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|
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8491621..5717486 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,26 +11,21 @@ set(CMAKE_CXX_COMPILER clang++ CACHE STRING "C++ compiler" FORCE)
project(TopPIC_Suite)
message(STATUS "Project name: " ${PROJECT_NAME})
-set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/../bin)
+SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
message(STATUS "System name: " ${CMAKE_SYSTEM_NAME})
-# C++ flags
-# -Wall is used to enable all compiler warnings
-# -Wno-unknown-pragmas is used to disable pragmas warnings
+# C++ flags
+# -Wall is used to enable all compiler warnings
+# -Wno-unknown-pragmas is used to disable pragmas warnings
# -DWITHOUT_MZ5 is used in pwiz to exclude code for mz5 format support
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unknown-pragmas --std=c++17 -O3 -DWITHOUT_MZ5")
IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DTOPPIC_LINUX")
# --disable-new-dtags is needed to first search the shared library in the lib/toppic directory
- SET(CMAKE_SHARED_LINKER_FLAGS "-Wl,-rpath=$ORIGIN/../lib/toppic,--disable-new-dtags")
-ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
-
-IF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
- # fpermissive is needed to compile ext/pwiz/utility/misc/Filesystem.cpp
- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fpermissive -DTOPPIC_WINDOWS -DWIN32")
-ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ # SET(CMAKE_SHARED_LINKER_FLAGS "-Wl,-rpath=$ORIGIN/../lib/toppic,--disable-new-dtags")
+ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
message(STATUS "Cmake cxx flags: " ${CMAKE_CXX_FLAGS})
@@ -51,20 +46,35 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src
${Qt5Core_INCLUDE_DIRS}
${Qt5Gui_INCLUDE_DIRS})
-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/lib/toppic)
+#link_directories(${CMAKE_CURRENT_SOURCE_DIR}/lib/toppic)
+
+# Find package PwizLite
+find_package(PwizLite REQUIRED)
+message(STATUS "PwizLite_INCLUDE_DIRS: ${PwizLite_INCLUDE_DIRS}")
+message(STATUS "PwizLite_LIBRARIES: ${PwizLite_LIBRARIES}")
+
+# To find package htslib, we first need to resort to the pkg-config
+# program. Find it first.
+find_package(PkgConfig REQUIRED)
+if(PKG_CONFIG_FOUND)
+ message("The PkgConfig package was found.")
+else()
+ message("The PkgConfig package was not found.")
+endif()
-# pwiz
-file(GLOB PWIZ_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/utility/minimxml/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/utility/misc/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/data/common/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/data/msdata/*.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/ext/pwiz/data/msdata/mzmlb/*.cpp)
+# Now use it to search htslib (that is the name of the pc file).
+pkg_search_module(HtsLib REQUIRED IMPORTED_TARGET GLOBAL htslib libhts hts)
-# hts
-file(GLOB HTS_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/ext/htslib/*.c)
+message(STATUS "HtsLib_INCLUDE_DIRS: ${HtsLib_INCLUDE_DIRS}")
+message(STATUS "HtsLib_LIBRARIES: ${HtsLib_LIBRARIES}")
-# nowide source code used for the Windows version of TopFD
-file(GLOB NOWIDE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/ext/boost/nowide/*.c)
+find_package(Boost REQUIRED)
+
+find_package(RapidJSON REQUIRED)
+# Note that ONNX needs libprotobuf-dev that uses pkgconfig.
