-<html>\r
-<head>\r
-<title>Sequence Feature Settings Dialog Box</title>\r
-</head>\r
-<body>\r
-<p><strong>Sequence Feature Settings Dialog Box</strong></p>\r
-<p>Select <strong>View→Feature Settings...</strong> menu entry in\r
-an alignment window to open the feature settings dialog box, which\r
-allows you to precisely control the presence and appearance of\r
-sequence features for the current alignment.</p>\r
-<center>\r
- <img src="featureSettings.gif" width="432" height="327"> <br>\r
- Sequence Feature\r
- Settings for the Jalview Application</img></center>\r
-<p>The top section of the dialog box lists all the sequence feature\r
- groups, along with a tickbox for each that controls whether its\r
- features are displayed. The table in the middle lists all the\r
- features in the currently selected groups, along with their display\r
- colour and whether they are currently being displayed (only the\r
- ticked features and groups are displayed). <strong><em>You can change the\r
- colour used for a feature in the associated alignment by clicking on\r
- its colour box.</em></strong></p>\r
-<p><strong>Transparency and Feature Ordering</strong></p><p>\r
- It is important to realise that sequence features are often not\r
- distinct and often overlap (for example, a metal binding site\r
- feature may be attached to one position along a stretch of sequence\r
- marked with a secondary structure feature).</p>\r
-<p>The ordering of the sequence features in the dialog box list is the\r
- order used by jalview for rendering sequence features. A feature at\r
- the bottom of the list is rendered <em>below</em> a feature higher\r
- up in the list.<br><em><strong>You can change the order of a feature\r
- by dragging it up and down the list with the\r
- mouse</strong></em>.</p>\r
-<p>\r
- The <strong><em>transparency slider setting</em></strong> (currently only available\r
- in the application version) controls the visibility of features\r
- rendered below other features. Reducing the transparency will mean\r
- that features at the top of the list can obscure features lower\r
- down, and increasing it allows the user to 'see through' the upper\r
- layers of a set of features.</p>\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>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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="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
+ 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>
+ <a name="selectbyfeature"><strong><em>Selecting
+ alignment columns by feature</em></strong></a><br> <strong>Double-clicking
+ a feature type</strong> in the <strong>Feature Settings</strong> dialog
+ allows you to select columns in the alignment that contain (or do
+ not contain) features of that type. If a region of the alignment is
+ currently selected, then only features in the current selection will
+ be searched. The following keys affect the way in which selections
+ are made:
+ <ul>
+ <li>Hold down <strong>Alt</strong> to select columns not
+ containing features of a particular type.
+ </li>
+ <li>Hold down <strong>Shift</strong> to add columns to the
+ current selection.
+ </li>
+ <li>Press <strong>Command/Windows key</strong> to toggle column
+ selection state (XOR)
+ </li>
+ </ul>
+ Options are also provided in the feature's pop-up menu (see below).
+ <br />
+ <em>Select columns by feature was added in Jalview 2.8.1</em>
+ </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 were 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>