X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=doc%2FAddingGroovySupport.html;h=e71c53b4515d54c4ca095ec44eaaa93eb48014f4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index e18e273..e71c53b 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,18 +1,61 @@ +Adding Groovy Support to Jalview + + +

+Adding Groovy Support to 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. +

Here are some scripts 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...

+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.

Making it easier

jalview.bin.JalviewScript could be a top level jalview instance of a script execution thread, creating and maintaining the context for scripts operating on the jalview datamodel and interfacing with the Jalview GUI. +

+ + +