X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2FAddingGroovySupport.html;h=ff9af0722e4d41090d1797792e1edd3bb13cfad8;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index e18e273..ff9af07 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,7 +1,7 @@ +
+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:
++def alf = Jalview.getAlignframes(); +print alf[0].getTitle(); +def alignment = alf[0].viewport.alignment; +def seq = alignment.getSequenceAt(0); ++
+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). +
++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.
+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. +
+ + +