3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Annotation Colouring</title>
28 <strong> Annotation Colouring </strong>
30 <p>Jalview allows the columns of an alignment to be coloured using
31 any numerical annotation rows added to that alignment.</p>
32 Select "Colour"
33 <strong>→</strong> ".. by Annotation" to bring up the
34 Colour by Annotation settings window.
38 <img src="annotationColourSetting.gif" width="471" height="256">
41 <li>Select which annotation to base the colouring scheme on using
42 the top left selection box.<br />If the <strong>Per-sequence
43 only</strong> tick box is not greyed out, then ticking it will limit the
44 available annotation rows to just those that are sequence associated
45 (e.g. T-COFFEE scores and <a
46 href="../webServices/proteinDisorder.html">protein disorder
47 predictions</a>), which will colour each sequence according to its own
48 per-residue scores.<br />
49 <em>Per-sequence associated annotation colouring was introduced
52 <li>If the "Use Original Colours" box is selected, the
53 colouring scheme will use the colouring scheme present on the
54 alignment before the Annotation Colour Settings window was displayed.
55 <br /> <em><strong>Please Note:</strong> If no colour scheme was
56 applied previously, then the colours for lines and labels at each
57 position in the annotation row will be used, for secondary structure
58 symbols and graphs, this may be black by default, so your alignment
59 will be coloured black.</em>
61 <li><em>Secondary structure annotation colouring</em><br />By
62 default, Jalview will employ the helix or sheet colours to shade
63 sequences and columns by available secondary structure annotation
64 tracks. In the case of RNA, each structure is processed to identify
65 distinct RNA helices and rendered in the same way as the <a
66 href="rnahelicesColouring.html">RNA Helices shading scheme</a>. <em>Structure based sequence shading was added in Jalview 2.8.2</em></li>
67 <li>The colour scheme can display a colour gradient from a colour
68 representing the minimum value in the selected annotation to a colour
69 representing the maximum value in the selected annotation. Use the
70 "Min Colour" and "Max Colour" to set the colour
73 <li>Press the "Defaults" button to reset the minimum
74 and maximum colours to their default settings (these are configured
75 in the applet's parameters or the <a
76 href="../features/preferences.html">application's user
77 preferences</a>.).<br />
78 <em>Default min and max colours were introduced in Jalview 2.7</em>
82 <li>Select whether to colour the alignment above or below an
83 adjustable threshold with the selection box center left of the
85 <li>Change the threshold value with the slider, or enter the
86 exact value in the text box.</li>
87 <li>Select the "Threshold is Min/Max" checkbox to
88 assign colours using the thresholded range's minimum and maximum
89 values, otherwise the scale will be defined by the range of values in
90 the annotation row.</li>
93 <img src="annotationColours.gif" width="582" height="464">