<html>
-<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>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><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 create a feature colourscheme 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 'Order by Score' and 'Order by Density' buttons will order the
-alignment based on the average score or total number of currently active
-features and groups on each sequence.<br>
-<em>Feature sorting and colour feature by score and description was
-introduced in jalview 2.4.1</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>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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/>.
+-->
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