Bioperl: Re: bioperl-ext Patch for extension portability (fwd)

Ewan Birney
Wed, 10 May 2000 12:05:07 +0100 (BST)

On Wed, 10 May 2000, James Gilbert wrote:

> P.S. Incidentally, I realize that this extension is essentially a
> direct port of part of WISE, without changes beyond those needed to
> get it to run with Perl. It looks like my Ph.D. thesis is going to be
> partially concerned with alignments and doing variations on how to run 
> them. Would there be interest in my (heavily) revising the C code in
> this to integrate it more fully with Perl (e.g., to have matrices
> entered through perl instead of external files), and/or introducing another
> alignment package module using C code from another public-domain source?

Definitely (!). You could do this by hacking that code, or by hacking
WISE. WISE is a pretty intertesting set of algorithms written by someone
who only vaguely grasped proper library design and software engineering.
In particular it based around a code generating langugage, called
Dynamite, which can only be described as ... interesting ...

If the author was to rewrite it, I am sure he would do it differently ;)
(I think he has improved alot...)

Take home message - feel free to

	a) rewrite/do your own thing looking at the WISE port for help

	b) hack wise that comes in bioperl-cext

	c) get a login from me to hack Wise directly on the cvs


> -- 
> Allen Smith

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420

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