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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 # This file is part of Jalview.
7 # Jalview is free software: you can redistribute it and/or
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11 # Jalview is distributed in the hope that it will be useful, but
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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
37 <title>DAS Features</title>
41 <p><strong>DAS Sequence Feature Retrieval</strong></p>
42 <p>Jalview includes a client for retrieving sequences and their features via
43 the <a href="http://www.biodas.org">Distributed Annotation System</a>.</p>
45 <li>Open the Feature Settings panel by selecting "View ->
46 Feature Settings..."</li>
47 <li>Click on the "<a href="dassettings.html">DAS Settings</a>"
49 <li>Select the sources to use for DAS feature retrieval, then
50 click the "Fetch DAS Features" button.
52 <li>Cancelling Feature Retrieval<br>
53 Press the <strong>Cancel Fetch</strong> button to immediately stop
54 feature retrieval. This will not remove any features already added to
55 the alignment, but will halt any outstanding DAS requests.<em>The
56 cancel fetch button is of particular use when one or more DAS
57 annotation servers are not responding!</em>
61 <p>If your DAS source selection contains sources which use Uniprot
62 accession ids, you will be asked whether Jalview should find Uniprot
63 Accession ids for the given sequence names. It is important to realise
64 that many DAS sources only use Uniprot accession ids, rather than
65 Swissprot/Uniprot sequence names.<br>
66 The <a href="../webservices/dbreffetcher.html">database reference
67 fetcher</a> documentation describes how Jalview discovers what database
68 references are appropriate for the sequences in the alignment.
71 Please remember to save your alignment if either the start/end
72 numbering, or the sequence IDs were updated during the ID
73 retrieval process.</li>
76 <p><em>DAS support was introduced in Jalview Version 2.1.</em></p>