X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2FAddingGroovySupport.html;h=e3e453f89a51bcc1286a7f9c6f52e3af2b15492d;hb=55b0b2a298681a72c6b47c35ce8b15bec6aac6dd;hp=6726612df0a7e84b0cd46d1d0fb4f45035f0b3ea;hpb=fdb9f5bbf2b5044a13131f1ad446a7967e20df34;p=jalview.git diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index 6726612..e3e453f 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,116 +1,41 @@ + Adding Groovy Support to Jalview

-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 been developed. + 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.

It is, however, really easy to embed scripting -engines within Jalview. We haven't done it -with the Bean Scripting Framework, but the -code snippets below show you how to get going -with groovy. -

Modifications

-For each class below, add the following objects and methods to their definitions. -

-jalview.jbgui.GDesktop +

Here are some scripts to get you started:

Getting the title, alignment and first sequence from the current alignFrame

-..
-protected JMenuItem groovyShell = new JMenuItem();
-..
-jbInit() {
-..
-groovyShell.setText("Groovy Shell...");
-groovyShell.addActionListener(new ActionListener() 
-{
-    public void actionPerformed(ActionEvent e) {
-        groovyShell_actionPerformed(e);
-    }  
-});
-..
-}
-..
-protected void groovyShell_actionPerformed(ActionEvent e) 
-{
-}
-..
-

jalview.gui.Desktop -

-..
-/** 
- * Accessor method to quickly get all the AlignmentFrames
- * loaded.  
- */    
-protected AlignFrame[] getAlignframes() {
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
-    if (frames == null)
-    {
-        return null;
-    }
-    Vector avp=new Vector();
-    try
-    {
-        //REVERSE ORDER
-        for (int i = frames.length - 1; i > -1; i--)
-        {
-            if (frames[i] instanceof AlignFrame)
-            {
-                AlignFrame af = (AlignFrame) frames[i];
-                avp.addElement(af);
-            }
-        }
-    }
-    catch (Exception ex)
-    {
-        ex.printStackTrace();
-    }
-    if (avp.size()==0)
-    {
-        return null;
-    }
-    AlignFrame afs[] = new AlignFrame[avp.size()];
-    for (int i=0,j=avp.size(); i<j; i++) {
-        afs[i] = (AlignFrame) avp.elementAt(i);
-    }
-    avp.clear();
-    return afs;
-}
-
-/**
-  * Add Groovy Support to Jalview
-  */
-public void groovyShell_actionPerformed(ActionEvent e) {
-    Console gc = new Console();
-    gc.setVariable("Jalview", this);
-    gc.run();
-}
-..
+def alf = Jalview.getAlignFrames();
+print alf[0].getTitle();
+def alignment = alf[0].viewport.alignment;
+def seq = alignment.getSequenceAt(0);

-Finally, compile and run with the groovy-all-*.jar (get the jar -from the embedded directory within the groovy distribution). -Then, you should be able to open the Groovy shell -window from the Desktop's Tools menu. To check things are working, -try a simple test script :
-

-  
-  print Jalview.getAlignframes()[0].getTitle();
-

-Executing this will print the title of the first alignment loaded into Jalview.

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.