+ 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+ 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();+
+ +