1 #-------------------------------------------------------------------------------
2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 # This file is part of Jalview.
7 # Jalview is free software: you can redistribute it and/or
8 # modify it under the terms of the GNU General Public License
9 # as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 # Jalview is distributed in the hope that it will be useful, but
12 # WITHOUT ANY WARRANTY; without even the implied warranty
13 # of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 # PURPOSE. See the GNU General Public License for more details.
16 # You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 #-------------------------------------------------------------------------------
20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
36 <head><title>Annotation Colouring</title></head>
39 <p><strong> Annotation Colouring </strong></p>
40 <p>Jalview 2.08 allows an alignment to be coloured on a per-column basis based
41 on any numerical annotation added to that alignment. </p>
42 Select "Colour" <strong>→</strong> "..
43 by Annotation" to bring up the Colour by Annotation settings window. <br>
44 <br><div align="center">
45 <img src="annotationColourSetting.jpg" width="426" height="140"> </div>
47 <li>Select which annotation to base the colouring scheme on using the top left
49 <li> If the "Use Original Colours" box is selected, the colouring
50 scheme will use the colouring scheme present on the alignment before the Annotation
51 Colour Settings window was displayed. </li>
52 <li>The colour scheme can display a colour gradient from a colour representing
53 the minimum value in the selected annotation to a colour representing the
54 maximum value in the selected annotation. Use the "Min Colour" and
55 "Max Colour" to set the colour gradient range.</li>
56 <li>Select whether to colour the alignment above or below an adjustable threshold
57 with the selection box center left of the window. </li>
58 <li>Change the threshold value with the slider, or enter the exact value in
61 <p align="center"><img src="annotationColours.jpg" width="475" height="262"> </p>