3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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/>.
20 <title>Annotation Colouring</title>
25 <strong> Annotation Colouring </strong>
27 <p>Jalview allows the columns of an alignment to be coloured using
28 any numerical annotation rows added to that alignment.</p>
29 Select "Colour"
30 <strong>→</strong> ".. by Annotation" to bring up the
31 Colour by Annotation settings window.
35 <img src="annotationColourSetting.gif" width="471" height="256">
38 <li>Select which annotation to base the colouring scheme on using
39 the top left selection box.<br />If the <strong>Per-sequence
40 only</strong> tick box is not greyed out, then ticking it will limit the
41 available annotation rows to just those that are sequence associated
42 (e.g. T-COFFEE scores and <a
43 href="../webServices/proteinDisorder.html">protein disorder
44 predictions</a>), which will colour each sequence according to its own
45 per-residue scores.<br />
46 <em>Per-sequence associated annotation colouring was introduced
49 <li>The colour scheme can display a colour gradient from a colour
50 representing the minimum value in the selected annotation to a colour
51 representing the maximum value in the selected annotation. Use the
52 "Min Colour" and "Max Colour" to set the colour
55 <li>Press the "Defaults" button to reset the minimum
56 and maximum colours to their default settings (these are configured
57 in the applet's parameters or the <a
58 href="../features/preferences.html">application's user
59 preferences</a>.).<br />
60 <em>Default min and max colours were introduced in Jalview 2.7</em>
64 <li>Select whether to colour the alignment above or below an
65 adjustable threshold with the selection box center left of the
67 <li>Change the threshold value with the slider, or enter the
68 exact value in the text box.</li>
69 <li>Select the "Threshold is Min/Max" checkbox to
70 assign colours using the thresholded range's minimum and maximum
71 values, otherwise the scale will be defined by the range of values in
72 the annotation row.</li>
75 <img src="annotationColourView.gif" width="581" height="148">