JAL-2446 merged to spike branch

[jalview.git] / help / html / features / groovy.html

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index 079cf9e..ead4436 100644 (file)
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -64,6 +64,7 @@
     public methods of the jalview class hierarchy can be called from
     Groovy scripts. In addition, the following objects are also defined:
 
+
   
   <ul>
     <li><strong>Jalview</strong> - this is bound to <code>jalview.bin.Jalview</code>.<br />Useful
@@ -90,9 +91,9 @@ def alignment = alf[0].viewport.alignment;
 def seq = alignment.getSequenceAt(0);
 </pre>
     </li>
-    <li>If you wanted to do the same thing from the command line, you can refer to
-      alignment that was just loaded with currentAlFrame:<br>
-      <pre>
+    <li>If you wanted to do the same thing from the command line,
+      you can refer to alignment that was just loaded with
+      currentAlFrame:<br> <pre>
 print currentAlFrame.getTitle();</pre>
   </ul>
   <p>
@@ -107,9 +108,18 @@ print currentAlFrame.getTitle();</pre>
     simplified the alignment analysis programming interface in Jalview
     2.10 to make it easy for you to add your own dynamic annotation
     tracks with Groovy. Have a look at the <a
-      href="../groovy/featureCounter.html">featureCounter.groovy</a>
+      href="../groovy/featuresCounter.html">featuresCounter.groovy</a>
     example for more information.
   </p>
+  <p><a name="groovyColours"/>
+    <em>Creating custom colourschemes</em><br/>
+    You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
+    <ul>
+    <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+    <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+    
+    </ul>
+  </p>
 
 </body>
 </html>