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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>User Defined Colours</title>
+</head>
+<body>
+ <p>
+ <strong>User Defined Colours</strong>
+ </p>
+ <p>
+ <img src="userDefined_java7.gif" width="815" height="402">
+ </p>
+ <p>
+ You may define any number of new colour schemes, each with a unique
+ name. <br> <br> Each of the residues in a colour scheme
+ may be assigned any chosen colour. <br> Select one or more
+ residues, then select the desired colour.<br /> Use Ctrl-click to
+ select multiple residues, or click then Shift-click to select a
+ block.<br /> Note that the currently selected buttons are
+ highlighted by a lighter text colour.
+ <p>
+ The <strong>Case Sensitive</strong> option allows you to choose
+ distinct colours for upper and lower case residue codes.
+ <p>
+ The <strong>Colour All Lower Case </strong> option allows you to apply a selected colour
+ to all lower case residues.
+ <p>
+ Click <strong>Apply</strong> or <strong>OK</strong> to set your new
+ colours on the active alignment window.<br /> Click <strong>Cancel</strong>
+ to undo your changes if you pressed the <strong>Apply</strong>
+ button.
+ </p>
+ If you save your colour scheme with a unique name, the colour scheme
+ name will be added to the
+ <strong>Colour</strong> menu on each new alignment window.
+ <br>
+ <br> Any saved colour schemes will be automatically loaded the
+ next time you use Jalview.
+ <br>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff