3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
4 * Copyright (C) 2014 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <title>DAS Features</title>
25 <p><strong>DAS Sequence Feature Retrieval</strong></p>
26 <p>Jalview includes a client for retrieving sequences and their features via
27 the <a href="http://www.biodas.org">Distributed Annotation System</a>.</p>
29 <li>Open the Feature Settings panel by selecting "View ->
30 Feature Settings..."</li>
31 <li>Click on the "<a href="dassettings.html">DAS Settings</a>"
33 <li>Select the sources to use for DAS feature retrieval, then
34 click the "Fetch DAS Features" button.
36 <li>Cancelling Feature Retrieval<br>
37 Press the <strong>Cancel Fetch</strong> button to immediately stop
38 feature retrieval. This will not remove any features already added to
39 the alignment, but will halt any outstanding DAS requests.<em>The
40 cancel fetch button is of particular use when one or more DAS
41 annotation servers are not responding!</em>
45 <p>If your DAS source selection contains sources which use Uniprot
46 accession ids, you will be asked whether Jalview should find Uniprot
47 Accession ids for the given sequence names. It is important to realise
48 that many DAS sources only use Uniprot accession ids, rather than
49 Swissprot/Uniprot sequence names.<br>
50 The <a href="../webServices/dbreffetcher.html">database reference
51 fetcher</a> documentation describes how Jalview discovers what database
52 references are appropriate for the sequences in the alignment.
55 Please remember to save your alignment if either the start/end
56 numbering, or the sequence IDs were updated during the ID
57 retrieval process.</li>
60 <p><em>DAS support was introduced in Jalview Version 2.1.</em></p>