3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 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 allows the columns of an alignment to be coloured using any
24 numerical annotation rows 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="507" height="202"> </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
36 representing the minimum value in the selected annotation to a colour
37 representing the maximum value in the selected annotation. Use the
38 "Min Colour" and "Max Colour" to set the colour
41 <li><em>New in Jalview 2.7</em>: Press the "Defaults"
42 button to reset the minimum and maximum colours to their default
43 settings (these are configured in the applet's parameters or the <a
44 href="../features/preferences.html">application's user
49 <li>Select whether to colour the alignment above or below an adjustable threshold
50 with the selection box center left of the window. </li>
51 <li>Change the threshold value with the slider, or enter the
52 exact value in the text box.
54 <li>Select the "Threshold is Min/Max" checkbox to
55 assign colours using the thresholded range's minimum and maximum
56 values, otherwise the scale will be defined by the range of values in
57 the annotation row.</li>
59 <p align="center"><img src="annotationColours.jpg" width="688" height="488"> </p>