-<html>\r
-<title>Adding Groovy Support to Jalview\r
-</title>\r
-<body>\r
-<h1>\r
-Adding Groovy Support to Jalview\r
-</h1>\r
-<p>\r
-There is currently no scripting language \r
-extension within Jalview, in part because a \r
-scripting API has not been developed.\r
-</p>\r
-<p>It is, however, really easy to embed scripting\r
-engines within Jalview. We haven't done it\r
-with the Bean Scripting Framework, but the\r
-code snippets below show you how to get going\r
-with groovy.\r
-</p>\r
-<h2>Modifications</h2>\r
-<p>\r
-For each class below, add the following objects and methods to their definitions.\r
-</p>\r
-<ul><li>\r
-jalview.jbgui.GDesktop\r
-<pre>\r
-..\r
-protected JMenuItem groovyShell = new JMenuItem();\r
-..\r
-jbInit() {\r
-..\r
-groovyShell.setText("Groovy Shell...");\r
-groovyShell.addActionListener(new ActionListener() \r
-{\r
- public void actionPerformed(ActionEvent e) {\r
- groovyShell_actionPerformed(e);\r
- } \r
-});\r
-..\r
-}\r
-..\r
-protected void groovyShell_actionPerformed(ActionEvent e) \r
-{\r
-}\r
-..\r
-</pre></li>\r
-<li>jalview.gui.Desktop\r
-<pre>\r
-..\r
-/** \r
- * Accessor method to quickly get all the AlignmentFrames\r
- * loaded. \r
- */ \r
-protected AlignFrame[] getAlignframes() {\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
-\r
- if (frames == null)\r
- {\r
- return null;\r
- }\r
- Vector avp=new Vector();\r
- try\r
- {\r
- //REVERSE ORDER\r
- for (int i = frames.length - 1; i > -1; i--)\r
- {\r
- if (frames[i] instanceof AlignFrame)\r
- {\r
- AlignFrame af = (AlignFrame) frames[i];\r
- avp.addElement(af);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- if (avp.size()==0)\r
- {\r
- return null;\r
- }\r
- AlignFrame afs[] = new AlignFrame[avp.size()];\r
- for (int i=0,j=avp.size(); i<j; i++) {\r
- afs[i] = (AlignFrame) avp.elementAt(i);\r
- }\r
- avp.clear();\r
- return afs;\r
-}\r
-\r
-/**\r
- * Add Groovy Support to Jalview\r
- */\r
-public void groovyShell_actionPerformed(ActionEvent e) {\r
- Console gc = new Console();\r
- gc.setVariable("Jalview", this);\r
- gc.run();\r
-}\r
-..\r
-</pre>\r
-</li>\r
-</ul>\r
-<p>\r
-Finally, compile and run with the groovy-all-*.jar (get the jar \r
-from the <em>embedded</em> directory within the <a \r
-href="http://dist.codehaus.org/groovy/distributions"/>groovy distribution</a>).\r
-Then, you should be able to open the Groovy shell \r
-window from the Desktop's Tools menu. To check things are working,\r
-try a simple test script :<br>\r
-<pre>\r
- \r
- print Jalview.getAlignframes()[0].getTitle();\r
-</pre>\r
-Executing this will print the title of the first alignment loaded into Jalview.</p>\r
-</hr>\r
-<h2>TODO</h2>\r
-<p>\r
-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>\r
-<h3>Making it easier</h3>\r
-<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.\r
-</p> \r
-</body>\r
-</html>\r
-\r
+<html>
+<title>Adding Groovy Support to Jalview
+</title>
+<body>
+<h1>
+Adding Groovy Support to Jalview
+</h1>
+<p>
+There is currently no scripting language
+extension within Jalview, in part because a
+scripting API has not been developed.
+</p>
+<p>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.
+</p>
+<h2>Modifications</h2>
+<p>
+For each class below, add the following objects and methods to their definitions.
+</p>
+<ul><li>
+jalview.jbgui.GDesktop
+<pre>
+..
+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)
+{
+}
+..
+</pre></li>
+<li>jalview.gui.Desktop
+<pre>
+..
+/**
+ * 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();
+}
+..
+</pre>
+</li>
+</ul>
+<p>
+Finally, compile and run with the groovy-all-*.jar (get the jar
+from the <em>embedded</em> directory within the <a
+href="http://dist.codehaus.org/groovy/distributions"/>groovy distribution</a>).
+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 :<br>
+<pre>
+
+ print Jalview.getAlignframes()[0].getTitle();
+</pre>
+Executing this will print the title of the first alignment loaded into Jalview.</p>
+</hr>
+<h2>TODO</h2>
+<p>
+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>
+<h3>Making it easier</h3>
+<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.
+</p>
+</body>
+</html>
+
git://source.jalview.org / jalview.git / commitdiff