2 <title>Adding Groovy Support to Jalview
6 Adding Groovy Support to Jalview
9 There is currently no scripting language
10 extension within Jalview, in part because a
11 scripting API has not yet been developed.
13 <p>It is, however, really easy to embed scripting
14 engines like groovy. If groovy is detected on the
15 classpath, a new menu entry on the Desktop's Tools
16 menu will open the GroovyShell.
18 <p>Here are some scripts to get you started:</p>
19 <ul><li>Getting the title, alignment and first sequence from the current alignFrame<br>
21 def alf = Jalview.getAlignframes();
22 print alf[0].getTitle();
23 def alignment = alf[0].viewport.alignment;
24 def seq = alignment.getSequenceAt(0);
28 <h1>Getting Groovy...</h1>
30 You need the core groovy jars which include the GroovyShell. The easiest way of doing
31 this is to add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.</p>
32 <p>The is obtained from the <em>embedded</em> directory within the <a
33 href="http://dist.codehaus.org/groovy/distributions"/>groovy distribution</a>).
37 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.</p>
38 <h3>Making it easier</h3>
39 <p>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.