JAL-1152 annotation sorting preferences and help documentation

[jalview.git] / help / html / menus / alwview.html

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index cb38708..e8fce84 100755 (executable)
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -38,43 +38,6 @@
     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 
-    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 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 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>
-       <strong>Group Conservation<br></strong>
-       When ticked, display a conservation row for all groups (only available for protein alignments).
-       </li>
-       <li>
-       <strong>Apply to all groups<br></strong>
-       When ticked, display a consensus row for all groups.
-       </li>
-       </ul>
-    </li>
   <li><strong>Automatic Scrolling<br>
     </strong><em>When selected, the view will automatically scroll to display the
     highlighted sequence position corresponding to the position under the mouse