From 9a0f8bd63ac90b6afad56e321a7556be3cfabd49 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 6 Feb 2009 14:51:48 +0000
Subject: [PATCH 1/1] show unconserved gui and annotation file attribute

---
 help/html/features/annotationsFormat.html |    3 ++-
 help/html/features/clarguments.html       |    4 ++--
 help/html/menus/alwformat.html            |    3 +++
 help/html/menus/popupMenu.html            |    5 ++++-
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index ef08774..cc73162 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -100,7 +100,8 @@ GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colo
   textColThreshold=0<br>
   idColour=ff3322<br>
   hide=false<br>
-  hidecols=false</p>
+  hidecols=false<br>
+  showunconserved=false</p>
 <ul><li>if the <strong>idColour</strong> property
 is given without specifying a colour scheme with the <strong>colour</strong>
 property, then the idColour will also be used to colour the sequence.</li>
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 28e605a..cf444a1 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -48,14 +48,14 @@
 		<div align="left">Run Jalview without User Interface</div>
 		</td>
 	</tr>
-	<tr>
+	<!--  <tr>
 		<td>
 		<div align="center">-props FILE</div>
 		<td>
 		<div align="left">Use the given Jalview properties file instead
 		of users default</div>
 		</td>
-	</tr>
+	</tr> -->
 	<tr>
 		<td>
 		<div align="center">-tree FILE</div>
diff --git a/help/html/menus/alwformat.html b/help/html/menus/alwformat.html
index 24bc5a1..97cb88e 100644
--- a/help/html/menus/alwformat.html
+++ b/help/html/menus/alwformat.html
@@ -50,6 +50,9 @@
     spaces. <br>
     You may set the default gap character in <a
 		href="../features/preferences.html">preferences</a>.</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>
 	<li><strong>Centre Column Labels<br>
     </strong><em>When this is selected, the text labels within each annotation row will be centred on the column that they are associated with.
     </em></li>
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9cf5358..abc7de7 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -66,7 +66,10 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
             </strong><em>Selecting this will display a &quot;Colour Chooser&quot; 
             window. Select a colour than press OK to set the border colour of 
             a group.</em></li>
-        </ul>
+	<li><strong>Show Unconserved<br>
+  	  </strong><em>When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
+    	</em></li>
+	    	    </ul>
       </li>
     </ul>
   </li>
-- 
1.7.10.2