<body>
<p>
<strong>Extending Jalview with Groovy - A customisable
- feature counter</strong><br />
- <br />The groovy script below shows how to add a new calculation
- track to a Jalview alignment window.</p><p>As currently written, it will
- add two tracks to a protein alignment view which count Pfam features
- in each column, and ones where a charge residue also occur.</p><p>To try
- it for yourself:</p><ol><li>Copy and paste it into the groovy script
- console</li><li>Load the example Feredoxin project (the one that opens
- by default when you first launched Jalview)</li><li>Select <strong>Calculations→Execute
- Groovy Script</strong> from the alignment window's menu bar to run the script on
- the current view.</li></ol>
+ feature counter</strong><br /> <br />The groovy script below shows how to
+ add a new calculation track to a Jalview alignment window.
+ </p>
+ <p>As currently written, it will add two tracks to a protein
+ alignment view which count Pfam features in each column, and ones
+ where a charge residue also occur.</p>
+ <p>To try it for yourself:</p>
+ <ol>
+ <li>Copy and paste it into the groovy script console</li>
+ <li>Load the example Feredoxin project (the one that opens by
+ default when you first launched Jalview)</li>
+ <li>Select <strong>Calculations→Execute Groovy
+ Script</strong> from the alignment window's menu bar to run the script on
+ the current view.
+ </li>
+ </ol>
<em><a
- href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a> - rendered with <a href="http://hilite.me">hilite.me</a></em>
+ href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a>
+ - rendered with <a href="http://hilite.me">hilite.me</a></em>
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