cmake_minimum_required(VERSION 2.8.11)

project(SwiSpot)

macro(use_c99)
  if (CMAKE_VERSION VERSION_LESS "3.1")
    if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
      set (CMAKE_C_FLAGS "--std=gnu99 ${CMAKE_C_FLAGS}")
    endif ()
  else ()
    set (CMAKE_C_STANDARD 99)
  endif ()
endmacro(use_c99)

find_package(OpenMP)
if (OPENMP_FOUND)
    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()

include_directories(
    .
    /usr/local/include/ViennaRNA

)

# Linker options
set(CMAKE_LDFLAGS "${CMAKE_LDFLAGS}  ")

# Library path
set(CMAKE_LDFLAGS "${CMAKE_LDFLAGS} -L\".\" -L\"/usr/local/lib\" ")

# Define the C sources
set ( C_SRCS
    cluster.c
    SwiSpot.c
    confparse.c
)

set_source_files_properties(
    ${C_SRCS} PROPERTIES COMPILE_FLAGS 
    " -g -O0 -Wall")

add_executable(SwiSpot ${CXX_SRCS} ${C_SRCS})

target_link_libraries(SwiSpot
    RNA
    m
)
use_c99()
