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.
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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.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Sequence feature colour schemes</title>
27 <p><strong>Sequence feature colour schemes</strong></p>
28 <p>Jalview can visualize annotation present on parts of a sequence by
29 overlaying colours according to the annotation present at each position.
30 It allows features to be colored either according to type, or for a
31 particular type, according to an individual feature's associated label
32 or score. The <a href="featuresettings.html">Feature Settings dialog
33 box</a> controls the order and display of each sequence annotation type, and
34 also allows the colour scheme used for the the feature to be changed <em>via</em>
35 the 'Graduated Colour' option in the sequence feature pop-up menu
36 (obtained by right-clicking on a sequence feature).</p>
38 <center><img src="featurecoloursettings.gif"><br/>Graduated
39 feature colour scheme settings dialog box</img></center>
40 <p>The Graduated Feature Colour dialog box has the following
43 <li><em>Colour by Label</em> - when checked this derives a colour
44 for each feature based on the label text.</li>
45 <li><em>Min and Max Color boxes</em> - Click on these boxes to set
46 the minimum and maximum colours used to shade features by their
47 associated score.</li>
48 <li><em>Threshold type combo box</em> - Allows features to be
49 hidden features if their score is below or above a given threshold.<br />
50 <em>Set the threshold using the slider or type it in to the text
51 box. The threshold cannot be set outside the available range of feature
54 <li><em>Threshold is Min/Max</em> - When checked, the threshold
55 will be used as the upper or lower limit when shading the features
56 according to their score using the Min and Max colour.</li>
59 <p><strong>Icon styles for graduated feature styles</strong><br/>
60 <p>When a graduated colourscheme is applied to a feature, it is indicated in the feature settings or amend feature dialog box by the following types of icon:<br/>
61 <center><table width="50%" border="1">
62 <tr><td><strong>Type of Colouring</strong></td><td><strong>Icon</strong></td></tr>
63 <tr><td><em>Graduated colour by Feature Score</em></td><td><img src="fcsminmax.gif"/></td></tr>
64 <tr><td><em>Graduated colour thresholded (less than) by feature Score</em></td><td><img src="fcsltthan.gif"/></td></tr>
65 <tr><td><em>Graduated colour thresholded (greater than) by feature Score</em></td><td><img src="fcsgtthan.gif"/></td></tr>
66 <tr><td><em>Colour by Feature Label (may also be thresholded)</em></td><td><img src="fcsntlabel.gif"/></td></tr>
68 <td align="center" colspan="2">
70 <strong>The current threshold is given in the
71 icon's tooltip.</strong>
73 </td></tr></table></center></p>
74 <em>Graduated feature colours were introduced in Jalview 2.5</em>