<html>
<!--
- * 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 2.8.1)
+ * 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.
- *
+ *
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head><title>Annotation Colouring</title></head>
+<head>
+<title>Annotation Colouring</title>
+</head>
<body>
-<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>
-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>
-<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
- 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>
+ <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>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>.).<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>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.gif" width="582" height="464">
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff