X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=2272503c682ac2f026766eea21a970f952d4cd32;hb=ecdbc96815298ac853543640881ef8d2384b48a1;hp=34d02556cca64770a086126407184536c850392f;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 34d0255..2272503 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -39,14 +39,17 @@
   </div>
   <ul>
     <li>Select which annotation to base the colouring scheme on
-      using the top left selection box.<br />If the <strong>Per-sequence
-        only</strong> tick box is not greyed out, then ticking it will limit the
-      available annotation rows to just those that are sequence
-      associated (e.g. T-COFFEE scores and <a
-      href="../webServices/proteinDisorder.html"
-    >protein disorder predictions</a>), which will colour each sequence
-      according to its own per-residue scores.<br /> <em>Per-sequence
-        associated annotation colouring was introduced in Jalview 2.8</em>
+      using the top left selection box. Sequence associated alignment
+      annotation are shown with the seuqence's name appended.<br />If
+      the <strong>Per-sequence only</strong> tick box is not greyed out,
+      then ticking it will limit the list of available annotation rows
+      to just the labels for those that are sequence associated.
+      Annotation rows on each sequence with the same label (e.g.
+      T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
+        disorder predictions</a>) will then be used to colour its
+      corresponding positions in the alignment.<br /> <em>Per-sequence
+        associated annotation colouring is currently only available in
+        the Desktop.</em>
     </li>
     <li>If the &quot;Use Original Colours&quot; box is selected,
       the colouring scheme will use the colouring scheme present on the
@@ -74,9 +77,9 @@
         <li>Press the &quot;Defaults&quot; button to reset the
           minimum and maximum colours to their default settings (these
           are configured in the applet's parameters or the <a
-          href="../features/preferences.html"
-        >application's user preferences</a>.).<br /> <em>Default min
-            and max colours were introduced in Jalview 2.7</em>
+          href="../features/preferences.html">application's
+            user preferences</a>.).<br /> <em>Default min and max
+            colours were introduced in Jalview 2.7</em>
       </ul>
     </li>
 