+pkg_search_module(ProtoBuf REQUIRED IMPORTED_TARGET GLOBAL protobuf)
+find_package(ONNX REQUIRED)
+find_package(onnxruntime REQUIRED)
# code shared by several executables
file(GLOB_RECURSE COMMON_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/common/*.cpp)
@@ -89,10 +99,10 @@ file(GLOB GUI_UTIL_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/util/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/common/xml/*.cpp)
-# topfd
+# topfd
file(GLOB_RECURSE TOPFD_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/topfd/*.cpp)
-# topfd console
+# topfd console
file(GLOB TOPFD_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd_argument.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topfd.cpp)
@@ -101,18 +111,18 @@ file(GLOB TOPFD_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/topfd/common/topfd_p
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topfd/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topfd/*.qrc)
-# topindex
+# topindex
file(GLOB FILTER_INDEX_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/filter/massmatch/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/filter/mng/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/filter/index/*.cpp)
# topindex console
file(GLOB TOPINDEX_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topindex_process.cpp
- ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topindex_argument.cpp)
+ ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topindex_argument.cpp)
file(GLOB TOPINDEX_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topindex.cpp)
-# topindex gui
+# topindex gui
file(GLOB TOPINDEX_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topindex/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topindex/*.qrc
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topindex_argument.cpp)
@@ -120,7 +130,7 @@ file(GLOB TOPINDEX_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topindex/*.cpp
# toppic
file(GLOB_RECURSE FILTER_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/filter/*.cpp)
-file(GLOB SEARCH_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/diag/*.cpp
+file(GLOB SEARCH_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/diag/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/search/zeroptmsearch/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/search/oneptmsearch/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/search/varptmsearch/*.cpp
@@ -139,7 +149,7 @@ file(GLOB TOPPIC_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/toppic_proce
file(GLOB TOPPIC_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/toppic.cpp)
-# toppic gui
+# toppic gui
file(GLOB TOPPIC_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/toppic/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/toppic/*.qrc
${CMAKE_CURRENT_SOURCE_DIR}/src/console/toppic_argument.cpp
@@ -154,7 +164,7 @@ file(GLOB GRAPH_ALIGN_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/diag/*.cpp
file(GLOB MCMC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/stat/count/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/stat/mcmc/*.cpp)
-# topmg console
+# topmg console
file(GLOB TOPMG_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg_process.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg_argument.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topindex_file_name.cpp
@@ -162,24 +172,24 @@ file(GLOB TOPMG_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg_proces
file(GLOB TOPMG_CONSOLE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg.cpp)
-# topmg gui
+# topmg gui
file(GLOB TOPMG_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topmg/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topmg/*.qrc
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topmg_argument.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/console_util.cpp)
-# topdiff
+# topdiff
file(GLOB DIFF_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/merge/*.cpp)
file(GLOB DIFF_SEARCH_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/search/duplicatematch/*.cpp)
-# topdiff console
+# topdiff console
file(GLOB TOPDIFF_PROC_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff_process.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff_argument.cpp)
