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JAL-1620 version bump and release notes
[jalview.git] / help / html / colourSchemes / index.html
diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html
index fc5e098..b072c38 100755 (executable)
--- a/help/html/colourSchemes/index.html
+++ b/help/html/colourSchemes/index.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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>Colour Schemes</title>
 <style type="text/css">
@@ -32,6 +52,7 @@ background, and the intensity threshold for transition between them.</p>
 <p>The default colour schemes are summarised in the table below:
 <div align="center">
 <p>&nbsp;</p>
+<p><strong>Protein Colour Schemes</strong></p>
 <table border="1">
        <tr>
                <td>
@@ -274,6 +295,81 @@ background, and the intensity threshold for transition between them.</p>
                </td>
        </tr>
 </table>
+<p>&nbsp;</p>
+<p><strong>Nucleotide Colour Schemes</strong></p>
+<table border="1">
+       <tr>
+               <td>
+               <table border="1">
+                       <tr>
+                               <td nowrap></td>
+                               <td>A</td> <!--Adenine-->
+                           <td>C</td> <!--Cytosine-->
+                       <td>G</td> <!--Guanine-->
+                       <td>T</td> <!--Thymine-->
+                       <td>U</td> <!--Uracil-->
+                       <td>I</td> <!--Inosine-->
+                       <td>X</td> <!--Xanthine-->
+                       <td>R</td> <!--Unknown Purine-->
+                       <td>Y</td> <!--Unknown Pyrimidine-->
+                       <td>N</td> <!--Unknown-->
+                       <td>W</td> <!--Weak nucleotide (A or T)-->
+                       <td>S</td> <!--Strong nucleotide (G or C)-->
+                       <td>M</td> <!--Amino (A or C)-->
+                       <td>K</td> <!--Keto (G or T)-->
+                       <td>B</td> <!--Not A (G or C or T)-->
+                       <td>H</td> <!--Not G (A or C or T)-->
+                       <td>D</td> <!--Not C (A or G or T)-->
+                       <td>V</td> <!--Not T (A or G or C-->
+                       </tr>
+                       <tr>
+                               <td height="24">Nucleotide</td>
+                               <td bgcolor="#64F73F"></td>
+                               <td bgcolor="#FFB340"></td>
+                       <td bgcolor="#EB413C"></td>
+                       <td bgcolor="#3C88EE"></td>
+                       <td bgcolor="#3C88EE"></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       </tr>
+                       <tr>
+                               <td height="24">Purine/Pyrimidine</td>
+                               <td bgcolor="#FF83FA"></td>
+                               <td bgcolor="#40E0D0"></td>
+                       <td bgcolor="#FF83FA"></td>
+                       <td bgcolor="#40E0D0"></td>
+                       <td bgcolor="#40E0D0"></td>
+                       <td></td>
+                       <td></td>
+                       <td bgcolor="#FF83FA"></td>
+                       <td bgcolor="#40E0D0"></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       <td></td>
+                       </tr>
+               </table>
+               </td>
+       </tr>
+</table>
+
+
 </div>
 <p align="center">&nbsp;</p>
 </body>