[Biococoa-dev] BioCocoa 2.1.0 release
schristley at mac.com
Fri Oct 3 23:25:23 EDT 2008
A new release of BioCocoa is now available; download is available from
the BioCocoa website Below is some news about what is available. If
you feel all excited and want to broadcast this all around, I ask to
maybe consider holding off for the moment :-)
Part of this is a run-through to document all the steps required to
make a release, this will help in making periodic consistent releases
in the future. For that purpose, it would be much more helpful if
people downloaded and prodded it and send back any comments. There
are some things definitely missing, most notably example programs to
show off the library, and who knows what else. This will give me a
chance to walk through the process a few times, and hopefully we will
have a true release soon!
BioCocoa 2.1.0 -- (found in Tags / 2.1.0)
- New BCSuffixArray and BCMCP classes for constructing disk-based
suffix arrays of sequences and finding the maximum common prefixes of
sequences using those suffix arrays. This is work based upon the
Scott Christley, Neil F. Lobo and Greg Madey.
Multiple Organism Algorithm for Finding Ultraconserved Elements.
BMC Bioinformatics, 9: 15, 2008.
- New BCCachedSequenceFile and BCCachedFastaFile classes that allow
for reading sequence data without reading the whole sequence into
memory. This is useful for working with very large sequences like
whole genomes. A future release will support a BCCachedSequence which
provides a consistent sequence interface regardless of whether the
sequence is in memory or cached on disk.
- File format can be explictly provided to BCSequenceReader using
- Documentation updates.
- More complete port to GNUstep, all BCFoundation functionality should
- Quad-fat binary supporting 32/64-bit and ppc/intel processors.
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