<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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>
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
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>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, or create a graduated feature colourscheme based on the
-scores associated with that feature.</p>
<p><strong><em>You can save all features, with their
current colours and visibility in a Jalview format file. </em></strong></p>
</body>
git://source.jalview.org / jalview.git / blobdiff