From fdb9f5bbf2b5044a13131f1ad446a7967e20df34 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 21 Dec 2006 14:11:18 +0000 Subject: [PATCH] type change --- doc/AddingGroovySupport.html | 244 +++++++++++++++++++++--------------------- 1 file changed, 122 insertions(+), 122 deletions(-) diff --git a/doc/AddingGroovySupport.html b/doc/AddingGroovySupport.html index efefcc2..6726612 100644 --- a/doc/AddingGroovySupport.html +++ b/doc/AddingGroovySupport.html @@ -1,122 +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. -

- - - + +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

+ + + -- 1.7.10.2