<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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>Alignment Window Menus</title>
</head>
<li><strong>Gather Views (G)</strong><em><br>
Each view associated with the alignment will be displayed within its own tab
on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences)</strong><em><br>
- All hidden Columns / Sequences will be revealed. </em></li>
- <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
- Hides the currently selected Columns / Sequences</em></li>
+ <li><strong>Show→(all Columns / Sequences / Sequences and Columns</strong> )</strong><em><br>
+ All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region)</strong><em><br>
+ Hides the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
<li><strong>Show Annotations<br>
</strong><em>If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the conservation
<li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
<ul><li>
<strong>Apply to all groups<br></strong>
- When ticked, any settings will be applied to all autocalculated annotation.
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
</li>
<li>
<strong>Show Consensus Histogram<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>