[Biopython-dev] Floats and Double in Cluster

[Bruce Southey]

Hi,
Actually just switch to the new numpy where ranlib is no longer used.
It uses  Mersenne Twister RNG from Jean-Sebastien Roy's random kit.
Robert Kern has also written additional code.

Of course, that really means moving BioPython to numpy from Numeric.
Is there a plan for this?

Bruce


On 6/20/06, Michiel Jan Laurens de Hoon <mdehoon at c2b2.columbia.edu> wrote:
> Peter (BioPython Dev) wrote:
> > One for Michiel, as the author of Bio.Cluster
> >
> > I've just been building the latest CVS code on Windows with MSVC 6.0
> > (Microsoft Visual C++) and noticed there are a lot of warnings about
> > double to float conversion (with associated data loss) from
> > Bio/Cluster/ranlib.c (see attached output).
> >
> > Does this matter?
> >
> Probably not. The ranlib library is quite old (maybe fifteen years or
> more). It was originally written in Fortran, and automatically converted
> into C. Such conversions are usually not so clean, so the resulting code
> tends to generate many warning messages. On the other hand, ranlib is a
> part of Numerical Python (the RandomArray module), so if there were a
> serious problem with it it would have been discovered by now.
> I did find out recently though that there may be a licensing problem
> with ranlib. Since we're using only a small part of ranlib in
> Bio.Cluster, I'm planning to replace it with a different random number
> generator for the next version.
>
> --Michiel.
>
> --
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1130 St Nicholas Avenue
> New York, NY 10032
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