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- * 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 ($$Version-Rel$$)
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* Jalview is free software: you can redistribute it and/or
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+ *
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+<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