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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 Consensus Annotation</title></head>
+<body>
+<p><strong>Alignment Consensus Annotation</strong></p>
+<p>The consensus displayed below the alignment is the percentage of the modal
+ residue per column. By default this calculation takes includes gaps in column.
+ You can choose to ignore gaps in the calculation by right clicking on the label
+ "Consensus" to the left of the consensus bar chart.
+<p>If the modal value is shared by more than 1 residue, a "+" symbol
+ is used in the display for the simple reason that it is not possible to display
+ multiple characters in a single character space.
+<p><strong>Copying the consensus sequence</strong></p>
+<p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
+the consensus annotation label to copy the alignment's consensus sequence to the
+clipboard.
+
+<p><strong>Sequence logo</strong></p>
+ By clicking on the label you can also activate the sequence logo. It
+ indicates the relative amount of residues per column which can be
+ estimated by it's size in the logo. The tooltip of a column gives the
+ exact numbers for all occuring residues.
+ <br />If columns of the alignment are very diverse, then it can
+ sometimes be difficult to see the sequence logo - in this case, right
+ click on the annotation row label and select
+ <strong>Normalise Consensus Logo</strong> to scale all columns of the
+ logo to the same height.
+ </p>
+</body>
+</html>