<head><title>Sequence Features</title></head>\r
<body>\r
<p><strong>View→Sequence Features</strong></p>\r
-<p>When this option is selected, sequence features extracted from the\r
- <a href="http://www.ebi.uniprot.org/">Uniprot</a> record for each\r
- sequence are displayed on the alignment.</p>\r
-<p>Currently, sequence features are rendered in red or blue, dependent\r
- upon their type:</p><ul>\r
- <li>Features associated with a particular residue are coloured\r
- red<br><em>e.g. an active site residue</em></li>\r
- <li>Features which span a region are coloured blue<br>\r
-<em>e.g. a region of sequence with known structure</em>\r
-</li>\r
-</ul></p>\r
+<p>When this option is selected, sequence features extracted from the <a href="http://www.ebi.uniprot.org/">Uniprot</a> \r
+ record for each sequence are displayed on the alignment.</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. A 100% match with \r
+ the Uniprot record is required to view the Sequence Features. If the match is \r
+ not 100%, Jalview will run EBI web service WUBlast to find unknown sequences. \r
+ You will be asked whether to proceed with this step, as it can take some time, \r
+ especially if the EBI servers are busy. </p>\r
<p>More information about the feature is given in a tooltip, which is\r
viewed by moving the mouse pointer over a sequence feature. The\r
description associated with the feature will then be displayed in a small\r
label near the pointer.</p>\r
-<p>After the Sequence Features option is selected, there may be some delay before\r
- the features are actually rendered, as jalview first determines if\r
- the sequences are contained in Uniprot and then retrieves any sequence\r
- records. This delay will normally only happen once for a particular\r
- set of sequences, as jalview caches uniprot records in a file in your home\r
- directory called '.jalview.uniprot.xml'.\r
-\r
- <p><strong>The Sequence Identification Process</strong>\r
+<p><strong>View→Feature Settings...</strong>\r
+<p>Once sequence features have been loaded onto an alignment features can be hidden \r
+ or have their rendering priority changed using the Feature Settings dialog. \r
+ This displays all the features loaded, the colour and whether to display the \r
+ feature or not. You can easily change the colour by clicking the colour box.<br>\r
+ It is important to realise that the order in which features are drawn to the \r
+ alignment may result in overlapping features being hidden. Features at the foot \r
+ of the table are rendered first. Therefore features higher up the table will \r
+ be drawn over the top of lower featrues. You can change the order of the feature \r
+ priority by dragging the feature with your mouse. <br>\r
+ Use the transparency setting as another way to visualise overlapping features. \r
+<p><strong><em>You can save all features, with their current colours and visibility \r
+ in a Jalview format file. </em></strong>\r
+<p><strong>The Sequence Identification Process</strong>\r
\r
</p>\r
<p>The first step in the procedure for matching uniprot IDs to\r
git://source.jalview.org / jalview.git / blobdiff