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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 2.8.2)
+ * 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.
- *
+ * 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/>.
--->
-<head><title>Annotation Colouring</title></head>
+ * 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>
+</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>
+ <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.gif" width="471" height="256">
+ </div>
+ <ul>
+ <li>Select which annotation to base the colouring scheme on using
+ the top left selection box.<br />If the <strong>Per-sequence
+ only</strong> tick box is not greyed out, then ticking it will limit the
+ available annotation rows to just those that are sequence associated
+ (e.g. T-COFFEE scores and <a
+ href="../webServices/proteinDisorder.html">protein disorder
+ predictions</a>), which will colour each sequence according to its own
+ per-residue scores.<br />
+ <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
"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
+ <li>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>.)
+ preferences</a>.).<br />
+ <em>Default min and max colours were introduced in Jalview 2.7</em>
</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>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>
+ 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>
+ <p align="center">
+ <img src="annotationColours.gif" width="582" height="464">
+ </p>
</body>
</html>