highlights are below.
</p>
<ul>
- <li><strong>New UI, and faster and more configurable implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
+ <li><strong>New UI, and faster and more configurable
+ implementation for PCA, Neighbour-Joining and UPGMA Trees</strong><br>
Menu entries for calculating PCA and different types of tree have
been replaced by a single <em>Calculations</em> dialog box. The
- underlying implementation for the PCA and tree calculations have been
- made faster and more memory efficient. A new framework has also been
- created for the score models used to calculate distances between
- sequences. This framework allows import of substitution matrices in
- NCBI and AAIndex format, and custom score models to be created via a
- groovy script.</li>
+ underlying implementation for the PCA and tree calculations have
+ been made faster and more memory efficient. A new framework has
+ also been created for the score models used to calculate distances
+ between sequences. This framework allows import of substitution
+ matrices in NCBI and AAIndex format, and custom score models to be
+ created via a groovy script.</li>
<li><strong>Update to JABAWS 2.2</strong><br />Jalview's
alignment, protein conservation analysis, and protein disorder and
RNA secondary structure prediction services are now provided by <a
the Chimera viewer's Chimera menu</a> allow positional annotation to
be exchanged between Chimera and Jalview.</li>
</ul>
+ <p>
+ <strong>Scripting</strong><br />New <a
+ href="http://www.jalview.org/examples/groovy">groovy examples</a>
+ demonstrate Jalview 2.10.2 APIs for creation of data-driven
+ colourschemes, and custom alignment file handlers. The <a
+ href="groovy/featuresCounter.html">FeatureAnnotationWorker</a>
+ introduced in Jalview 2.10 has also been refactored to allow
+ efficient counting across multiple feature types. Please be aware
+ that feature counter scripts created for earlier versions will not
+ execute in Jalview 2.10.2.
+ </p>
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