+ 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 its 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+ object 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); ++
+print currentAlFrame.getTitle();+