<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head>
<title>Sequence Feature Settings Dialog Box</title>
</head>
in an alignment window to open the feature settings dialog box, which
allows you to precisely control the presence and appearance of sequence
features for the current alignment.</p>
-<center><img src="featureSettings.gif" width="351" height="350">
+<center><img src="featureSettings.gif" width="400" height="452">
<br>
Sequence Feature Settings for the Jalview Application</img></center>
<p>The top section of the dialog box lists all the sequence feature
groups, along with a tickbox for each that controls whether its features
are displayed. The table in the middle lists all the features in the
-currently selected groups, along with their display colour and whether
+currently selected groups, along with their display style and whether
they are currently being displayed (only the ticked features and groups
-are displayed). <strong><em>You can change the colour used
-for a feature in the associated alignment by clicking on its colour box.</em></strong></p>
+are displayed). <strong><em>You can change the colour or
+shading style used for a feature in the associated alignment by clicking
+on its colour box.</em></strong></p>
+<p><strong><em>Feature settings pop-up menu</em></strong><br>
+<strong>Right-click</strong> on a feature to open a pop-up menu that
+allows you to sort the alignment or current selection using that feature
+type (see below), or toggle the type of colouring used for the feature.
+Features may be highlighted with either a single colour or a <a
+ href="featureschemes.html">feature colourscheme</a> based on either the
+scores associated with that feature or from the feature's description
+(e.g. to distinguish different names associated with a DOMAIN feature).</p>
<p><strong>Ordering alignment by features</strong><br>
-Right click on a feature type to order the alignment by either the
-feature's score, or the number of features of that type. The 'Order by
-Score' and 'Order by Density' buttons will order the alignnment based on
-the average score or total number of currently active features and
-groups on each sequence. (Experimental - added in jalview 2.4.1)</p>
+The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort the
+alignment based on the average score or total number of currently active
+features and groups on each sequence. To order the alignment using a
+specific feature type, use the <em>sort by ..</em> entries in the pop-up
+menu for that type.<br>
+<em>Feature sorting and graduated feature colouring was introduced
+in jalview 2.5</em></p>
+
<p><strong>Transparency and Feature Ordering</strong></p>
<p>It is important to realise that sequence features are often not
distinct and often overlap (for example, a metal binding site feature