I have a couple of questions regarding codon bias measurements.
1) Is there a codon usage object in Biojava?
2) How easy would it be to integrate it into Artemis (to add things to the Graph menu)?
I've seen references to CrossProductAlphabet codonAlphabet = AlphabetManager
in the archive, so I think I can manage to generate a codon usage table, and compute codon bias statistics from that, but I was wondering if something more complete has already been written.
I have been using TreeMaps to make codon usage tables within Artemis classes, but they seem to be very slow, eg:
Collator co = Collator.getInstance();
TreeMap codonUsageTable = new TreeMap(co);
and then accessing them using .put() and .get() TreeMap methods. But the performance is poor compared to the Artemis classes that just read single chars, eg GCFrameAlgorithm.
Cheers Derek
_________________________
Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR
Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: [EMAIL PROTECTED] Website: http://www.vir.gla.ac.uk
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