X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fsorting.html;h=d12a518355326a82d209a19cf7f002627efe243c;hb=cedd8bb81245ba719e6d54688d763e341b3cc695;hp=c61481f5fff5f9b0789fbae5ebd902f1e7b79959;hpb=15acf4db2949be30f3aabf2916b6609b19e8afb3;p=jalview.git

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index c61481f..d12a518 100755
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <head>
 <title>Sorting Sequences</title>
 </head>
@@ -6,7 +26,7 @@
 <p><strong>Sorting Sequences</strong></p>
 <p>Any group of selected sequences may be reordered by pressing the
 up or down arrow keys. The whole alignment may also be reordered by
-the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
+the use of the functions in the Sort menu (<strong>Calculate&#8594;Sort</strong>):
 </p>
 <ul>
 <li><p><strong>Sort by ID</strong></p>
@@ -14,11 +34,11 @@ the use of the functions in the Sort menu (<em>Calculate->Sort</em>):
 precedence of their names.</p><p>
 </li>
 <li><p><strong>Sort by Group</strong></p>
-<p>Places sequences in the same group adjacent to eachother.</p><p>
+<p>Places sequences in the same group adjacent to each other.</p><p>
 </li>
 <li><p><strong>Sort by Pairwise Identity</strong></p>
 <p>Places pairs of sequences together that align with the greatest
-fraction of conserved residues. 
+fraction of conserved residues.
 </p><p>
 </li>
 <li><p><strong>Sort by Tree Order</strong></p>
@@ -26,7 +46,7 @@ fraction of conserved residues.
 order the sequences corresponding to those leaves in the
 alignment.<br>
 If a tree has been calculated from or associated with the current
-alignment, its name will appear in the submenu <em>Sort-&gt;By Tree Order</em>.</p><p>
+alignment, its name will appear in the submenu <strong>Sort&#8594;By Tree Order</strong>.</p><p>
 </li>
 <li><p><strong>Sort by alignment ordering</strong></p>
 <p>Multiple alignment methods often order the sequences in their
@@ -34,8 +54,13 @@ 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
