AC_INIT([exp007], [0.1], [don@drexel.edu])
AM_INIT_AUTOMAKE([-Wall, -Werror, -Wno-portability])
AC_PROG_CC
AM_CONFIG_HEADER([config.h])
AC_CONFIG_FILES([
	Makefile
	src/Makefile
])

# Headers Checks

AC_CHECK_HEADERS([ncbi.h],[],
[AC_MSG_ERROR("The NCBI Toolkit headers are needed to build the system.")])

AC_CHECK_HEADERS([hdf5.h],[],
[AC_MSG_ERROR("The HDF5 headers are needed to build the system.")])

AC_CHECK_HEADERS([petscconf.h],[],
[AC_MSG_ERROR("The PETSc headers are needed to build the system.")])

AC_CHECK_HEADERS([petscmat.h],[],
[AC_MSG_ERROR("The PETSc headers are needed to build the system.")])

AC_CHECK_HEADERS([libxml/parser.h],[],
[AC_MSG_ERROR("The libxml2 headers are needed to build the system.")])

########################
# MODULE: NCBI Toolkit #
########################

# Check for the NCBI ToolBox libraries.
AC_SEARCH_LIBS([log10],[m],[],
[AC_MSG_ERROR("The C Math Library is needed to build the system.")])

AC_SEARCH_LIBS([NlmThreadsAvailable],[ncbi],[],
[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")])

AC_SEARCH_LIBS([SeqAlignNew],[ncbiobj],[],
[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")])

AC_SEARCH_LIBS([Blast_RedoOneMatch],[blastcompadj],[],
[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")])

AC_SEARCH_LIBS([BioseqBlastEngine],[ncbitool],[],
[AC_MSG_ERROR("The NCBI ToolBox is needed to build the system. Information on this API can be found on-line at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi. Debian users can add the package libncbi6-dev to fulfill this dependency.")])

################
# MODULE: HDF5 #
################

AC_SEARCH_LIBS([__intel_rtc_uninit_use],[irc])
AC_SEARCH_LIBS([MPI_File_open],[mpi])
AC_SEARCH_LIBS([compress2],[z])
AC_SEARCH_LIBS([SZ_BufftoBuffCompress],[sz])

AC_SEARCH_LIBS([H5Fcreate],[hdf5],[],
[AC_MSG_ERROR("The HDF5 libraries are needed to build the system.")])

AC_SEARCH_LIBS([H5TBmake_table],[hdf5_hl],[],
[AC_MSG_ERROR("The HDF5 libraries are needed to build the system.")])

#################
# MODULE: PETSc #
#################

AC_SEARCH_LIBS([pthread_atfork],[pthread])

AC_SEARCH_LIBS([PetscInitialize],[petsc],[],
[AC_MSG_ERROR("The Portable Extensible Toolkit for Scientific Computation (PETSc) is needed to build the system.")])

# The AC_SEARCH_LIBS other-libraries list is not particularly useful.
# Autoconf determines if the other-libraries are necessary however in
# the cases where they are indeed necessary they are not actually
# added to the library list.

# These are the dependencies.  Random functions are selected from
# these libraries from the list of otherwise undefined references at
# link time.
AC_SEARCH_LIBS([VecNorm],[petscvec])

# MatCreateSeqAIJ is acutally used in the code for this project.
AC_SEARCH_LIBS([MatCreateSeqAIJ],[petscmat],[],
[AC_MSG_ERROR("The Portable Extensible Toolkit for Scientific Computation (PETSc) is needed to build the system.")])

###################
# MODULE: libxml2 #
###################
AC_SEARCH_LIBS([xmlCreatePushParserCtxt],[xml2],[],
[AC_MSG_ERROR("The libxml2 library is needed to build the system.")])

AC_OUTPUT