3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Annotation Colouring</title></head>
22 <p><strong> Annotation Colouring </strong></p>
23 <p>Jalview 2.08 allows an alignment to be coloured on a per-column basis based
24 on any numerical annotation added to that alignment. </p>
25 Select "Colour" <strong>→</strong> "..
26 by Annotation" to bring up the Colour by Annotation settings window. <br>
27 <br><div align="center">
28 <img src="annotationColourSetting.jpg" width="426" height="140"> </div>
30 <li>Select which annotation to base the colouring scheme on using the top left
32 <li> If the "Use Original Colours" box is selected, the colouring
33 scheme will use the colouring scheme present on the alignment before the Annotation
34 Colour Settings window was displayed. </li>
35 <li>The colour scheme can display a colour gradient from a colour representing
36 the minimum value in the selected annotation to a colour representing the
37 maximum value in the selected annotation. Use the "Min Colour" and
38 "Max Colour" to set the colour gradient range.</li>
39 <li>Select whether to colour the alignment above or below an adjustable threshold
40 with the selection box center left of the window. </li>
41 <li>Change the threshold value with the slider, or enter the exact value in
44 <p align="center"><img src="annotationColours.jpg" width="475" height="262"> </p>