<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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
+</h1>
+<p>
+There is currently no scripting language
+extension within Jalview, in part because a
+scripting API has not yet been developed.
+</p>
+<p>It is, however, really easy to embed scripting
+engines like groovy. If groovy is detected on the
+classpath, a new menu entry on the Desktop's Tools
+menu will open the GroovyShell.
+</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>
+<h1>Getting Groovy...</h1>
+<p>
+You need the core groovy jars which include the GroovyShell. The easiest way of doing
+this is to add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.</p>
+<p>The is obtained from the <em>embedded</em> directory within the <a
+href="http://dist.codehaus.org/groovy/distributions"/>groovy distribution</a>).
+</p>
+<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