X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=cb3870816a13d7b5eab42c3b3a5f57a65972d8c3;hb=d305e02d8b425bb501141ad32142aeb8572adc57;hp=85ffe3639faf8b26ee894be88c6e69b7da451df4;hpb=aff93619ba53584f9b01970832558331951d9dbf;p=jalview.git

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 85ffe36..cb38708 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * 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.
+ *  
+ * 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>Alignment Window Menus</title>
 </head>
@@ -22,20 +42,30 @@
     </strong><em>If this is selected the &quot;Annotation Panel&quot; 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> 
+    &nbsp;or <a href="../features/annotation.html">Annotation</a>&nbsp;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>
-    	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>
@@ -52,7 +82,7 @@
   </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>
