<html>
-
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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/>.
+-->
<head>
<title>Preferences</title>
</head>
<body>
<p><strong>Preferences</strong></p>
-<p>There are four tabs in the Preferences dialog box:
+<p>There are four 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
<li>The <a href="#editing"><strong>"Editing"</strong>
Preferences</a> tab contains settings affecting the export of sequence
alignments and EPS files.</li>
- <li>The <a href="#editing"><strong>"DAS
+ <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>
</ul>
will display an annotation panel below the sequences. This annotation
panel may have several rows describing the whole alignment. The 3
standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
- may be shown or hidden by default.</p>
+for the alignment may be shown or hidden by default using the checkboxes
+below.</p>
+<p><em>Show group: Conservation and Consensus</em> controls the
+display of per-group automatic annotation.</p>
+<p><em>Consensus: Histogram and Logo</em> checkboxes control the
+display of the consensus histogram and sequence logo for consensus
+annotation rows.</p>
<p><em>Full Sequence ID</em> - If selected the ID panel will display
the name of a sequence plus the start and end residues in the format
name/start-end. If not selected, the displayed ID will be the name of
edge of the alignment display window.</p>
<p><em>Font</em> - The default font name, size and style can be set
for a new alignment window.</p>
+<p><em>Sequence ID Tooltip</em>: Control the display of Database
+References and Non-positional annotation in the tooltip displayed when
+the mouse is over a sequence's ID.</p>
<p><em>Sequence Name Italics</em> - select to apply the italicised
vbersion of the font to sequence labels.</p>
<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
<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
-sequence positions appended to each sequence id:
-<pre>
+sequence positions appended to each sequence id: <pre>
>ID/1-10
AACDEAAFEA
</pre>
Consensus" option set according to this setting.</p>
<p><em>Pad gaps when editing</em> - New alignment windows will
"Pad Gaps" according to this setting.</p>
-<p><a name="editing"><strong>DAS Settings </strong></a></p>
-<p>See <a href="dassettings.html">DAS Settings</a></p>
<p> </p>
<p> </p>
</body>
git://source.jalview.org / jalview.git / blobdiff