<body>
<p><strong>DAS Sequence Feature Retrieval</strong></p>
-<p>Jalview includes a client for retrieving sequence features via
+<p>Jalview includes a client for retrieving sequences and their features via
the <a href="http://www.biodas.org">Distributed Annotation System</a>.</p>
<ol>
<li>Open the Feature Settings panel by selecting "View ->
Feature Settings..."</li>
<li>Click on the "<a href="dassettings.html">DAS Settings</a>"
tabbed pane.</li>
- <li>Select the sources to use for DAS feature retireval, then
+ <li>Select the sources to use for DAS feature retrieval, then
click the "Fetch DAS Features" button.
<ul>
<li>Cancelling Feature Retrieval<br>
<html>
-<head><title>DAS Settings</title></head>
+<head>
+<title>DAS Settings</title>
+</head>
<body>
<p><strong>DAS Settings</strong></p>
-<p>Jalview can retrieve and visualize features from many <a href="http://biodas.org/">DAS</a>
- sources at once. The DAS sources are discovered and selected <em>via</em> the DAS settings panel.</p>
+<p>Jalview can retrieve sequences or features from many <a
+ href="http://biodas.org/">DAS</a> sources at once. 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.
+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>
+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>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>
<body>
<p><strong>Sequence Fetcher</strong></p>
<p>Jalview can retrieve sequences from certain databases using either the
-WSDBFetch service provided by the European Bioinformatics Institute, and DAS servers capable of the <em>sequence</em> command (<em>since version 2.4</em>).</p>
+WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the <em>sequence</em> command (configured in <a href="dassettings.html">DAS settings</a>).</p>
<img src="seqfetcher.gif" align="center" alt="The Jalview Sequence Fetcher Dialog Box">
<p>The Sequence Fetcher dialog box can be opened via the "File"
menu on the main desktop in order to retrieve sequences as a new
git://source.jalview.org / jalview.git / commitdiff