-<html>\r
-\r
-<head><title>DAS Features</title></head>\r
-\r
-<body>\r
-<p><strong>DAS Sequence Feature Retrieval</strong></p>\r
-<p>Jalview 2.1 can be set up to retrieve sequence features using the <a href="http://www.biodas.org">Distributed \r
- Annotation System</a></p>\r
-<ol>\r
- <li>Open the Feature Settings panel by selecting "View -> Feature Settings..."</li>\r
- <li>Click on the "<a href="dassettings.html">DAS Settings</a>" tabbed \r
- pane.</li>\r
- <li>Select the sources to use for DAS feature retireval, then click the "Fetch \r
- DAS Features" button.</li>\r
-</ol>\r
-<p>If your DAS source selection contains sources which use Uniprot accession ids, \r
- you will be asked whether Jalview should find Uniprot Accession ids for the \r
- given sequence names. It is important to realise that many DAS sources only \r
- use Uniprot accession ids, not names of sequences. <br>\r
- The method of Uniprot accession id discovery is the same method which earlier \r
- Jalview versions used for sequence feature retrieval, ie WSDbFetch provided \r
- by the EBI.</p>\r
-<p>The process is as described:</p>\r
-<p><strong>The Sequence Identification Process</strong> </p>\r
-<p>Jalview will attempt to retrieve sequence features from Uniprot files using \r
- the EBI dbFetch web service using the given sequence names (or Uniprot ID, if \r
- available). A 100% match with the Uniprot record is required for Uniprot features \r
- to be view on a sequence.</p>\r
-<p>The first step in the procedure for matching uniprot IDs to sequences is to \r
- use the ID (name) of each sequence to retrieve Uniprot records directly.</p>\r
-<p> If a uniprot record (or set of records) is found for a sequence, then the \r
- sequence is aligned to the one in the Uniprot record to determine the correct \r
- start and end residue positions (which are displayed when the 'Show Full Sequence \r
- ID' option is set). </p>\r
-<p>If the alignment reveals differences between the sequence in the alignment \r
- and the one in the record, then Jalview will assume that the aligned sequence \r
- is not the one in the uniprot record. </p>\r
-<p> In some cases, the ID used to retrieve Uniprot records may be out of date \r
- and you will be notified of that a 100% match between the sequence and a Uniprot \r
- record was identified, but the sequence name must be manually changed (by right \r
- clicking on the sequence ID and selecting <strong>Sequence→Edit Name</strong>), \r
- before Jalview will show its sequence features. \r
-<ul>\r
- <li>remember to save your alignment if you have updated any of the sequence \r
- IDs! </li>\r
-</ul>\r
-<p> \r
-<p>\r
-<p> \r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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/>.
+ * 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 Distributed Annotation System.</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>
+ <br />
+ <p>
+ <em>The DAS registry at http://www.dasregistry.org was
+ decommissioned early in 2015. An unmaintained mirror is currently
+ hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+ </p>
+ <p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff