X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2FAddingGroovySupport.html;fp=doc%2FAddingGroovySupport.html;h=63e7170f81328c07807026ea341fe8d64e62fb39;hb=99d5f1d805e530f23a53dad4484d44ecd0fbfdf3;hp=41e34ce41d6a58fd6f4af1235a285a978552d205;hpb=e6134bccddc2c7faad28fad1a4e77ccd0ceb3d84;p=jalview.git diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index 41e34ce..63e7170 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -21,17 +21,10 @@

-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
@@ -43,13 +36,6 @@ 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.