- associated text for the feature will then be displayed in a small\r
- label will appear 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 must first determine if a\r
- sequence is contained in uniprot and then retrieve its sequence\r
- record. This delay should only happen once for a particular\r
- alignment, as jalview caches uniprot records in a file in your home\r
- directory called '.jalview.uniprot.xml'.\r
+ description associated with the feature will then be displayed in a small\r
+ label near the pointer.</p>\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