<strong>The Groovy Shell</strong>
</p>
<p>
- <a href="http://groovy.codehaus.org/">Groovy</a> is an "<em>agile
- and dynamic language for the Java platform</em>". The groovy
- scripting language makes it extremely easy to programmatically
- interact with Java programs, in much the same way that Javascript is
- used to generate and interact with applets and other objects on the
- page.
+ Groovy (<a href="http://www.groovy-lang.org/">www.groovy-lang.org</a>)
+ is an "<em>agile and dynamic language for the Java
+ platform</em>". The groovy scripting language makes it extremely
+ easy to programmatically interact with Java programs, in much the
+ same way that Javascript is used to generate and interact with
+ applets and other objects on the page.
</p>
<p>
- <strong><em>Getting Groovy...</em> </strong><br> Jalview Groovy
- support is only possible if the core groovy jars which include the
- GroovyShell are present on the CLASSPATH when Jalview is started.
- </p>
- <p>
- The jars are obtained from the <em>embedded</em> directory within
- the <a href="http://dist.codehaus.org/groovy/distributions">groovy
- distribution</a>. The easiest way of adding them to the Jalview
- classpath is to download and build Jalview from its source
- distribution, and then add the groovy-all-*.jar to the lib directory
- whose path is given in the java.ext.dirs property.
- </p>
- <p>
- <strong>Opening Jalview's Groovy Console</strong><br>If groovy
- is available, then the <strong>Tools→Groovy
- Console...</strong> menu entry will be available from the Jalview Desktop's
- drop-down menu. Selecting this will open the <a
- href="http://groovy.codehaus.org/Groovy+Console"
- >Groovy Console</a> which allows you to interactively execute Groovy
- scripts within the Jalview run-time environment.
+ <em>Getting Groovy...</em><br> Jalview comes with an embedded
+ installation of Groovy. Just select <strong>Tools→Groovy
+ Console...</strong> from the Jalview Desktop's drop-down menu. After a
+ short pause, you should then see the <a
+ href="http://groovy-lang.org/groovyconsole.html">Groovy
+ Console</a> appear. This allows you to interactively execute Groovy
+ scripts whilst Jalview is running. We've also provided a <strong>Calculations→Execute
+ Groovy Script</strong> button so you can execute the currently loaded
+ groovy script whilst viewing an alignment.
</p>
<p>
<strong>Executing groovy scripts on Jalview startup</strong><br>
</p>
<p>
<strong>Access to Jalview's functions from Groovy Scripts</strong><br>
- There is as yet no properly defined scripting interface to Jalview,
- but all the public methods of the jalview class hierarchy can be
- called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
- object defined in the groovy environment which corresponds to the
- <pre>jalview.gui.Desktop</pre>
- object which manages all the Jalview windows. Here's an example to get
- you started:
- <br>
+ The scripting interface to Jalview is still a work in progress, so
+ we recommend you also take a look at Jalview's source, since all the
+ public methods of the jalview class hierarchy can be called from
+ Groovy scripts. In addition, the following objects are also defined:
+
+
+
+ <ul>
+ <li><strong>Jalview</strong> - this is bound to <code>jalview.bin.Jalview</code>.<br />Useful
+ methods include:
+ <ul>
+ <li>Jalview.getAlignFrames() - returns a list of
+ jalview.gui.AlignFrame objects</li>
+ <li>Jalview.getCurrentAlignFrame() - returns the alignment
+ window which is currently being looked at by the user</li>
+ </ul></li>
+ <li><strong>currentAlFrame</strong> - this is only defined when
+ running a Groovy script via the -groovy command line argument. It
+ returns the first alignment window created after acting on the
+ other arguments passed on the command line.</li>
+ </ul>
+ <p>
+ <em>A simple script</em><br />
<ul>
<li>Getting the title, alignment and first sequence from the
current alignFrame<br> <pre>
def seq = alignment.getSequenceAt(0);
</pre>
</li>
- <li>When running a groovy script from the command line, the
- alignment that was just loaded can be referred to like so:<br>
- <pre>
+ <li>If you wanted to do the same thing from the command line,
+ you can refer to alignment that was just loaded with
+ currentAlFrame:<br> <pre>
print currentAlFrame.getTitle();</pre>
</ul>
- If you have downloaded the InstallAnywhere version of Jalview, you can
- find additional groovy scripts in the examples/groovy subfolder of the
- installation directory.
+ <p>
+ <em>Example scripts</em><br />If you have downloaded the
+ InstallAnywhere version of Jalview, you can find additional groovy
+ scripts in the examples/groovy subfolder of the installation
+ directory. The examples are also available at <a
+ href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+ </p>
+ <p>
+ <em>Using Groovy to add new Alignment Calculations</em><br />We've
+ simplified the alignment analysis programming interface in Jalview
+ 2.10 to make it easy for you to add your own dynamic annotation
+ tracks with Groovy. Have a look at the <a
+ href="../groovy/featureCounter.html">featureCounter.groovy</a>
+ example for more information.
+ </p>
+
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