CMakeLists.txt

cmake_minimum_required(VERSION 3.13)  # CMake version check
project(simple_example)               # Create project "simple_example"
set(CMAKE_CXX_STANDARD 20)            # Enable c++20 standard

option(AVX_2 "Add compiler flags to support avx2 instructions" OFF)
option(AVX_512 "Add compiler flags to support avx512 instruction" OFF)

if (AVX_2)
    set(AVX_COMPILE_FLAGS "-mavx2 -march=skylake -DUSE_AVX_2=true")
endif ()

if (AVX_512)
    set(AVX_COMPILE_FLAGS "-mavx2 -march=skylake-avx512 -mavx512f -DUSE_AVX_512=true")
endif ()

set(CMAKE_CXX_FLAGS "-Ofast -pthread ${AVX_COMPILE_FLAGS} ")
# Add main.cpp file of project root directory as source file
set(SOURCE_FILES src/spectrum.cpp src/msp_reader.cpp src/scores.cpp src/library.cpp src/library.h src/mgf_reader.cpp src/mgf_reader.h src/spectral_search.h src/match.cpp src/match.h src/fragment_ion_index.cpp src/fragment_ion_index.h src/precursor_index.cpp src/precursor_index.h src/index_file_reader.h src/index_file_reader.cpp src/index_file_writer.cpp src/index_file_writer.h) #deleted src/spectral_search.cpp

include_directories(include) # Added argument_parser header-only library


# Add executable target with source files listed in SOURCE_FILES variable
#add_executable(test_executable src/main.cpp ${SOURCE_FILES})
#add_executable(quick_scan src/quick_scan.cpp ${SOURCE_FILES} src/scanner.cpp src/scanner.h)
add_executable(mistle-build src/build_index.cpp src/indexing_manager.cpp src/indexing_manager.h src/msp_reader.cpp src/msp_reader.h src/mgf_reader.cpp src/mgf_reader.h src/spectrum.h src/spectrum.cpp src/index_file_writer.cpp src/index_file_writer.h src/precursor_index.cpp src/precursor_index.h src/fragment_ion_index.cpp src/fragment_ion_index.h src/index_file_reader.cpp src/index_file_reader.h src/configuration.cpp src/configuration.h src/thread_pool.cpp src/thread_pool.h src/settings.cpp src/settings.h)
add_executable(mistle-search src/search_index.cpp src/indexing_manager.cpp src/indexing_manager.h src/msp_reader.cpp src/msp_reader.h src/spectrum.h src/spectrum.cpp src/index_file_writer.cpp src/index_file_writer.h src/precursor_index.cpp src/precursor_index.h src/fragment_ion_index.cpp src/fragment_ion_index.h src/index_file_reader.cpp src/index_file_reader.h src/search_manager.cpp src/search_manager.h src/configuration.cpp src/configuration.h src/library.cpp src/library.h src/mgf_reader.cpp src/mgf_reader.h src/match.cpp src/match.h src/thread_pool.cpp src/thread_pool.h src/settings.cpp src/settings.h)
#add_executable(naive-search src/naive_search.cpp src/library.cpp src/precursor_index.cpp src/msp_reader.cpp src/mgf_reader.cpp src/spectrum.cpp src/fragment_ion_index.cpp src/index_file_writer.cpp src/spectral_search.cpp src/scores.cpp src/match.cpp)
#add_executable(test-SIMD src/test_SIMD.cpp)