-<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>
+<!--
+ * 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>
+Groovy Support in Jalview
+</h1>
+<p>
+ <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>Here are some scripts to get you started:</p>
+<ul><li>Getting the title, alignment and first sequence from the current alignFrame<br>
+<pre>
+def alf = Jalview.getAlignFrames();
+print alf[0].getTitle();
+def alignment = alf[0].viewport.alignment;
+def seq = alignment.getSequenceAt(0);
+</pre>
+</li>
+</ul>
+<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 / blobdiff