<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 2.9.0b2)
+ * 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 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. Note that the registry hosted at
+ http://www.dasregistry.org/das/ was retired at the start of 2015. An
+ alternative service is currently hosted at
+ http://www.ebi.ac.uk/das-srv/registry/das/. To connect to this
+ service, ensure your .jalview_properties file includes the following
+ line:<br> <b>DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/</b>
+ </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