+++ /dev/null
-<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>