Modified for 2.08

[jalview.git] / help / html / menus / alwcolour.html

diff --git a/help/html/menus/alwcolour.html b/help/html/menus/alwcolour.html
index 4d28163..9a7d43b 100755 (executable)
--- a/help/html/menus/alwcolour.html
+++ b/help/html/menus/alwcolour.html
@@ -6,33 +6,39 @@
 <ul>\r
   <li><strong>Colour</strong></li>\r
 </ul>\r
-<blockquote>\r
+<blockquote> \r
   <ul>\r
     <li><strong>Apply Colour To All Groups<br>\r
-      </strong><em>If this is selected, any changes made to the background colour\r
+      </strong><em>If this is selected, any changes made to the background colour \r
       will be applied to all currently defined groups.<br>\r
       </em></li>\r
-    <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,\r
-      Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried\r
-      Index, Nucleotide, User Defined<br>\r
-      </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for\r
+    <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage \r
+      Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity, \r
+      Turn Propensity, Buried Index, Nucleotide, User Defined<br>\r
+      </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for \r
       a description of all colour schemes.</em><br>\r
     </li>\r
     <li><strong>By Conservation<br>\r
-      </strong><em>See <a href="../colourSchemes/conservation.html">Colouring\r
+      </strong><em>See <a href="../colourSchemes/conservation.html">Colouring \r
       by Conservation</a>.</em><br>\r
     </li>\r
     <li><strong>Modify Conservation Threshold<br>\r
-      </strong><em>Use this to display the conservation threshold slider window.\r
-      Useful if the window has been closed, or if the 'by\r
-      conservation' option appears to be doing nothing!</em><br></li>\r
+      </strong><em>Use this to display the conservation threshold slider window. \r
+      Useful if the window has been closed, or if the 'by conservation' option \r
+      appears to be doing nothing!</em><br>\r
+    </li>\r
     <li><strong>Above Identity Threshold<br>\r
-      </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage\r
+      </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage \r
       Identity</a></em><strong>.<br>\r
       </strong></li>\r
     <li><strong>Modify Identity Threshold<br>\r
-      </strong><em>Use this to set the threshold value for colouring above Identity.\r
-      Useful if the window has been closed. </em></li>\r
+      </strong><em>Use this to set the threshold value for colouring above Identity. \r
+      Useful if the window has been closed.<br>\r
+      </em></li>\r
+    <li><strong>By Annotation</strong><br>\r
+      <em>Colours the alignment on a per-column value from a specified annotation. \r
+      See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>\r
+    </li>\r
   </ul>\r
 </blockquote>\r
 </body>\r