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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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
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* 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.
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+ *
* 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
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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/>.
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+<head><title>Alignment Window Menus</title></head>
+
+<body>
+<p><strong>Alignment Window Colour Menu</strong></p>
+ <ul>
+ <li><strong>Apply Colour To All Groups<br>
+ </strong><em>If this is selected, any changes made to the background colour
+ will be applied to all currently defined groups.<br>
+ </em></li>
+ <li><strong><a href="../colourSchemes/textcolour.html">Colour
+ Text ...</a></strong><em><br>
+ Opens the Colour Text dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
+ </em></li>
+ <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
+ Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
+ Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br>
+ </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
+ a description of all colour schemes.</em><br>
+ </li>
+ <li><strong>By Conservation<br>
+ </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
+ by Conservation</a>.</em><br>
+ </li>
+ <li><strong>Modify Conservation Threshold<br>
+ </strong><em>Use this to display the conservation threshold slider window.
+ Useful if the window has been closed, or if the 'by conservation' option
+ appears to be doing nothing!</em><br>
+ </li>
+ <li><strong>Above Identity Threshold<br>
+ </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
+ Identity</a></em><strong>.<br>
+ </strong></li>
+ <li><strong>Modify Identity Threshold<br>
+ </strong><em>Use this to set the threshold value for colouring above Identity.
+ Useful if the window has been closed.<br>
+ </em></li>
+ <li><strong>By Annotation</strong><br>
+ <em>Colours the alignment on a per-column value from a specified annotation.
+ See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
+ </li>
+ <li><strong>By RNA Helices</strong><br>
+ <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
+ Colouring</a>.</em><br>
+ </li>
+ </ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff