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JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this...
[jalview.git] / help / html / io / tcoffeescores.html
diff --git a/help/html/io/tcoffeescores.html b/help/html/io/tcoffeescores.html
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--- a/help/html/io/tcoffeescores.html
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-<html>
-<!--
- * 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.
- *  
- * 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>T-COFFEE Annotation Scores</title>
-</head>
-<body>
-  <p>
-    <strong>Loading and viewing T-COFFEE Annotation Scores</strong>
-  </p>
-  <p>
-    T-COFFEE score files like the <a href="#tcoffeeeg">one below</a> can
-    be displayed on the alignment using the <strong><em>Colours&rarr;T-COFFEE
-        Scores</em></strong> or <strong><em>Colour &rarr; <a
-        href="../colourSchemes/annotationColouring.html">Colour
-          by Annotation</a></em></strong> options.
-  </p>
-  <img src="../colourSchemes/colbytcoffee.png" />
-  <p>
-    <strong><a name="tcoffeeeg">Example T-COFFEE Score file</a></strong><br />
-    T-COFFEE score files like the one below can be dropped directly onto
-    the corresponding alignment to visualize alignment confidence
-    scores.
-  </p>
-  <pre>
-T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
-Cedric Notredame 
-CPU TIME:0 sec.
-SCORE=90
-*
- BAD AVG GOOD
-*
-1PHT   :  89
-1BB9   :  90
-1UHC   :  94
-1YCS   :  94
-1OOT   :  93
-1ABO   :  94
-1FYN   :  94
-1QCF   :  94
-cons   :  90
-
-1PHT   999999999999999999999999998762112222543211112134
-1BB9   99999999999999999999999999987-------4322----2234
-1UHC   99999999999999999999999999987-------5321----2246
-1YCS   99999999999999999999999999986-------4321----1-35
-1OOT   999999999999999999999999999861-------3------1135
-1ABO   99999999999999999999999999986-------422-------34
-1FYN   99999999999999999999999999985-------32--------35
-1QCF   99999999999999999999999999974-------2---------24
-cons   999999999999999999999999999851000110321100001134
-
-
-1PHT   ----------5666642367889999999999889
-1BB9   1111111111676653-355679999999999889
-1UHC   ----------788774--66789999999999889
-1YCS   ----------78777--356789999999999889
-1OOT   ----------78877--356789999999997-67
-1ABO   ----------687774--56779999999999889
-1FYN   ----------6888842356789999999999889
-1QCF   ----------6878742356789999999999889
-cons   00100000006877641356789999999999889
-</pre>
-<table border="1">
-<tr><th>Score</th><th>0</th><th>1</th><th>2</th><th>3</th><th>4</th><th>5</th><th>6</th><th>7</th><th>8</th><th>9</th></tr>
-<tr>
-<td>RGB colour</td>
-<td bgcolor="#6666FF">102, 102, 255</td>
-<td bgcolor="#00FF00">0, 255, 0</td>
-<td bgcolor="#66FF00">102, 255, 0</td>
-<td bgcolor="#CCFF00">204, 255, 0</td>
-<td bgcolor="#FFFF00">255, 255, 0</td>
-<td bgcolor="#FFCC00">255, 204, 0</td>
-<td bgcolor="#FF9900">255, 153, 0</td>
-<td bgcolor="#FF6600">255, 102, 0</td>
-<td bgcolor="#FF3300">255, 51, 0</td>
-<td bgcolor="#FF2000">255, 34, 0</td></tr>
-</table>
-</body>
-</html>