X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmenus%2Falwannotations.html;h=4e1d84453b8ded89cb89903079ebb983add2b971;hb=b9b0c4c90f6ac88f6f5a1300d1dc4f3e83c79eb2;hp=c63354604014fd1abe529a54779047a7dacc79f4;hpb=990fd5f012601024aaeeb09e2901791d242636c4;p=jalview.git

diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index c633546..4e1d844 100755
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -1,4 +1,22 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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>Annotation Panel Menus</title>
 </head>
@@ -29,12 +47,26 @@
         This is useful to export alignment quality measurements for further analysis.</em> 
       </li>
    </ul>
-   <em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em> 
+   <em>The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:</em> 
    <ul>
+   
       <li><strong>Ignore Gaps in Consensus</strong><br>
         If this checkbox is selected, all consensus calculations performed in 
         the current Alignment window will be done without counting gaps as a consensus 
         character.</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 Logo<br></strong>
+    Enable or disable the display of the sequence logo above the consensus sequence.
+      </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>
       <li><strong>Copy Consensus Sequence</strong><br>
         Copies the consensus sequence to the clipboard in Fasta format, to allow 
         the consensus sequence to be added to an alignment. Note the copied sequence 
