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. All you need is to select Tools→Groovy Console... menu option 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 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.

Executing a groovy script on a particular alignment

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 environment 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();