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

Adam Kraut adamnkraut at gmail.com
Thu May 18 17:07:42 EDT 2006

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

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.


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