<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 2.8.2)
+ * Copyright (C) 2014 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 Settings</title>
+</head>
+
+<body>
+<p><strong>DAS Settings</strong></p>
+<p>Jalview can retrieve sequences and features from many <a
+ href="http://biodas.org/">DAS</a> sources. The DAS sources that
+it uses are discovered and selected <em>via</em> the DAS settings panel,
+opened either from the <a href="featuresettings.html">View→Feature
+Settings</a> dialog box from the alignment window's menu bar, or the <a
+ href="featuresettings.html">Tools→Preferences</a> dialog box
+opened from the Desktop menu bar.</p>
+<p><img src="das.gif">
+<p>The available sources are listed in the table using each source's
+Nickname as its identifier. Clicking on a source's entry in the table
+reveals more information about that service in the panel to the right.
+Select the tickbox in the "Use Source" column for a source to
+add it to the set Jalview queries for alignment and sequence features.</p>
+<p>You can filter the visible DAS sources by authority, type and
+"label". You should read the DAS documentation to understand
+more about these values.
+<p><strong>Updating the list of sources</strong></p>
+<p>When the DAS Settings panel is first opened, and when the <strong>'Refresh
+source'</strong> buton is pressed, a list of DAS sources is retrieved from the
+DAS registry URL (set by default to the DAS registration server at
+http://das.sanger.ac.uk/registry/das1/sources/).</p>
+<p><strong>Adding your own DAS Sources</strong></p>
+<p>You can add your own DAS source to the list by clicking the
+"Add Local Source" button. Enter the URL and nickname of your
+additional service. It should be noted that Jalview 2.1 will not query
+additional sources for more information, but this will be implemented in
+future editions.
+<p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff