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JAL-2446 merged to spike branch
[jalview.git] / help / html / colourSchemes / clustal.html
diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html
index 3531330..b3d44db 100755 (executable)
--- a/help/html/colourSchemes/clustal.html
+++ b/help/html/colourSchemes/clustal.html
@@ -1,21 +1,137 @@
-<html>\r
-<head><title>Clustal Colour Scheme</title>\r
-<style type="text/css">\r
-<!--\r
-td {\r
-       text-align: center;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<p><em>Clustal X</em></p>\r
-  <p>Clustal X is a graphical interface for the ClustalW multiple sequence alignment\r
-    program. Sequences can be coloured either by assigning a colour to specific\r
-    residues, or on the basis of an alignment consensus. The residues in each\r
-    column are coloured according to the consensus character assigned to that column.\r
-    In this way, you can choose to highlight, for example, conserved hydrophilic\r
-    or hydrophobic positions in the alignment. </p>\r
-</body>\r
-</html>\r
+<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>