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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required (VERSION 3.1)
project (MeshClust2)
include_directories(src/exception src/nonltr src/utility src/cluster src/prediction src/clutil src/fastcar)
set(CMAKE_BINARY_DIR ${CMAKE_SOURCE_DIR}/bin)
set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR})
set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR})
add_library(Fastcar
${CMAKE_SOURCE_DIR}/src/fastcar/FC_Runner.cpp
)
add_library(ClusterUtil
${CMAKE_SOURCE_DIR}/src/clutil/DivergencePoint.cpp
${CMAKE_SOURCE_DIR}/src/clutil/Histogram.cpp
${CMAKE_SOURCE_DIR}/src/clutil/Loader.cpp
${CMAKE_SOURCE_DIR}/src/clutil/SingleFileLoader.cpp
${CMAKE_SOURCE_DIR}/src/clutil/Progress.cpp
${CMAKE_SOURCE_DIR}/src/clutil/Datatype.cpp
${CMAKE_SOURCE_DIR}/src/clutil/Clock.cpp
)
add_library(Predict
${CMAKE_SOURCE_DIR}/src/predict/Feature.cpp
${CMAKE_SOURCE_DIR}/src/predict/GLM.cpp
${CMAKE_SOURCE_DIR}/src/predict/HandleSeq.cpp
${CMAKE_SOURCE_DIR}/src/predict/Matrix.cpp
${CMAKE_SOURCE_DIR}/src/predict/MultiMute.cpp
${CMAKE_SOURCE_DIR}/src/predict/Predictor.cpp
${CMAKE_SOURCE_DIR}/src/predict/SingMute.cpp
${CMAKE_SOURCE_DIR}/src/predict/FeatureSelector.cpp
${CMAKE_SOURCE_DIR}/src/predict/GreedySelector.cpp
${CMAKE_SOURCE_DIR}/src/predict/BestFirstSelector.cpp
)
add_library(Cluster
${CMAKE_SOURCE_DIR}/src/cluster/ClusterFactory.cpp
${CMAKE_SOURCE_DIR}/src/cluster/CRunner.cpp
${CMAKE_SOURCE_DIR}/src/cluster/Trainer.cpp
${CMAKE_SOURCE_DIR}/src/cluster/bvec.cpp
${CMAKE_SOURCE_DIR}/src/cluster/bvec_iterator.cpp
)
add_library(Exception
${CMAKE_SOURCE_DIR}/src/exception/FileDoesNotExistException.cpp
${CMAKE_SOURCE_DIR}/src/exception/InvalidInputException.cpp
${CMAKE_SOURCE_DIR}/src/exception/InvalidOperationException.cpp
${CMAKE_SOURCE_DIR}/src/exception/InvalidOrderOfOperationsException.cpp
${CMAKE_SOURCE_DIR}/src/exception/InvalidScoreException.cpp
${CMAKE_SOURCE_DIR}/src/exception/InvalidStateException.cpp
)
add_library(Nonltr
${CMAKE_SOURCE_DIR}/src/nonltr/ChromDetectorMaxima.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/ChromListMaker.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/Chromosome.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/ChromosomeOneDigit.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/ChromosomeOneDigitDna.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/ChromosomeOneDigitProtein.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/ChromosomeRandom.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/DetectorMaxima.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/HMM.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/LocationList.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/LocationListCollection.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/Scanner.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/Scorer.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/TableBuilder.cpp
${CMAKE_SOURCE_DIR}/src/nonltr/Trainer.cpp
)
add_library(Utility
${CMAKE_SOURCE_DIR}/src/utility/EmptyLocation.cpp
${CMAKE_SOURCE_DIR}/src/utility/GlobAlignE.cpp
${CMAKE_SOURCE_DIR}/src/utility/Location.cpp
${CMAKE_SOURCE_DIR}/src/utility/Util.cpp
)
target_include_directories(Exception PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(Nonltr PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(Utility PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(Cluster PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(Fastcar PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(ClusterUtil PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
target_include_directories(Predict PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
set (HEADER_FILES
${CMAKE_SOURCE_DIR}/src/nonltr/KmerHashTable.h
${CMAKE_SOURCE_DIR}/src/nonltr/EnrichmentMarkovView.h
${CMAKE_SOURCE_DIR}/src/nonltr/TableBuilder.h
)
set (CMAKE_CXX_COMPILER g++)
set (CMAKE_CXX_STANDARD 11)
set (CMAKE_CXX_STANDARD_REQUIRED on)
set (CMAKE_CXX_FLAGS "-fopenmp -g -O3 -march=native -std=c++11")
target_compile_definitions(Cluster PRIVATE VERSION="2.3.0")
target_compile_definitions(Fastcar PRIVATE VERSION="0.7.1")
add_executable(Red ${CMAKE_SOURCE_DIR}/src/nonltr/RepeatsDetector.cpp )
add_executable(meshclust2 ${CMAKE_SOURCE_DIR}/src/cluster/meshclust2.cpp)
add_executable(fastcar ${CMAKE_SOURCE_DIR}/src/fastcar/fastcar.cpp)
target_link_libraries(Red Exception Nonltr Utility ${HEADER_FILES})
target_link_libraries(Utility Exception ${HEADER_FILES})
target_link_libraries(Nonltr Utility Exception ${HEADER_FILES})
target_link_libraries(ClusterUtil Nonltr ${HEADER_FILES})
target_link_libraries(Predict ClusterUtil Nonltr ${HEADER_FILES})
target_link_libraries(meshclust2 Cluster Nonltr ClusterUtil Predict ${HEADER_FILES})
target_link_libraries(fastcar Nonltr ClusterUtil Fastcar Predict ${HEADER_FILES})