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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
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- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
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- * of the License, or (at your option) any later version.
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- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Groovy Shell</title>
-</head>
-<body>
- <p>
- <strong>The Groovy Shell</strong>
- </p>
- <p>
- 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>
- <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>
- 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>
- 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 alf = Jalview.getAlignFrames();
-print alf[0].getTitle();
-def alignment = alf[0].viewport.alignment;
-def seq = alignment.getSequenceAt(0);
-</pre>
- </li>
- <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>
- <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/featuresCounter.html">featuresCounter.groovy</a>
- example for more information.
- </p>
- <p><a name="groovyColours"/>
- <em>Creating custom colourschemes</em><br/>
- You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
- <ul>
- <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
- <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
-
- </ul>
- </p>
-
-</body>
-</html>
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