X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=doc%2FAddingGroovySupport.html;h=e3e453f89a51bcc1286a7f9c6f52e3af2b15492d;hp=275ddb087ca197c0b898cf31a737b439e94c5648;hb=ec606034401293ba2700c18bdd8b5c62000f7810;hpb=c53aeee9a688f68d64106a968876e542f701fbc6 diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index 275ddb0..e3e453f 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,54 +1,41 @@ Adding Groovy Support to Jalview

-Adding Groovy Support to Jalview +Groovy Support in 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. + Groovy has been bundled with the Jalview desktop since circa 2012. The program supports interactive execution of groovy scripts via the Groovy Console, and command line execution via the '-groovy' option. The main source for documentation about Groovy in Jalview is the online help pages.

Here are some scripts to get you started:

Getting the title, alignment and first sequence from the current alignFrame

-def alf = Jalview.getAlignframes();
+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.