<title>Groovy Shell</title>
</head>
<body>
- <p>
- <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.
- </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.
- </p>
- <p>
- <strong>Executing groovy scripts on Jalview startup</strong><br>
- 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
- analysis workflows with groovy.</em>
- </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 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();
+ <p>
+ <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.
+ </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.
+ </p>
+ <p>
+ <strong>Executing groovy scripts on Jalview startup</strong><br>
+ 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
+ analysis workflows with groovy.
+ </em>
+ </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>
+ <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>
-<li>When running a groovy script from the command line, the alignment that was just loaded can be referred to like so:<br><pre>
+</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>
print currentAlFrame.getTitle();</pre>
- </ul>
- </p>
-
- <p> </p>
+ </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.
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff