<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
<title>Adding Groovy Support to Jalview
</title>
<body>
<h1>
-Adding Groovy Support to Jalview
+Groovy Support in Jalview
</h1>
<p>
-There is currently no scripting language
-extension within Jalview, in part because a
-scripting API has not been developed.
+ <a href="http://www.groovy-lang.org">Groovy</a> 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 <a href="http://www.jalview.org/help/html/features/groovy.html">online help pages</a>.
</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
+<p>Here are some scripts to get you started:</p>
+<ul><li>Getting the title, alignment and first sequence from the current alignFrame<br>
<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();
-}
-..
+def alf = Jalview.getAlignFrames();
+print alf[0].getTitle();
+def alignment = alf[0].viewport.alignment;
+def seq = alignment.getSequenceAt(0);
</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>
git://source.jalview.org / jalview.git / blobdiff