<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
--->
+ * 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>DAS Features</title>
+</head>
+
+<body>
+ <p>
+ <strong>DAS Sequence Feature Retrieval</strong>
+ </p>
+ <p>
+ Jalview includes a client for retrieving sequences and their
+ features via the <a href="http://www.biodas.org">Distributed
+ Annotation System</a>.
+ </p>
+ <ol>
+ <li>Open the Feature Settings panel by selecting "View
+ -> Feature Settings..."</li>
+ <li>Click on the "<a href="dassettings.html">DAS
+ Settings</a>" tabbed pane.
+ </li>
+ <li>Select the sources to use for DAS feature retrieval, then
+ click the "Fetch DAS Features" button.
+ <ul>
+ <li>Cancelling Feature Retrieval<br> Press the <strong>Cancel
+ Fetch</strong> button to immediately stop feature retrieval. This
+ will not remove any features already added to the alignment,
+ but will halt any outstanding DAS requests.<em>The cancel
+ fetch button is of particular use when one or more DAS
+ annotation servers are not responding!</em>
+ </ul>
+ </li>
+ </ol>
+ <p>
+ If your DAS source selection contains sources which use Uniprot
+ accession ids, you will be asked whether Jalview should find Uniprot
+ Accession ids for the given sequence names. It is important to
+ realise that many DAS sources only use Uniprot accession ids, rather
+ than Swissprot/Uniprot sequence names.<br> The <a
+ href="../webServices/dbreffetcher.html"
+ >database reference fetcher</a> documentation describes how Jalview
+ discovers what database references are appropriate for the sequences
+ in the alignment.
+ <ul>
+ <li><em>Note</em><br> Please remember to save your
+ alignment if either the start/end numbering, or the sequence IDs
+ were updated during the ID retrieval process.</li>
+ </ul>
+ <p>
+ <p>
+ <em>DAS support was introduced in Jalview Version 2.1.</em>
+ </p>
+ <p>
+</body>
+</html>