3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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>If the "Use Original Colours" box is selected, the
50 colouring scheme will use the colouring scheme present on the
51 alignment before the Annotation Colour Settings window was displayed.
52 <br /> <em><strong>Please Note:</strong> If no colour scheme was
53 applied previously, then the colours for lines and labels at each
54 position in the annotation row will be used, for secondary structure
55 symbols and graphs, this may be black by default, so your alignment
56 will be coloured black.</em>
58 <li>The colour scheme can display a colour gradient from a colour
59 representing the minimum value in the selected annotation to a colour
60 representing the maximum value in the selected annotation. Use the
61 "Min Colour" and "Max Colour" to set the colour
64 <li>Press the "Defaults" button to reset the minimum
65 and maximum colours to their default settings (these are configured
66 in the applet's parameters or the <a
67 href="../features/preferences.html">application's user
68 preferences</a>.).<br />
69 <em>Default min and max colours were introduced in Jalview 2.7</em>
73 <li>Select whether to colour the alignment above or below an
74 adjustable threshold with the selection box center left of the
76 <li>Change the threshold value with the slider, or enter the
77 exact value in the text box.</li>
78 <li>Select the "Threshold is Min/Max" checkbox to
79 assign colours using the thresholded range's minimum and maximum
80 values, otherwise the scale will be defined by the range of values in
81 the annotation row.</li>
84 <img src="annotationColours.gif" width="582" height="464">