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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
+<head><title>Annotation Colouring</title></head>
+
+<body>
+<p><strong> Annotation Colouring </strong></p>
+<p>Jalview allows the columns of an alignment to be coloured using any
+ numerical annotation rows added to that alignment. </p>
+Select "Colour" <strong>→</strong> "..
+ by Annotation" to bring up the Colour by Annotation settings window. <br>
+ <br><div align="center">
+ <img src="annotationColourSetting.jpg" width="507" height="202"> </div>
+<ul>
+ <li>Select which annotation to base the colouring scheme on using the top left
+ selection box.</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. </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
+ "Min Colour" and "Max Colour" to set the colour
+ gradient range.
+ <ul>
+ <li><em>New in Jalview 2.7</em>: Press the "Defaults"
+ 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>.)
+ </ul>
+ </li>
+
+ <li>Select whether to colour the alignment above or below an adjustable threshold
+ with the selection box center left of the window. </li>
+ <li>Change the threshold value with the slider, or enter the
+ exact value in the text box.
+ </li>
+ <li>Select the "Threshold is Min/Max" checkbox to
+ assign colours using the thresholded range's minimum and maximum
+ values, otherwise the scale will be defined by the range of values in
+ the annotation row.</li>
+ </ul>
+<p align="center"><img src="annotationColours.jpg" width="688" height="488"> </p>
+</body>
+</html>