<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>
<body>
<p><strong>Sequence Feature Settings Dialog Box</strong></p>
-<p>Select <strong>View→Feature Settings...</strong> menu entry 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"> <br>
- Sequence Feature
- Settings for the Jalview Application</img></center>
+<p>Select <strong>View→Feature Settings...</strong> menu entry
+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="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 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>
-<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 may be attached to one position along a stretch of sequence
- marked with a secondary structure feature).</p>
-<p>The ordering of the sequence features in the dialog box list is the
- order used by jalview for rendering sequence features. A feature at
- the bottom of the list is rendered <em>below</em> a feature higher
- up in the list.<br><em><strong>You can change the order of a feature
- by dragging it up and down the list with the
- mouse</strong></em>.</p>
-<p>The <strong><em>Optimise order</em></strong> button (currently only available in the application) will re-order the feature render ordering based on the average length of each feature type.</p>
-<p>
- The <strong><em>transparency slider setting</em></strong> (currently only available
- in the application version) controls the visibility of features
- rendered below other features. Reducing the transparency will mean
- that features at the top of the list can obscure features lower
- down, and increasing it allows the user to 'see through' the upper
- layers of a set of features.</p>
-<p><strong><em>You can save all features, with their current colours and visibility
- in a Jalview format file. </em></strong>
-</p>
+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 style and whether
+they are currently being displayed (only the ticked features and groups
+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>
+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
+may be attached to one position along a stretch of sequence marked with
+a secondary structure feature).</p>
+<p>The ordering of the sequence features in the dialog box list is
+the order used by jalview for rendering sequence features. A feature at
+the bottom of the list is rendered <em>below</em> a feature higher up in
+the list.<br>
+<em><strong>You can change the order of a feature by
+dragging it up and down the list with the mouse</strong></em>.</p>
+<p>The <strong><em>Optimise order</em></strong> button (currently
+only available in the application) will re-order the feature render
+ordering based on the average length of each feature type.</p>
+<p>The <strong><em>transparency slider setting</em></strong>
+(currently only available in the application version) controls the
+visibility of features rendered below other features. Reducing the
+transparency will mean that features at the top of the list can obscure
+features lower down, and increasing it allows the user to 'see through'
+the upper layers of a set of features.</p>
+<p><strong><em>You can save all features, with their
+current colours and visibility in a Jalview format file. </em></strong></p>
</body>
</html>
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