show unconserved gui and annotation file attribute

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index ef08774..cc73162 100755 (executable)
--- 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 (file)
--- 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 (file)
--- 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 (executable)
--- 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>