X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=ba9cbdd115d5cf24ce4f37c21bc54ff249953277;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=3d40a3e82d4539532adf37225958f5594b1cb50b;hpb=7bc3c614b6d38f11d3f804d5dab2df8dd2bf7204;p=jalview.git

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 3d40a3e..ba9cbdd 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,20 +1,21 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <head>
 <title>Annotation Colouring</title>
@@ -46,6 +47,15 @@
 		<em>Per-sequence associated annotation colouring was introduced
 				in Jalview 2.8</em>
 		</li>
+		<li>If the &quot;Use Original Colours&quot; box is selected, the
+			colouring scheme will use the colouring scheme present on the
+			alignment before the Annotation Colour Settings window was displayed.
+			<br /> <em><strong>Please Note:</strong> If no colour scheme was
+				applied previously, then the colours for lines and labels at each
+				position in the annotation row will be used, for secondary structure
+				symbols and graphs, this may be black by default, so your alignment
+				will be coloured black.</em>
+		</li>
 		<li>The colour scheme can display a colour gradient from a colour
 			representing the minimum value in the selected annotation to a colour
 			representing the maximum value in the selected annotation. Use the
@@ -72,7 +82,7 @@
 			the annotation row.</li>
 	</ul>
 	<p align="center">
-		<img src="annotationColourView.gif" width="581" height="148">
+		<img src="annotationColours.gif" width="582" height="464">
 	</p>
 </body>
 </html>
