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, or alternatively if it is "STDIN"
then the standard input will be used.
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.Desktopobject which manages all the Jalview windows. Here's an example to get you started:
def alf = Jalview.getAlignframes(); print alf[0].getTitle(); def alignment = alf[0].viewport.alignment; def seq = alignment.getSequenceAt(0);