<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.
*
* 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>Preferences</title>
<body>
<p><strong>Preferences</strong></p>
-<p>There are four tabs in the Preferences dialog box:
+<p>The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong> menu.</p>
+<p>There are six tabs in the Preferences dialog box:
<ul>
<li>The <a href="#visual"><strong>"Visual"</strong>
Preferences</a> tab allows you to configure the default display for a new
alignment window.</li>
+ <li>The <a href="#colours"><strong>"Colours"</strong>
+ Preferences</a> tab allows you to configure default colourschemes for a new
+ alignment window.</li>
<li>The <a href="#connections"><strong>"Connections"</strong>
Preferences</a> tab allows you to change the links made from Jalview to
your default web browser.</li>
<li>The <a href="dassettings.html"><strong>"DAS
Settings"</strong> Preferences</a> tab allows you to select which DAS sources
to use when fetching DAS Features.</li>
+ <li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web Service"</strong> Preferences</a> tab allows you to configure the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a> servers that Jalview uses, and change the layout of the alignment's Web Services menu.</li>
</ul>
</p>
<p><strong><a name="visual">Visual</a> Preferences tab</strong></p>
windows in wrapped mode or not.</p>
<p><em>Gap Symbol</em> - The default gap symbol may be set to either
"-" or "."</p>
-<p><em>Colour</em> - The default colour scheme for a new alignment
-window. If the chosen option is "User Defined" then the last
-User Defined Colour loaded or saved via the User Defined Colours panel
-will be loaded.</p>
<p><em>Sort by</em> - When the alignment is loaded in, it will can
be sorted by Id or pairwise identity.</p>
<p><em>Open file</em> - If this is selected then the default
alignment file will be opened when Jalview is started. You can change
the default file by clicking on file name and either typing in the file
-path or selecting it from the file chooser window.</p>
+path or selecting it from the file chooser window.<br/><em>Note: The default example alignment is updated periodically to demonstrate new features in Jalview.</em></p>
+<p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
+<p><em>Alignment Colour</em> - The default colour scheme for a new alignment
+window. If the chosen option is "User Defined" then the last
+User Defined Colour loaded or saved via the User Defined Colours panel
+will be loaded.</p>
+ <p>
+ <em>Annotation Shading Default</em> - set the default minimum
+ and maximum colours used when <a
+ href="../colourSchemes/annotationColouring.html">Colour by
+ Annotation ..</a> is selected from the alignment window's colours menu.
+ </p>
+ <br>
+ </p>
<p><a name="connections"><strong>"Connections"
Preferences tab</strong></a></p>
<p><em>URL Link From Sequence ID</em><br>
make an EPS file.</li>
</ul>
</p>
+<p><em>Automatically set ID width</em><br>
+When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.</p>
+<p><em>Figure ID column width</em><br>
+Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if <em>"Automatically set ID width"</em> is set.
+</p>
<p><em>Sequence//Start-End Numbering</em><br>
The output tab also has a group of checkboxes for each file format. If
these are ticked, then Jalview will write files with the start and end
git://source.jalview.org / jalview.git / blobdiff