[Bioperl-l] Bio::SeqAnalysisParserI, Bio::Factory::SeqAnalysisParserFactory

Hilmar Lapp hlapp@gmx.net
Sun, 04 Feb 2001 15:56:47 -0800

The SeqAnalysisParser framework is now refactored. Please check
out and review the respective modules (Bio::SeqAnalysisParserI,
Bio::Factory::*). Bio::Factory::SeqAnalysisParserFactory
implements the corresponding interface (append an 'I') and
basically takes over most of Bio::SeqFeatureProducer's

Note that I dropped parse() from the Bio::SeqAnalysisParserI
interface because of the potential problems in a multi-threaded
environment (CORBA). In order to still allow a rather generic way
of instantiating implementing classes (which the factory does) I
added a note about what new() in implementing classes is expected
to recognize. I adapted Bio::Tools::AnalysisParser accordingly.

SeqFeatureProducer test now of course fails completely. I'd be
glad if someone jumps in and migrates the test to
Bio::Factory::SeqAnalysisParserFactory, should be fairly easy.
Otherwise I'll do it myself as soon as there's time.

Right now we have 3 parsers implementing Bio::SeqAnalyisParserI
(Genscan.pm, MZEF.pm, ESTScan.pm). BPlite and HMMER should be
additional well-suitable candidates. Anyone willing to change
these modules to implement the interface? (It's only one method

Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757