JAL-958 documented logo menu items

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 4a1a200..eb51c62 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -287,9 +287,13 @@
                                                <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>

diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html
index 9508b24..146c862 100755 (executable)
--- a/help/html/menus/alwannotations.html
+++ b/help/html/menus/alwannotations.html
@@ -52,6 +52,19 @@
         If this checkbox is selected, all consensus calculations performed in 
         the current Alignment window will be done without counting gaps as a consensus 
         character.</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>
       <li><strong>Copy Consensus Sequence</strong><br>
         Copies the consensus sequence to the clipboard in Fasta format, to allow 
         the consensus sequence to be added to an alignment. Note the copied sequence 

diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 2cf52db..99eff31 100755 (executable)
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -49,10 +49,15 @@
        Enable or disable the display of the histogram above the consensus sequence.
        </li>
        <li>
-       <strong>Show Consensus Profile<br></strong>
+       <strong>Show Consensus Logo<br></strong>
                Enable or disable the display of the sequence logo above the consensus sequence.
        </li>
-       <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>