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<p><strong> Annotation Colouring </strong></p>
-<p>Jalview 2.08 allows an alignment to be coloured on a per-column basis based
- on any numerical annotation added to that alignment. </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="426" height="140"> </div>
+ <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.</li>
- <li>Select whether to colour the alignment above or below an adjustable threshold
+ <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>
-</ul>
-<p align="center"><img src="annotationColours.jpg" width="475" height="262"> </p>
+ <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>
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git://source.jalview.org / jalview.git / commitdiff
