
# add the library that runs 
add_library(Aln align.cc align_smx.cc asset.cc cmafull.cc cmsa.cc cmsa_emit_sq.cc cmsa_io.cc cmsa_map.cc cmsa_operations.cc cmsa_put.cc cmsa_recombine.cc cmsa_recombine_gaps.cc cmsa_rtf.cc cmsa_sample.cc cmsa_sma.cc colwt.cc dfps.cc dom_typ.cc eblocks.cc evalue.cc fmodel.cc fsm.cc genetic.cc gibbs.cc mdl.cc mem_typ.cc msaheap.cc msites.cc oscan.cc pah_typ.cc pairaln.cc pattern.cc pheap.cc profile.cc prtn_model.cc psialn.cc sample_smx.cc scanheap.cc scaninfo.cc sites.cc sma.cc smatrix.cc smooth.cc sseq.cc strctprof.cc swt_hsw.cc swt_typ.cc watchgibbs.cc wmodel.cc )

# state that anybody linking to us needs to include the current source dir
# to find MathFunctions.h, while we don't.
include_directories("${PROJECT_SOURCE_DIR}/lib/libaln"
	"${PROJECT_SOURCE_DIR}/lib/libgsq"
	"${PROJECT_SOURCE_DIR}/lib/libafn"
	"${PROJECT_SOURCE_DIR}/lib/include") 

target_link_libraries(Aln Afn Gsq )

list(APPEND EXTRA_LIBS Afn Gsq)
#list(APPEND EXTRA_INCLUDES "${PROJECT_SOURCE_DIR}/lib/libafn"
#        "${PROJECT_SOURCE_DIR}/lib/libgsq"
#        "${PROJECT_SOURCE_DIR}/lib/libaln"
#        "${PROJECT_SOURCE_DIR}/lib/include" )

target_include_directories(Aln
                           INTERFACE
                            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
                            $<INSTALL_INTERFACE:include>)

#target_compile_definitions(Aln PRIVATE "$<$<BOOL:${USE_MYMATH}>:USE_MYMATH>")

# define the symbol stating we are using the declspec(dllexport) when
# building on windows
#target_compile_definitions(Aln PRIVATE "EXPORTING_MYMATH")

# setup the version numbering
set_property(TARGET Aln PROPERTY VERSION "1.0.0")
set_property(TARGET Aln PROPERTY SOVERSION "1")

install(TARGETS Aln
        DESTINATION lib
        EXPORT AlnTargets)
install(FILES MathFunctions.h DESTINATION include)

