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- * 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)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* 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
<em>Per-sequence associated annotation colouring was introduced
in Jalview 2.8</em>
</li>
+ <li>If the "Use Original Colours" 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
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>
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