<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
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* 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.
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* 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>
<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>
-<p><strong><em>Feature settings pop-up menu</em></strong><br>
+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>Selecting alignment columns by feature</em></strong><br>
+ <strong>Double-click</strong> a feature to add all the columns where
+ that feature is found to the current column selection. <strong>Shift+Double-click</strong>
+ will add all the columns where that feature is <strong>not</strong>
+ found. You can also find these options 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 create 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>
+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
git://source.jalview.org / jalview.git / blobdiff