[Bioperl-l] Bio::SeqAnalysisParserI, Bio::Factory::SeqAnalysisPar serFactory

[Jason Stajich]

On Sun, 4 Feb 2001, Hilmar Lapp wrote:

> 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
> functionality.
> 
> 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.
done, renamed to SeqFeatureProducer to SeqAnalysisParser.t
> 
> 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
> ...)
I'll take a looksie at BPlite.
> 
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/