[Biojava-l] Biojava in Artemis

[Derek Gatherer]

Hi

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:	      d.gatherer at vir.gla.ac.uk
Website:    http://www.vir.gla.ac.uk