2.5 release doc

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

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index aceabce..b39bf25 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -215,17 +215,40 @@
                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 all 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>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>
+               <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>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 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>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>
@@ -236,7 +259,10 @@
     <br>This submenu's options allow the inclusion or exclusion of 
     non-positional sequence features or database cross references 
     from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li> 
-               
+  <li><strong>Alignment Properties...<br/>
+    </strong><em>Displays some simple statistics computed for the
+    current alignment view and any named properties defined on the
+    whole alignment.</em></li>
                <li><strong><a href="../features/overview.html">Overview
                Window</a><br>
                </strong><em>A scaled version of the alignment will be displayed in a
@@ -299,6 +325,10 @@
                        <li><strong>Centre Annotation Labels<br>
                        </strong><em>Select this to center labels along an annotation row 
                        relative to their associated column (default is off, i.e. left-justified).</em></li>
+                           <li><strong>Show Unconserved<br>
+    </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
+    </em></li>
+                       
        </ul>
        <li><strong>Colour</strong>
        <ul>
@@ -349,7 +379,10 @@
                        <li><strong>by ID</strong><em><br>
                        This will sort the sequences according to sequence name. If the sort
                        is repeated, the order of the sorted sequences will be inverted. </em></li>
-                       <li><strong>by Group</strong><strong><br>
+                       <li><strong>by Length</strong><em><br>
+        This will sort the sequences according to their length (excluding gap characters). If the sort is 
+        repeated, the order of the sorted sequences will be inverted. </em></li>
+               <li><strong>by Group</strong><strong><br>
                        </strong><em>This will sort the sequences according to sequence name. If
                        the sort is repeated, the order of the sorted sequences will be
                        inverted. </em><strong></strong></li>