das feature fetch followed by png output fixed (bug #0059977). Trial of utf8 decoding...

[jalview.git] / help / html / menus / alwcalculate.html

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 9d40868..700ce51 100755 (executable)
--- 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>
@@ -44,6 +45,12 @@
     in the alignment. See <a href="../calculations/pca.html">Principal Component 
     Analysis</a>.</em> <br>
   </li>
+       <li><strong>Extract Scores ... (optional)</strong><br>
+               <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
+               When selected, these numbers are parsed into sequence associated annotation which can 
+               then be used to sort the alignment via the Sort by&#8594;Score menu.</em> <br>
+       </li>
+  
   <li><strong>Autocalculate Consensus</strong><br>
     <em>For large alignments it can be useful to deselect &quot;Autocalculate 
     Consensus&quot; when editing. This prevents the sometimes lengthy calculations