group autoannotation and consensus display settings

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

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index a2aa0c9..10ab511 100755 (executable)
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -22,6 +22,34 @@
     </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>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.
+       </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>
+               Enable or disable the display of the sequence logo above the consensus sequence.
+       </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 
+    pointer in a linked alignment or structure view.</em>
+  </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>