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<html>
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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>
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