file(GLOB TOPDIFF_CONSOLE_SRCS
${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff.cpp)
-# topdiff gui
+# topdiff gui
file(GLOB TOPDIFF_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdiff_argument.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topdiff/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topdiff/*.qrc)
@@ -198,36 +208,36 @@ file(GLOB TOPDIA_GUI_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/console/topdia_argumen
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topdia/*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/gui/topdia/*.qrc)
-# unit test
+# unit test
file(GLOB UNIT_TEST_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/src/test/*.cpp)
-add_executable(topfd
- ${TOPFD_CONSOLE_SRCS} ${TOPFD_SRCS} ${COMMON_SRCS} ${SQL_SRCS} ${PARA_SRCS}
- ${SPEC_SRCS} ${MZML_SRCS} ${PWIZ_SRCS} ${NOWIDE_SRCS})
+add_executable(topfd
+ ${TOPFD_CONSOLE_SRCS} ${TOPFD_SRCS} ${COMMON_SRCS} ${SQL_SRCS} ${PARA_SRCS}
+ ${SPEC_SRCS} ${MZML_SRCS})
-add_executable(topindex
- ${TOPINDEX_CONSOLE_SRCS} ${TOPINDEX_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
- ${SEQ_SRCS} ${PARA_SRCS} ${FILTER_INDEX_SRCS})
+add_executable(topindex
+ ${TOPINDEX_CONSOLE_SRCS} ${TOPINDEX_PROC_SRCS} ${COMMON_SRCS}
+ ${SEQ_SRCS} ${PARA_SRCS} ${FILTER_INDEX_SRCS})
-add_executable(toppic
- ${TOPPIC_CONSOLE_SRCS} ${TOPPIC_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
- ${SEQ_SRCS} ${PARA_SRCS} ${SPEC_SRCS}
- ${PRSM_SRCS} ${FILTER_SRCS} ${SEARCH_SRCS}
+add_executable(toppic
+ ${TOPPIC_CONSOLE_SRCS} ${TOPPIC_PROC_SRCS} ${COMMON_SRCS}
+ ${SEQ_SRCS} ${PARA_SRCS} ${SPEC_SRCS}
+ ${PRSM_SRCS} ${FILTER_SRCS} ${SEARCH_SRCS}
${TDGF_SRCS} ${LOCAL_SRCS} ${VISUAL_SRCS})
-add_executable(topmg
- ${TOPMG_CONSOLE_SRCS} ${TOPMG_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
- ${SEQ_SRCS} ${PARA_SRCS} ${SPEC_SRCS} ${PRSM_SRCS} ${FILTER_SRCS}
+add_executable(topmg
+ ${TOPMG_CONSOLE_SRCS} ${TOPMG_PROC_SRCS} ${COMMON_SRCS}
+ ${SEQ_SRCS} ${PARA_SRCS} ${SPEC_SRCS} ${PRSM_SRCS} ${FILTER_SRCS}
${GRAPH_ALIGN_SRCS} ${MCMC_SRCS} ${VISUAL_SRCS})
-add_executable(topdiff
- ${TOPDIFF_CONSOLE_SRCS} ${TOPDIFF_PROC_SRCS} ${HTS_SRCS} ${COMMON_SRCS}
- ${DIFF_SEARCH_SRCS} ${SEQ_SRCS} ${PARA_SRCS} ${SPEC_SRCS} ${PRSM_SRCS}
+add_executable(topdiff
+ ${TOPDIFF_CONSOLE_SRCS} ${TOPDIFF_PROC_SRCS} ${COMMON_SRCS}
+ ${DIFF_SEARCH_SRCS} ${SEQ_SRCS} ${PARA_SRCS} ${SPEC_SRCS} ${PRSM_SRCS}
${DIFF_SRCS})
add_executable(topdia
${TOPDIA_CONSOLE_SRCS} ${TOPDIA_SRCS} ${COMMON_SRCS} ${SQL_SRCS} ${PARA_SRCS}
- ${SPEC_SRCS} ${MZML_SRCS} ${TOPFD_SRCS} ${PWIZ_SRCS} ${NOWIDE_SRCS})
+ ${SPEC_SRCS} ${MZML_SRCS} ${TOPFD_SRCS})
add_executable(topfd_gui ${TOPFD_GUI_SRCS} ${GUI_UTIL_SRCS} ${SQL_SRCS})
@@ -241,96 +251,50 @@ add_executable(topdiff_gui ${TOPDIFF_GUI_SRCS} ${GUI_UTIL_SRCS})
add_executable(topdia_gui ${TOPDIA_GUI_SRCS} ${GUI_UTIL_SRCS} ${SQL_SRCS})
-IF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
- # onnx runtime library
- add_library(onnx_lib SHARED IMPORTED)
- set_property(TARGET onnx_lib PROPERTY IMPORTED_LOCATION ${CMAKE_CURRENT_SOURCE_DIR}/lib/windows/onnxruntime.dll)
- set_property(TARGET onnx_lib PROPERTY IMPORTED_IMPLIB ${CMAKE_CURRENT_SOURCE_DIR}/lib/windows/onnxruntime.lib)
-
- target_link_libraries(topfd boost_chrono-mt boost_filesystem-mt
- boost_program_options-mt boost_iostreams-mt boost_thread-mt
- boost_nowide-mt xerces-c sqlite3 z psapi Ws2_32 onnx_lib)
-
- target_link_libraries(topindex boost_program_options-mt
- boost_serialization-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(toppic boost_program_options-mt
- boost_serialization-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(topmg boost_program_options-mt
- boost_serialization-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(topdiff boost_program_options-mt
- boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(topdia boost_chrono-mt boost_filesystem-mt
- boost_program_options-mt boost_iostreams-mt boost_thread-mt
- boost_nowide-mt xerces-c sqlite3 z psapi Ws2_32 onnx_lib)
-
- # Qt
- SET(QTOPTION -Wl,-subsystem,windows)
- target_link_libraries(topfd_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
- boost_thread-mt xerces-c sqlite3 z Ws2_32)
