From cd5042310088854fc941b55011fd152f463b982b Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 May 2017 16:51:31 +0100
Subject: [PATCH] JAL-384 documentation on custom colours groovy examples

---
 help/help.jhm                  |    1 +
 help/helpTOC.xml               |    1 +
 help/html/features/groovy.html |    9 +++++++++
 3 files changed, 11 insertions(+)

diff --git a/help/help.jhm b/help/help.jhm
index 53b86d2..54cce2a 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -131,6 +131,7 @@
    
    <mapID target="memory" url="html/memory.html" />
    <mapID target="groovy" url="html/features/groovy.html" />
+   <mapID target="groovy.colours" url="html/features/groovy.html#groovyColours" />
    <mapID target="groovy.featurescounter" url="html/groovy/featuresCounter.html" />
    <mapID target="privacy" url="html/privacy.html" />
    <mapID target="vamsas" url="html/vamsas/index.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 62df81f..a8aadf5 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -25,6 +25,7 @@
 			<tocitem text="What's new" target="new" expand="true">
 				<tocitem text="Latest Release Notes" target="release"/>
 				<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
+				<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
 				<tocitem text="Omit hidden regions in Overview" target="overview"/>
 				<tocitem text="identifers.org for URL Links" target="linksprefs" />
 				<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index d9bf76e..ead4436 100644
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -111,6 +111,15 @@ print currentAlFrame.getTitle();</pre>
       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>
-- 
1.7.10.2