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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git] / help / html / colourSchemes / clustal.html
diff --git a/help/html/colourSchemes/clustal.html b/help/html/colourSchemes/clustal.html
index 33455dc..7b68c84 100755 (executable)
--- a/help/html/colourSchemes/clustal.html
+++ b/help/html/colourSchemes/clustal.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -19,7 +19,8 @@
  * 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>
+<head>
+<title>Clustal Colour Scheme</title>
 <style type="text/css">
 <!--
 td {
@@ -30,36 +31,95 @@ td {
 </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: {+X%,xx,y},
-     where X is the minimum percentage presence for any of the xx (or y) residue types.</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>Residue at position</th><th>Applied Colour</th><th>{ Threshhold, Residue group }</th></tr>
-<tr><td>A,I,L,M,F,W,V</td><td bgcolor="#80a0f0">BLUE</td><td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>R,K</td><td bgcolor="#f01505">RED</td><td>{+60%,KR},{+80%, K,R,Q}</td></tr>
-<tr><td>N</td><td bgcolor="#15c015">GREEN</td><td>{+50%, N}, {+85%, N,Y}</td></tr>
-<tr><td>C</td><td bgcolor="#80a0f0">BLUE</td>
-<td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>C</td><td bgcolor="#f08080">PINK</td>
-<td>{100%, C}</td></tr>
-<tr><td>Q</td><td bgcolor="#15c015">GREEN</td><td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td></tr>
-<tr><td>E</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td></tr>
-<tr><td>D</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td></tr>
-<tr><td>G</td><td bgcolor="#f09048">ORANGE</td><td>{+0%, G}</td></tr>
-<tr><td>H,Y</td><td bgcolor="#15a4a4">CYAN</td><td>{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}</td></tr>
-<tr><td>P</td><td bgcolor="#c0c000">YELLOW</td><td>{+0%, P}</td></tr>
-<tr><td>S,T</td><td bgcolor="#15c015">GREEN</td><td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td></tr>
-</table>
-</td></tr></table>
-</div>
+  <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: {+X%,xx,y},
+    where X is the minimum percentage presence for any of the xx (or y)
+    residue types.</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>Residue at position</th>
+              <th>Applied Colour</th>
+              <th>{ Threshhold, Residue group }</th>
+            </tr>
+            <tr>
+              <td>A,I,L,M,F,W,V</td>
+              <td bgcolor="#80a0f0">BLUE</td>
+              <td>{+60%, WLVIMAFCHP}</td>
+            </tr>
+            <tr>
+              <td>R,K</td>
+              <td bgcolor="#f01505">RED</td>
+              <td>{+60%,KR},{+80%, K,R,Q}</td>
+            </tr>
+            <tr>
+              <td>N</td>
+              <td bgcolor="#15c015">GREEN</td>
+              <td>{+50%, N}, {+85%, N,Y}</td>
+            </tr>
+            <tr>
+              <td>C</td>
+              <td bgcolor="#80a0f0">BLUE</td>
+              <td>{+60%, WLVIMAFCHP}</td>
+            </tr>
+            <tr>
+              <td>C</td>
+              <td bgcolor="#f08080">PINK</td>
+              <td>{100%, C}</td>
+            </tr>
+            <tr>
+              <td>Q</td>
+              <td bgcolor="#15c015">GREEN</td>
+              <td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td>
+            </tr>
+            <tr>
+              <td>E</td>
+              <td bgcolor="#c048c0">MAGENTA</td>
+              <td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td>
+            </tr>
+            <tr>
+              <td>D</td>
+              <td bgcolor="#c048c0">MAGENTA</td>
+              <td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td>
+            </tr>
+            <tr>
+              <td>G</td>
+              <td bgcolor="#f09048">ORANGE</td>
+              <td>{+0%, G}</td>
+            </tr>
+            <tr>
+              <td>H,Y</td>
+              <td bgcolor="#15a4a4">CYAN</td>
+              <td>{+60%, WLVIMAFCHP}, {+85%,
+                W,Y,A,C,P,Q,F,H,I,L,M,V}</td>
+            </tr>
+            <tr>
+              <td>P</td>
+              <td bgcolor="#c0c000">YELLOW</td>
+              <td>{+0%, P}</td>
+            </tr>
+            <tr>
+              <td>S,T</td>
+              <td bgcolor="#15c015">GREEN</td>
+              <td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td>
+            </tr>
+          </table></td>
+      </tr>
+    </table>
+  </div>
 </body>
 </html>