From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 17 Sep 2024 20:39:49 +0000 (+0100)
Subject: JAL-4418 fix link case for linkcheck and window menu documentation update
X-Git-Tag: Release_2_11_4_0~4^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab3055b2ebd93e8265cb193e7b6a79f326732316;p=jalview.git

JAL-4418 fix link case for linkcheck and window menu documentation update
---

diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html
index 33534b5..351a8c5 100755
--- a/help/help/html/menus/alignmentMenu.html
+++ b/help/help/html/menus/alignmentMenu.html
@@ -376,7 +376,7 @@
             of the annotations.</em></li>
         <li><strong>Show Secondary Structure</strong> (since 2.11.4.0)<em>
         <br><strong><em>All</em></strong> and <strong><em>None</em></strong> control display of secondary structure annotations on the alignment. 
-        Additional options allow just a specific source of protein secondary structure to be shown.</li> 
+        Additional options allow just a specific source of <a href="../calculations/protssconsensus.html">Protein secondary structure</a> to be shown.</li> 
         <li><strong>Autocalculated Annotation<br>
         </strong><em>Settings for the display of autocalculated annotation.</em>
           <ul>
@@ -399,7 +399,14 @@
             </strong><em> Enable or disable the display of the Consensus
                 Logo above the consensus sequence.</em></li>
             <li><strong>Show SS Consensus Histogram<br>
-            </strong><em> Enable or disable the display of histogram for Secondary Structure Consensus.</em></li>
+        </strong><em> Enable or disable the display of histogram for 
+        Secondary Structure Consensus.</em><br/><br/><em>Note: 
+        consensus secondary structure rows are not shown when no secondary 
+        structure annotations are present for sequences in the alignment. 
+        Use <strong><a href="popupMenu.html#addrefannot">Add Reference Annotation</a></strong>
+         from the sequence or selection popup menu to add annotations from 
+         structures or secondary structure predictions associated with 
+         the sequences in the alignment.</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
@@ -410,6 +417,9 @@
             <li><strong>Group Consensus<br>
             </strong><em> When ticked, display a consensus row for all
                 groups.</em></li>
+            <li><strong>Group Secondary Structure Consensus<br>
+        	</strong><em> When ticked, display a consensus secondary 
+        	structure row for all groups.</em></li>
           </ul></li>
       </ul></li>
     <li><strong>Alignment Window Format Menu</strong>
diff --git a/help/help/html/menus/alwannotation.html b/help/help/html/menus/alwannotation.html
index 9f014ea..d6a7eb9 100755
--- a/help/help/html/menus/alwannotation.html
+++ b/help/help/html/menus/alwannotation.html
@@ -29,6 +29,11 @@
       Jalview 2.8.2</em>
   </p>
   <ul>
+	<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 Alignment Related</strong><em><br>
         Show all annotations that are for the alignment as a whole (for
         example, Consensus, or secondary structure prediction from
@@ -82,7 +87,7 @@
         Secondary Structure Consensus.</em><br/><br/><em>Note: 
         consensus secondary structure rows are not shown when no secondary 
         structure annotations are present for sequences in the alignment. 
-        Use <strong><a href="popupmenu.html#addrefannot">Add Reference Annotation</a></strong>
+        Use <strong><a href="popupMenu.html#addrefannot">Add Reference Annotation</a></strong>
          from the sequence or selection popup menu to add annotations from 
          structures or secondary structure predictions associated with 
          the sequences in the alignment.</em></li>