-
- target_link_libraries(topindex_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
- boost_program_options-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(toppic_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
- boost_program_options-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(topmg_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
- boost_program_options-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(topdiff_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
- boost_program_options-mt boost_thread-mt xerces-c z Ws2_32)
-
- target_link_libraries(topdia_gui ${QTOPTION} Qt5Widgets Qt5Core Qt5Gui
- boost_program_options-mt boost_thread-mt xerces-c sqlite3 z Ws2_32)
-
-ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
-
# boost_chrono boost_file_system boost_iostreams boost_thread z are required by ProteoWizard
# boost_serialization boost_thread xerces-c z are required by toppic suite
IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
- target_link_libraries(topfd boost_chrono boost_filesystem boost_program_options
- boost_iostreams boost_thread xerces-c sqlite3 z onnxruntime)
+ target_link_libraries(topfd boost_chrono boost_filesystem boost_program_options
+ boost_iostreams boost_thread xerces-c sqlite3 PwizLite::PwizLite
+ z ONNX::onnx onnxruntime::onnxruntime)
- target_link_libraries(topindex boost_program_options
- boost_serialization boost_thread xerces-c z)
+ target_link_libraries(topindex boost_program_options
+ boost_serialization boost_thread xerces-c z PkgConfig::HtsLib)
target_link_libraries(toppic boost_program_options
- boost_serialization boost_thread xerces-c z)
+ boost_serialization boost_thread xerces-c z PkgConfig::HtsLib)
target_link_libraries(topmg boost_program_options
- boost_serialization boost_thread xerces-c z)
+ boost_serialization boost_thread xerces-c z PkgConfig::HtsLib)
target_link_libraries(topdiff boost_program_options
- boost_thread sqlite3 xerces-c z)
+ boost_thread sqlite3 xerces-c z PkgConfig::HtsLib)
- target_link_libraries(topdia boost_chrono boost_filesystem boost_program_options
- boost_iostreams boost_thread xerces-c sqlite3 z onnxruntime)
+ target_link_libraries(topdia boost_chrono boost_filesystem boost_program_options
+ boost_iostreams boost_thread xerces-c sqlite3 z onnxruntime PwizLite::PwizLite)
- target_link_libraries(topfd_gui Qt5Widgets Qt5Core Qt5Gui boost_thread xerces-c sqlite3)
+ target_link_libraries(topfd_gui Qt5Widgets Qt5Core Qt5Gui boost_thread xerces-c sqlite3 PwizLite::PwizLite)
target_link_libraries(topindex_gui Qt5Widgets Qt5Core Qt5Gui
- boost_program_options boost_thread xerces-c)
+ boost_program_options boost_thread xerces-c PwizLite::PwizLite)
- target_link_libraries(toppic_gui Qt5Widgets Qt5Core Qt5Gui
- boost_program_options boost_thread xerces-c)
+ target_link_libraries(toppic_gui Qt5Widgets Qt5Core Qt5Gui
+ boost_program_options boost_thread xerces-c PwizLite::PwizLite)
- target_link_libraries(topmg_gui Qt5Widgets Qt5Core Qt5Gui
- boost_program_options boost_thread xerces-c)
+ target_link_libraries(topmg_gui Qt5Widgets Qt5Core Qt5Gui
+ boost_program_options boost_thread xerces-c PwizLite::PwizLite)
target_link_libraries(topdiff_gui Qt5Widgets Qt5Core Qt5Gui
- boost_program_options boost_thread xerces-c)
+ boost_program_options boost_thread xerces-c PwizLite::PwizLite)
- target_link_libraries(topdia_gui Qt5Widgets Qt5Core Qt5Gui
+ target_link_libraries(topdia_gui Qt5Widgets Qt5Core Qt5Gui
boost_thread boost_program_options xerces-c sqlite3)
-install (TARGETS topfd topindex toppic topmg topdiff topdia topfd_gui topindex_gui
- toppic_gui topmg_gui topdiff_gui topdia_gui DESTINATION bin/)
-install (DIRECTORY resources/ DESTINATION etc/toppic)
-install (DIRECTORY lib/toppic DESTINATION lib/toppic)
+# Required for the canonical path for installations below.
+include(GNUInstallDirs)
-ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+install (TARGETS topfd topindex toppic topmg topdiff topdia topfd_gui topindex_gui
+ toppic_gui topmg_gui topdiff_gui topdia_gui DESTINATION ${CMAKE_INSTALL_BINDIR})
+install (DIRECTORY resources/ DESTINATION ${CMAKE_INSTALL_DATADIR}/toppic)
+ENDIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
|
