[Biojava-l] Recent changes

[Keith James]

On your next cvs update it may look like I've made sweeping changes,
but that's not really the case.

Fixed all Javadoc warnings/errors on 1.4, general Javadoc cleaning
Fixed a couple of things which turned up in a grep for 'fixme'

Enhanced RestrictionEnzyme and RestrictionEnzymeManager. Added a
RestrictionSite feature. This involved pulling RestrictionEnzyme back
into the main code tree (it was in src-1.4) because I added
SimpleRestrictionSite to the default FeatureRealizer. (Adding to the
default FeatureRealizer seems to be the approach used most often).

Added RestrictionMapper which implements SequenceAnnotator for marking
RestrictionSite features on a Sequence by creating a ViewSequence. The
searching is configurably multithreaded via a basic thread pool
interface. This class is not unit tested yet - only by visual
inspection of annotated EMBL dumps. As you might expect, it's only
about 30-40% of the speed of EMBOSS restrict (by highly accurate
wristwatch benchmarking... ). However, I guess native threads on a
multi-cpu machine will close the gap.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -