<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
- *
+ * 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/>.
--->
+ * 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>Alignment Window Menus</title>
</head>
</strong><em>If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the conservation
calculation, quality calculation and consensus values as bar charts. </em></li>
+ <li><strong>Show All Annotations</strong><em><br>
+ Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Hide All Annotations</strong><em><br>
+ Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
<li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
<ul><li>
<strong>Apply to all groups<br></strong>
Enable or disable the display of the histogram above the consensus sequence.
</li>
<li>
- <strong>Show Consensus Profile<br></strong>
+ <strong>Show Consensus Logo<br></strong>
Enable or disable the display of the sequence logo above the consensus sequence.
</li>
- <li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.</em></li>
+
+ <li>
<strong>Group Conservation<br></strong>
When ticked, display a conservation row for all groups (only available for protein alignments).
</li>
</li>
<li><strong>Show Sequence Features</strong><br>
<em>Show or hide sequence features on this alignment.</em></li>
- <li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
+ <li><strong><a href="../features/featuresettings.html">Sequence Feature Settings...</a></strong><em><br>
Opens the Sequence Feature Settings dialog box to control the colour and display
of sequence features on the alignment, and configure and retrieve features
from DAS annotation servers.</em></li>
git://source.jalview.org / jalview.git / blobdiff