The Groovy Shell

Groovy ( is an "agile and dynamic language for the Java platform". The groovy scripting language makes it extremely easy to programmatically interact with Java programs, in much the same way that Javascript is used to generate and interact with applets and other objects on the page.

Getting Groovy...
Jalview comes with an embedded installation of Groovy. Just select Tools→Groovy Console... from the Jalview Desktop's drop-down menu. After a short pause, you should then see the Groovy Console appear. This allows you to interactively execute Groovy scripts whilst Jalview is running. We've also provided a Calculations→Execute Groovy Script button so you can execute the currently loaded groovy script whilst viewing an alignment.

Executing groovy scripts on Jalview startup
The -groovy <script> option on the Jalview command line will execute the contents of <script>. <script> may be a file, a URL, or alternatively if it is "STDIN" then the standard input will be used.
Note: The groovy script will be executed after any data is loaded, and before images or any output files are written. This allows you to perform customised Jalview analysis workflows with groovy.

Access to Jalview's functions from Groovy Scripts
The scripting interface to Jalview is still a work in progress, so we recommend you also take a look at Jalview's source, since all the public methods of the jalview class hierarchy can be called from Groovy scripts. In addition, the following objects are also defined:

A simple script

Example scripts
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

Using Groovy to add new Alignment Calculations
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 featuresCounter.groovy example for more information.

Creating custom colourschemes
You can create your own alignment colourschemes with a groovy script. We've provided two examples: