10.2