X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfetch.html;h=d4a00f14b3b4af04ff2887f3ece0a70f6d4ea3fd;hb=66830878ef77fb7030de00ab6e302ef9936f0a3b;hp=a956d6d1148339ccf1ef1ac1f70cbc56fda52009;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html
index a956d6d..d4a00f1 100755
--- a/help/html/features/seqfetch.html
+++ b/help/html/features/seqfetch.html
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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 
@@ -23,24 +23,42 @@
 <p><strong>Sequence Fetcher</strong></p>
 <p>Jalview can retrieve sequences from certain databases using either the
 WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
-<img src="seqfetcher.gif" align="center" alt="The Jalview Sequence Fetcher Dialog Box">
-<p>The Sequence Fetcher dialog box can be opened via the &quot;File&quot; 
+	<img src="seqfetcher.gif" align="center"
+		alt="The Jalview Sequence Fetcher Dialog Box">
+	<p>The Sequence Fetcher dialog box can be opened via the &quot;File&quot; 
   menu on the main desktop in order to retrieve sequences as a new
   alignment, or opened via the &quot;File&quot; menu of an existing alignment
-  to import additional sequences. Please note, there will be a short delay when the sequence fetcher is first opened, 
+  to import additional sequences. There may be a short delay when the sequence fetcher is first opened, 
   whilst Jalview compiles the list of available sequence datasources from the 
-  currently defined DAS server registry.</strong>
+  currently defined DAS server registry.
 </p>
-<p>First, select the database you want to retrieve sequences from. Then, enter
+	<p>First, select the database you want to retrieve sequences from
+		by clicking the button labeled 'Select database retrieval source'. If
+		a database source is already selected, then the button's label will
+		change to show the currently selected database.</p>
+		<img src="selectfetchdb.gif" align="left" alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+		<p>Since Jalview 2.8, the
+		available databases are shown as a tree in a popup dialog box. The
+		databases are ordered alphabetically, and if there are many sources
+		for the same type of sequence identifier, they will be grouped
+		together in a sub-branch branch labeled with the identifier.</p>
+	<p>Once you have selected the sequence database using the popup dialog box, enter
   one or more accession ids (as a semi-colon separated list), or press the 
   &quot;Example&quot; button to paste the example accession for the currently selected database into the retrieval box.
    Finally, press &quot;OK&quot; to initiate the retrieval.</p>
-<p>
+	<p><strong>Specifying chains for PDB IDs</strong>
   If you are retrieving sequences from the PDB, you can retrieve
   specific chains by appending a colon and the chain id to the PDB
-  id. For example :<br><pre> 1GAQ:A</pre><br>When retrieving from DAS sequence sources,
-  coordinate range arguments can be passed to the server using the standard DAS 
-  sequence command format (<strong>:&lt;start&gt;,&lt;end&gt;</strong>)</p>
+  id. For example :<br/><pre> 1GAQ:A</pre>
+  </p>
+   <p>
+    <strong>Only retrieving part of a sequence</strong> DAS sources
+    (indicated by a &quot;<em>(DAS)</em>&quot;) allow a range to be
+    specified in addition to a sequence ID. To retrieve 50 residues
+    starting at position 35 in UNIPROT sequence P73137 using the UNIPROT
+    DAS server, you would enter &quot;'P73137:35,84'.<br/><em>Full support for DAS range queries was introduced in Jalview 2.8</em>
+    </p>
+  
 <p>If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB, PFAM, and RFAM)
    in work for publication, please cite:</p>
 <p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar 
