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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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>
+ -->
+<head>
+<title>User Defined Colours</title>
+</head>
<body>
-<p><em>User Defined Colours</em></p>
-<p><img src="userDefined.gif" width="719" height="368"> </p>
-<p>You may define any number of new colour schemes, each with a unique name. <br>
+ <p>
+ <strong>User Defined Colours</strong>
+ </p>
+ <p>
+ <img src="userDefined_java6.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>
+ 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>
- Each of the residues in a new colour scheme may be assigned a new user defined
- colour. <br>
+ <br> Any saved colour schemes will be automatically loaded the
+ next time you use Jalview.
<br>
- Click "Apply" or "OK" to set your new colours on the active
- alignment window. </p>
-<p>Click "Cancel" to undo your changes if you pressed the "Apply"
- button. <br>
<br>
- 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>
+ <em>Note: the screenshot shows the appearance when running Java
+ version 6. For Java 7 (from Jalview 2.8.2) only the Swatches colour
+ chooser is currently supported (for reasons of available screen
+ space).</em>
+ <p />
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff