[Bioperl-l] conservative amino acid change?

[Hilmar Lapp]

Heikki Lehvaslaiho wrote:
> 
> Hilmar Lapp wrote:
> >
> > Heikki Lehvaslaiho wrote:
> > >
> > > My implementation has the BLOSUM62 matrix inside the package. I can
> > > not remember matrixes never being discussed in bioperl context. Other
> > > bio* projects might have a selection of standard similarity matrixes
> > > included. (?) Should we have them? And classes dealing with them?
> > >
> >
> > I think we should. It is definitely going to be useful for other
> > modules, too.
> 
> OK. I'll write the modules:
> 
> Bio::Matrix::SimilarityMatrixI
>         id()
>         name()
>         moltype()
>         pam()
>         max()
>         min()
>         def()
>         deletion()
>         similarity_score()
> 
> Bio::Matrix::SimilarityMatrix
> Bio::Matrix::SimilarityMatrixIO
> Bio::Matrix::SimilarityMatrixIO::full
> Bio::Matrix::SimilarityMatrixIO::half
> 

Cool! :-)

I agree with naming etc.

> 
> We'll need a data directory to place the default matrixes in. What
> would be the best (platform independent) way of refering to files
> within bioperl?
> 

Couldn't that be loaded through a 'require' utilizing the standard
perl search mechanism?

	Hilmar

-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
A-1120 Vienna
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