Merge branch 'fix_JAL-1423' into Release_2_8_1_Branch
[jalview.git] / help / html / menus / alignmentMenu.html
index 6a5ec9f..d53b3eb 100755 (executable)
@@ -1,14 +1,14 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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 
                                </strong><em>Any columns currently not selected will replace the current
                                                column selection. </em>
                                </li>
-                               <li><strong>Undefine Groups (Control U)<br> </strong><em>The
-                                               alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
-                                               This cannot be undone.</em>
-                               </li>
-                               <li><strong>Make Groups<br /> </strong> <em>The currently
+                                 <li><strong>Create Group (Control G)<br></strong>
+  <em>Create a group containing the currently selected sequences.</em></li>
+  <li><strong>Remove Group (Shift Control G)<br></strong>
+  <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
+                       <li><strong>Make Groups for selection<br /> </strong> <em>The currently
                                                selected groups of the alignment will be subdivided according to
                                                the contents of the currently selected region. <br />Use this to
                                                subdivide an alignment based on the different combinations of
                                                residues observed at specific positions. (new in jalview 2.5)</em>
                                </li>
-                       </ul></li>
+       <li><strong>Undefine Groups (Control U)<br> </strong><em>The
+            alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
+            This cannot be undone.</em>
+        </li>
+               </ul></li>
                <li><strong>View</strong>
                        <ul>
                                <li><strong>New View (Control T)</strong><em><br>
                                                <li><strong>Show Consensus Histogram<br> </strong><em>
                                                        Enable or disable the display of the histogram above the
                                                        consensus sequence.</em></li>
-                                               <li><strong>Show Consensus Profile<br> </strong><em> Enable
-                                                       or disable the display of the sequence logo above the consensus
+                                               <li><strong>Show Consensus Logo<br> </strong><em> Enable
+                                                       or disable the display of the Consensus Logo above the consensus
                                                        sequence.</em></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><em> When
                                                        ticked, display a conservation row for all groups (only available
                                                        for protein alignments).</em></li>