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
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>
+ <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>
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>
+ 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>
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