# Adding Groovy Support to Jalview

There is currently no scripting language extension within Jalview, in part because a scripting API has not yet been developed.

It is, however, really easy to embed scripting engines like groovy. If groovy is detected on the classpath, a new menu entry on the Desktop's Tools menu will open the GroovyShell.

Here are some scripts to get you started:

- 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);

# Getting Groovy...

You need the core groovy jars which include the GroovyShell. The easiest way of doing this is to add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.

The is obtained from the embedded directory within the groovy distribution).

## TODO

Using Java class methods from Groovy is straightforward, but currently, there isn't a set of easy to use methods for the jalview objects. A Jalview Scripting API needs to be developed to make this easier.

### Making it easier

jalview.bin.JalviewScript could be a top level jalview instance of a script execution thread, creating and maintaining the context for scripts operating on the jalview datamodel and interfacing with the Jalview GUI.