</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://www.dasregistry.org/das/).</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>
+ <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