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JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this...
[jalview.git] / help / html / colourSchemes / clustal.html
diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html
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--- a/help/html/colourSchemes/clustal.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>Clustal Colour Scheme</title>
-<style type="text/css">
-<!--
-td {
-       text-align: center;
-}
--->
-</style>
-</head>
-
-<body>
-  <p>
-    <strong>Clustal X Colour Scheme</strong>
-  </p>
-  <p>This is an emulation of the default colourscheme used for
-    alignments in Clustal X, a graphical interface for the ClustalW
-    multiple sequence alignment program. Each residue in the alignment
-    is assigned a colour if the amino acid profile of the alignment at
-    that position meets some minimum criteria specific for the residue
-    type.</p>
-  <p>The table below gives these criteria as clauses: {&gt;X%,xx,y},
-    where X is the threshold percentage presence for any of the xx (or y)
-    residue types.
-    <br>For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).</p>
-  <div align="center">
-    <p>&nbsp;</p>
-    <table border="1">
-      <tr>
-        <th>Clustal X Default Colouring</th>
-      </tr>
-      <tr>
-        <td><table border="1">
-            <tr>
-              <th>Category</th>
-              <th>Colour</th>
-              <th>Residue at position</th>
-              <th>{ Threshold, Residue group }</th>
-            </tr>
-            <tr>
-              <td rowspan="2">Hydrophobic</td>
-              <td rowspan="2" bgcolor="#80a0f0">BLUE</td>
-              <td>A,I,L,M,F,W,V</td>
-              <td>{&gt;60%, WLVIMAFCHP}</td>
-            </tr>
-            <tr>
-              <td>C</td>
-              <td>{&gt;60%, WLVIMAFCHP}</td>
-            </tr>
-            <tr>
-              <td>Positive charge</td>
-              <td bgcolor="#f01505">RED</td>
-              <td>K,R</td>
-              <td>{&gt;60%,KR},{&gt;80%, K,R,Q}</td>
-            </tr>
-            <tr>
-              <td rowspan="2">Negative charge</td>
-              <td rowspan="2" bgcolor="#c048c0">MAGENTA</td>
-              <td>E</td>
-              <td>{&gt;60%,KR},{&gt;50%,QE},{&gt;85%,E,Q,D}</td>
-            </tr>
-            <tr>
-              <td>D</td>
-              <td>{&gt;60%,KR}, {&gt;85%, K,R,Q}, {&gt;50%,ED}</td>
-            </tr>
-            <tr>
-              <td rowspan="3">Polar</td>
-              <td rowspan="3" bgcolor="#15c015">GREEN</td>
-              <td>N</td>
-              <td>{&gt;50%, N}, {&gt;85%, N,Y}</td>
-            </tr>
-            <tr>
-              <td>Q</td>
-              <td>{&gt;60%,KR},{&gt;50%,QE},{&gt;85%,Q,E,K,R}</td>
-            </tr>
-            <tr>
-              <td>S,T</td>
-              <td>{&gt;60%, WLVIMAFCHP}, {&gt;50%, TS}, {&gt;85%,S,T}</td>
-            </tr>
-            <tr>
-              <td>Cysteines</td>
-              <td bgcolor="#f08080">PINK</td>
-              <td>C</td>
-              <td>{>85%, C}</td>
-            </tr>
-            <tr>
-              <td>Glycines</td>
-              <td bgcolor="#f09048">ORANGE</td>
-              <td>G</td>
-              <td>{&gt;0%, G}</td>
-            </tr>
-            <tr>
-              <td>Prolines</td>
-              <td bgcolor="#c0c000">YELLOW</td>
-              <td>P</td>
-              <td>{&gt;0%, P}</td>
-            </tr>
-            <tr>
-              <td>Aromatic</td>
-              <td bgcolor="#15a4a4">CYAN</td>
-              <td>H,Y</td>
-              <td>{&gt;60%, WLVIMAFCHP}, {&gt;85%,
-                W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
-            </tr>
-            <tr>
-              <td>Unconserved</td>
-              <td>WHITE</td>
-              <td>any / gap</td>
-              <td>If none of the above criteria are met</td>
-            </tr>
-          </table></td>
-      </tr>
-    </table>
-  </div>
-</body>
-</html>