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
+ 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>
<p>
<strong>Executing groovy scripts on Jalview startup</strong><br>
- The -groovy <script> option on the <a href="commandline.html" />
+ The -groovy <script> option on the <a href="commandline.html">
Jalview command line</a> will execute the contents of <script>.
<script> may be a file, a URL, or alternatively if it is
"STDIN" then the standard input will be used.<br>
<em>Note: The groovy script will be executed <strong>after</strong>
any data is loaded, and <strong>before</strong> images or any output
- files are written. This allows you to perform customised jalview
+ files are written. This allows you to perform customised Jalview
analysis workflows with groovy.</em>
</p>
<p>
object defined in the groovy environent which corresponds to the
<pre>jalview.gui.Desktop</pre>
object which manages all the Jalview windows.
- </p>
Here's an example to get you started:
<br>
<ul>
<li>Getting the title, alignment and first sequence from the
current alignFrame<br> <pre>
-def alf = Jalview.getAlignframes();
+def alf = Jalview.getAlignFrames();
print alf[0].getTitle();
def alignment = alf[0].viewport.alignment;
def seq = alignment.getSequenceAt(0);
<li>When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:<br><pre>
print currentAlFrame.getTitle();</pre>
</ul>
- </p>
-
- <p> </p>
+If you have downloaded the InstallAnywhere version of Jalview, you can find additional groovy scripts in the examples/groovy subfolder of the installation directory.
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