X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=f59e0146b15420cccd3c1d5e6a00913c634a2d9a;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=10ab5112a0fc0d95dfeac4ee746c5620a59d4a4a;hpb=be5a6a44e9eb355110f3b414d6b0fd5419f5936c;p=jalview.git

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 10ab511..f59e014 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,4 +1,22 @@
 <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>
@@ -14,10 +32,10 @@
   <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&#8594;(all Columns / Sequences)</strong><em><br>
-    All hidden Columns / Sequences will be revealed. </em></li>
-  <li><strong>Hide&#8594;(all Columns / Sequences)</strong><em><br>
-    Hides the currently selected Columns / Sequences</em></li>
+  <li><strong>Show&#8594;(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&#8594;(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 &quot;Annotation Panel&quot; will be 
     displayed below the alignment. The default setting is to display the conservation 
@@ -25,17 +43,22 @@
     <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>
