Groovy Shell

From: jprocter Date: Fri, 11 Jan 2008 13:53:39 +0000 (+0000) Subject: documentation for groovy console and basic groovy scripting support X-Git-Tag: Release_2_4~157 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a1d3c3dd9366660e8bff47f9e072ed3f9394d071;p=jalview.git documentation for groovy console and basic groovy scripting support --- diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html new file mode 100644 index 0000000..1a0b83c --- /dev/null +++ b/help/html/features/groovy.html @@ -0,0 +1,46 @@ + +Groovy Shell + +

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.

Opening the 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 linecommand line option will

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:
+

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...
+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.

+ +