-<html>\r
-\r
-<head><title>DAS Settings</title></head>\r
-\r
-<body>\r
-<p><strong>DAS Settings</strong></p>\r
-<p>Jalview can retrieve features from multiple <a href="http://biodas.org/">DAS</a> \r
- sources. The DAS sources are selected in the DAS settings panel.</p>\r
-<p><img src="das.jpg" width="497" height="365">\r
-<p>On start up of the DAS Settings panel, Jalview will use the registry URL (default \r
- is http://das.sanger.ac.uk/registry/das1/sources/) to retrieve a list of currently \r
- available DAS sources. These are all listed in the table using the sources' \r
- Nickname as an identifier. <br>\r
- Click on a Nickname in the table to reveal more information about that service \r
- in the panel to the right of the table. \r
-<p>You can filter the visible DAS sources by authority, type and "label". \r
- You should read the DAS documentation to understand more about these values.\r
-<p>Tick the box "Use Source" so that Jalview will use a particular source \r
- when fetching features. \r
-<p>You can add your own DAS source to the list by clicking the "Add Local \r
- Source" button. Enter the URL and nickname of your additional service. \r
- It should be noted that Jalview 2.1 will not query additional sources for more \r
- information, but this will be implemented in future editions. \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 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