[Bioperl-l] writing a pairwise alignment module: XS and Inline C?

[aaron.j.mackey at gsk.com]

bioperl-ext is the package in which alignment algorithms and/or BioPerl 
"wrapped" external C libraries live.  Subprojects in bioperl-ext use both 
XS and Inline::C, that's up to you.

You'll need to get your C code compiled to a dynamically loaded library 
(.so) to use either XS or Inline::C; this precludes any reuse of the C 
main() function (although your Inline::C wrapper might recapitulate/copy 
the main() function code).

Out of curiosity, what pairwise alignment algorithm are you using?  This 
is a heavily beaten path, you might want to dig around first to see if 
someone else already has what you need.

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 05/18/2006 05:07:42 PM:

> I am currently using a pairwise alignment algorithm written in C (not by
> me).  The program consists of a library of routines, structures, and
> definitions which I do not want to spend a lot of time abstracting.  I
> already have a hack method of writing the parameters and inputs I want 
from
> perl, calling the c program with system( ), and then parsing the output 
in
> Perl.  Any good programmer would probably smack me but I'm just an 
undergrad
> and I needed to show my boss that this works in order to spend more time 
on
> it.
> 
> So on to my question, what is the preferred method of extending Bioperl 
to
> use this algorithm?  I have just read the XS tutorial and a bit about 
Inline
> C.  Can I put the main function in my script using Inline, and then just
> point Inline at the rest of the C library?  The program has several
> C-structures that are semantically equivalent to Bioperl objects, so 
just
> need somewhere to start.  I will spend some more time so that I have a 
more
> specific question, I just wanted a little feedback, this is my first 
post to
> the bioperl list.
> 
> Thanks,
> Adam
> 
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