Compiling project requiring w/ source requiring different compilers

[jasond]

Hi everyone,

I am currently learning the ins and outs of automake and I am attempting to
incorporate it into a project I am working on.  I have run into an issue
that has me at wits end as I can't seem to find a way around it.  I have a
project that will be comprised of two key subbranches: one containing C++
code that can be compiled into a couple of different libs and a second
branch that contains "mex" files.  When I say, "mex" file I specifically
mean a Matlab executable that can be compiled using mex.  I'd like to have
all of the C++ libraries built first and then all of the mex files second. 
The problem is that I don't know how to tell automake to switch to using the
mex compiler as opposed to g++.  This includes setting the options I want,
etc.  I looked into resetting the CC, CPP, etc... flags, but that seems
shady.  Even when I tried that, mex bailed b/c of unrecognized options that
automake is throwing at it.  Is there a clean way to accomplish what I am
trying do? If not, does anyone have any ideas on possible ways around this?

Bear with me, I am new to automake and am still learning :o)
Any advice would be greatly appreciated!

Thanks in advance!
Jason
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