From 8a6e4d35873d3e938a4e4d73467ffbd9b317f0d0 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 6 Sep 2012 22:36:13 +0100
Subject: [PATCH] JAL-958 documented logo menu items

---
 help/html/menus/alignmentMenu.html  |    8 ++++++--
 help/html/menus/alwannotations.html |   13 +++++++++++++
 help/html/menus/alwview.html        |    9 +++++++--
 3 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 4a1a200..eb51c62 100755
--- 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
--- 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
--- 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>
-- 
1.7.10.2