From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 4 Sep 2012 16:18:56 +0000 (+0100)
Subject: JAL-975 note about black colouring bug
X-Git-Tag: Jalview_2_9~339
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=cf96462693b8944caaedf638a1a0099b339ccdb4

JAL-975 note about black colouring bug
---

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 3d40a3e..4847e71 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -46,6 +46,15 @@
 		<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