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 Groovy support is only possible if the core groovy jars which include the GroovyShell are present on the CLASSPATH when Jalview is started.

The jars are obtained from the embedded directory within the groovy distribution. The easiest way of adding them to the Jalview classpath is to download and build jalview from it's source distribution, and then add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.

Opening Jalview's Groovy Console
If groovy is available, then the Tools→Groovy Console... menu entry will be available from the Jalview Desktop's drop-down menu. Selecting this will open the Groovy Console which allows you to interactively execute Groovy scripts within the Jalview run-time environment.

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
There is as yet no properly defined scripting interface to Jalview, but all the public methods of the jalview class hierarchy can be called from Groovy scripts. The access point for this is the Jalview object defined in the groovy environent which corresponds to the

jalview.gui.Desktop

• Getting the title, alignment and first sequence from the current alignFrame
  

  def alf = Jalview.getAlignframes();
  print alf[0].getTitle();
  def alignment = alf[0].viewport.alignment;
  def seq = alignment.getSequenceAt(0);
  

• When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:
  

  print currentAlFrame.getTitle();