-<html>\r
-\r
-<head><title>DAS Features</title></head>\r
-\r
-<body>\r
-<p><strong>DAS Sequence Feature Retrieval</strong></p>\r
-<p>Jalview 2.1 can be set up to retrieve sequence features using the <a href="http://www.biodas.org">Distributed \r
- Annotation System</a></p>\r
-<ol>\r
- <li>Open the Feature Settings panel by selecting "View -> Feature Settings..."</li>\r
- <li>Click on the "<a href="dassettings.html">DAS Settings</a>" tabbed \r
- pane.</li>\r
- <li>Select the sources to use for DAS feature retireval, then click the "Fetch \r
- DAS Features" button.</li>\r
-</ol>\r
-<p>If your DAS source selection contains sources which use Uniprot accession ids, \r
- you will be asked whether Jalview should find Uniprot Accession ids for the \r
- given sequence names. It is important to realise that many DAS sources only \r
- use Uniprot accession ids, not names of sequences. <br>\r
- The method of Uniprot accession id discovery is the same method which earlier \r
- Jalview versions used for sequence feature retrieval, ie WSDbFetch provided \r
- by the EBI.</p>\r
-<p>The process is as described:</p>\r
-<p><strong>The Sequence Identification Process</strong> </p>\r
-<p>Jalview will attempt to retrieve sequence features from Uniprot files using \r
- the EBI dbFetch web service using the given sequence names (or Uniprot ID, if \r
- available). A 100% match with the Uniprot record is required for Uniprot features \r
- to be view on a sequence.</p>\r
-<p>The first step in the procedure for matching uniprot IDs to sequences is to \r
- use the ID (name) of each sequence to retrieve Uniprot records directly.</p>\r
-<p> If a uniprot record (or set of records) is found for a sequence, then the \r
- sequence is aligned to the one in the Uniprot record to determine the correct \r
- start and end residue positions (which are displayed when the 'Show Full Sequence \r
- ID' option is set). </p>\r
-<p>If the alignment reveals differences between the sequence in the alignment \r
- and the one in the record, then Jalview will assume that the aligned sequence \r
- is not the one in the uniprot record. </p>\r
-<p> In some cases, the ID used to retrieve Uniprot records may be out of date \r
- and you will be notified of that a 100% match between the sequence and a Uniprot \r
- record was identified, but the sequence name must be manually changed (by right \r
- clicking on the sequence ID and selecting <strong>Sequence→Edit Name</strong>), \r
- before Jalview will show its sequence features. \r
-<ul>\r
- <li>remember to save your alignment if you have updated any of the sequence \r
- IDs! </li>\r
-</ul>\r
-<p> \r
-<p>\r
-<p> \r
-</body>\r
-</html>\r
+<html>
+
+<head>
+<title>DAS Features</title>
+</head>
+
+<body>
+<p><strong>DAS Sequence Feature Retrieval</strong></p>
+<p>Jalview includes a client for retrieving sequence 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
+ click the "Fetch DAS Features" button.
+ <ul>
+ <li>Cancelling Feature Retrieval<br>
+ Press the <strong>Cancel Fetch</strong> button to immediately stop
+ feature retrieval. This will not remove any features already added to
+ the alignment, but will halt any outstanding DAS requests.<em>The
+ cancel fetch button is of particular use when one or more DAS
+ annotation servers are not responding!</em>
+ </ul>
+ </li>
+</ol>
+<p>If your DAS source selection contains sources which use Uniprot
+accession ids, you will be asked whether Jalview should find Uniprot
+Accession ids for the given sequence names. It is important to realise
+that many DAS sources only use Uniprot accession ids, rather than
+Swissprot/Uniprot sequence names.<br>
+<p><strong>The Sequence Identification Process</strong></p>
+The method of Uniprot accession id discovery is the same method which
+earlier Jalview versions used for sequence feature retrieval, and is now
+also used for
+<a href="viewingpdbs.html">PDB ID discovery</a>
+. Essentially, Jalview will try to retrieve Uniprot records via the
+EBI's WSDbFetch interface using each sequence's ID string (or each
+string in the ID separated by the '∣' symbol).
+</p>
+<p>If a uniprot record (or set of records) is found for a sequence,
+then the sequence is aligned to the one in the Uniprot record to
+determine the correct start and end residue positions (which are
+displayed when the 'Show Full Sequence ID' option is set).</p>
+<p>If the alignment reveals differences between the sequence in the
+alignment and the one in the record, then Jalview will assume that the
+aligned sequence is not the one in the uniprot record.</p>
+<p>In some cases, the ID used to retrieve Uniprot records may be out
+of date and a dialog box will be opened indicating that a 100% match
+between the sequence and a Uniprot record was identified, but the
+sequence name is different. In this case, the ID must be manually
+changed (by right clicking on the sequence ID and selecting <strong>Sequence→Edit
+Name</strong>), before Jalview will show its sequence features.
+<ul>
+ <li><em>Note</em><br>
+ Please remember to save your alignment if either the start/end
+ numbering, or the sequence IDs were updated during the Uniprot ID
+ retrieval process.</li>
+</ul>
+<p>
+<p><em>DAS support was introduced in Jalview Version 2.1.</em></p>
+<p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff