X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2FAddingGroovySupport.html;h=e3e453f89a51bcc1286a7f9c6f52e3af2b15492d;hb=c09c4d7c3e34cf37ed91fc66615d7c1cc86d0909;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index e18e273..e3e453f 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,18 +1,47 @@ +Adding Groovy Support to Jalview + + +

+Groovy Support in Jalview +

+ 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();
+print alf[0].getTitle();
+def alignment = alf[0].viewport.alignment;
+def seq = alignment.getSequenceAt(0);
+

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. +

+ + +