[emboss-dev] External Libraries, C++ App

Brandon Barker brandon.barker at gmail.com
Thu Aug 2 04:05:23 UTC 2007

Thanks for the tips and info, sounds good.  Another question is
regarding the interoperability between AJAX and GMP.  Would it be
acceptable for me to add some GMP oriented functions that are
analogous to existing functions in AJAX and add an optional check in
configure.in for GMP?  Since building EMBOSS with GMP would still be
optional, my parametric alignment package could still be part of
EMBASSY, but the AJAX GMP functions would be part of EMBOSS (but only
built if the user has GMP, and maybe only if the user explicitly tells
configure they want it).

If not, I can try to make my own AJAX-like library for GMP types, but
this doesn't seem ideal.

On 8/1/07, Peter Rice <pmr at ebi.ac.uk> wrote:
> Brandon Barker wrote:
> > Hello, I'm currently developing a software package that I would like to try
> > to add to EMBOSS or EMBASSY.  There are two potential problems: the package
> > I'm working on is in C++, and most likely won't be changed to C.  Also, it
> > makes heavy use (in innermost loops, unfortunately, but this can't be
> > avoided) of arbitrary precision rationals (or integers) so I need to  use an
> > external library (GMP). All the licensing should be fine, since all of the
> > software and libraries I'm using are under the LGPL or the GPL.  The
> > application area is parametric and inverse parametric sequence alignment (or
> >  regular alignment with arbitrary precision parameters, but I don't think too
> >  many people are interested in that aspect).
> C++ should not be a problem. Licensing is also not a problem.
> But because you do need to compile with C++ and add an external library I
> suggest you make this an EMBASSY package. The reason is that you can tailor the
> EMBASSY package's configure.in and Makefile.am files for your build.
> The EMBOSS CVS server has an EMBASSY directory "myemboss" that can be used as a
> template for new EMBASSY packages.
> You have a choice of requiring users to install GMP or providing a copy in the
> EMBASSY package distribution.
> Please mail emboss-bug at emboss.open-bio.org for any help in configuring (or
> emboss-dev if it is of enough general interest)
> regards,
> Peter Rice

Brandon Barker
Phone: (859) 948-5335

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