From dc5507ccf4bf0c8b20f86aee7175c16b68ef52ea Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 4 Dec 2006 17:28:34 +0000 Subject: [PATCH] random notes on putting a Groovy interpreter into Jalview. --- doc/AddingGroovySupport.html | 122 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 doc/AddingGroovySupport.html diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html new file mode 100644 index 0000000..efefcc2 --- /dev/null +++ b/doc/AddingGroovySupport.html @@ -0,0 +1,122 @@ + +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 been developed. +

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 +

+..
+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();
+}
+..
+

+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.

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. +

+ + + -- 1.7.10.2