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.
22 <head><title>User Defined Colours</title></head>
24 <p><em>User Defined Colours</em></p>
25 <p><img src="userDefined_java6.gif" width="719" height="368"> </p>
26 <p>You may define any number of new colour schemes, each with a unique name. <br>
28 Each of the residues in a colour scheme may be assigned any chosen colour. <br>
29 Select one or more residues, then select the desired colour.<br/>
30 Use Ctrl-click to select multiple residues, or click then Shift-click to select a block.<br/>
31 Note that the currently selected buttons are highlighted by a lighter text colour.
33 The 'Case Sensitive' option allows you to choose distinct colours for upper and
34 lower case residue codes.
36 Click "Apply" or "OK" to set your new colours on the active
37 alignment window.<br/>
38 Click "Cancel" to undo your changes if you pressed the "Apply"
41 If you save your colour scheme with a unique name, the colour scheme name will
42 be added to the "Colour" menu on each new alignment window.<br>
44 Any saved colour schemes will be automatically loaded the next time you use
46 Note: the screenshot shows the appearance when running Java version 6. For Java 7, only the Swatches colour chooser is
47 currently supported (for reasons of available screen space).