- If you have downloaded the InstallAnywhere version of Jalview, you can
- find additional groovy scripts in the examples/groovy subfolder of the
- installation directory.
+ <p>
+ <em>Example scripts</em><br />If you have downloaded the
+ InstallAnywhere version of Jalview, you can find additional groovy
+ scripts in the examples/groovy subfolder of the installation
+ directory. The examples are also available at <a
+ href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+ </p>
+ <p>
+ <em>Using Groovy to add new Alignment Calculations</em><br />We've
+ 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/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>
+