-<html>\r
-\r
-<body>\r
-<p><em>User Defined Colours</em></p>\r
-<p>Each of the residues may be assigned a new user defined colour. </p>\r
-<p>You may save this colour scheme and reuse it at a later time.</p>\r
-<p>The default user defined colour is the last user colour scheme which was defined.</p>\r
-<p> </p>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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.
+ *
+ * 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><em>User Defined Colours</em></p>
+<p><img src="userDefined_java6.gif" width="719" height="368"> </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 'Case Sensitive' option allows you to choose distinct colours for upper and
+ lower case residue codes.
+ <p>
+ Click "Apply" or "OK" to set your new colours on the active
+ alignment window.<br/>
+ Click "Cancel" to undo your changes if you pressed the "Apply"
+ button.
+ </p>
+ If you save your colour scheme with a unique name, the colour scheme name will
+ be added to the "Colour" menu on each new alignment window.<br>
+ <br>
+ Any saved colour schemes will be automatically loaded the next time you use
+ Jalview.</p>
+ Note: the screenshot shows the appearance when running Java version 6. For Java 7, only the Swatches colour chooser is
+ currently supported (for reasons of available screen space).
+ <p/>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff