CMakeLists.txt

# this command finds Qt4 libraries and sets all required variables
# note that it's Qt4, not QT4 or qt4

SET (QT_USE_QTXML true)
SET (QT_USE_QTXMLPATTERNS true)

SET(masschroq_RCCS resources.qrc)

if (MINGW32)
  FIND_PACKAGE( Qt4 REQUIRED )
ELSE (MINGW32)
  FIND_PACKAGE( Qt4 REQUIRED )
endif (MINGW32)

if (NOT ODSSTREAM_INCLUDE_DIR) 
FIND_PACKAGE( Odsstream REQUIRED )
endif (NOT ODSSTREAM_INCLUDE_DIR) 

INCLUDE_DIRECTORIES(${ODSSTREAM_INCLUDE_DIR})


# (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
INCLUDE( ${QT_USE_FILE} )

#sudo apt-get install libpappsomspp-dev
if (NOT PAPPSOMSPP_DIR) 
	FIND_PACKAGE( Pappsomspp REQUIRED )
endif (NOT PAPPSOMSPP_DIR)
#SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
#  SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
#  SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
#  SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/build/src/libpappsomspp-qt4.so")

INCLUDE_DIRECTORIES( ${PAPPSOMSPP_INCLUDE_DIR})


SET (GUI_UIS
	./gui/mcqgui.ui
)

SET(MASSCHROQ_LIB_MOC_HDRS
   ./masschroq_cli.h
)

SET(MASSCHROQ_LIB_SRCS
  ./masschroq_cli.cpp
  ./lib/consoleout.cpp
  ./lib/mcq_error.h
  ./lib/share/utilities.cpp

  ./lib/peptides/protein.cpp
  ./lib/peptides/peptide.cpp
  ./lib/peptides/peptide_isotope.cpp
  ./lib/peptides/peptide_observed_in.cpp
  ./lib/peptides/peptide_list.cpp
  ./lib/peptides/isotope_label.cpp
  ./lib/peptides/peptidert.cpp

  ./lib/quanti_items/quantiItemBase.cpp
  ./lib/quanti_items/quantiItemMzRt.cpp
  ./lib/quanti_items/quantiItemPeptide.cpp
  ./lib/quanti_items/quantiitempeptidenaturalisotope.cpp

  ./lib/msrun/spectrum.cpp
  ./lib/msrun/precursor.cpp

  ./lib/msrun/msrun.cpp
  ./lib/msrun/msrun_classic.cpp
  ./lib/msrun/slice.cpp
  ./lib/msrun/slicer.cpp
  ./lib/msrun/msrun_sliced.cpp
  ./lib/msrun/ms_run_hash_group.cpp

  ./lib/quantifications/quantificationMethod.cpp
  ./lib/quantifications/mapquanti.cpp
  ./lib/quantifications/mapquantirealxic.cpp
  ./lib/quantificator.cpp
  ./lib/mass_chroq.cpp

  ./lib/alignments/alignment_base.cpp
  ./lib/alignments/alignment_obiwarp.cpp
  ./lib/alignments/alignment_ms2.cpp
  ./lib/alignments/lmatreader.cpp

  ./lib/alignments/monitors/monitor_alignment_base.cpp
  ./lib/alignments/monitors/monitor_alignment_time.cpp
  ./lib/alignments/monitors/monitor_alignment_plot.cpp

  ./lib/xicExtractionMethods/xicExtractionMethodBase.cpp
  ./lib/xicExtractionMethods/xicExtractionMethodMzRange.cpp
  ./lib/xicExtractionMethods/xicExtractionMethodPpmRange.cpp

  ./lib/xic/alignedxicpeak.cpp
  ./lib/xic/xic_base.cpp
  ./lib/xic/xicfilterdetectmatch.cpp
  ./lib/xic/xicfilterdetectmatchrealrt.cpp
  ./lib/xic/xictracebase.cpp
  ./lib/xic/xictracepeptide.cpp
  ./lib/xic/xictracepeptidenaturalisotope.cpp
  ./lib/monitors/mcq_qxmlstreamwriter.cpp
  ./lib/monitors/masschroqWriter.cpp
  ./lib/monitors/monitorspeedinterface.cpp
  ./lib/monitors/monitorodsoutput.cpp
  ./lib/monitors/monitorspeedlist.cpp
  ./lib/monitors/monitorcomparoutput.cpp
  ./reporters/ReporterConsole.cpp

  )

SET(SAXLIB_SRCS
  ./encode/decodeBinary.cpp
  ./saxparsers/xmlSimpleParser.cpp
  ./saxparsers/mzxmlSimpleParser.cpp
  ./saxparsers/mzmlSimpleParser.cpp
  ./saxparsers/xmlSpectrumParser.cpp
  ./saxparsers/mzxmlSpectrumParser.cpp
  ./saxparsers/mzmlSpectrumParser.cpp
  ./saxparsers/xmlParserFactory.cpp
  ./saxparsers/xmlToLmatParser.cpp
  ./saxparsers/mzxmlToLmatParser.cpp
  ./saxparsers/mzmlToLmatParser.cpp
  ./saxparsers/masschroqmlParser.cpp
  ./pepfileparser/masschroq_dom_engine.cpp
  ./pepfileparser/pepParser.cpp
  )

SET(OBIWARP_SRCS
  ./libobiwarp/lmat.cpp
  ./libobiwarp/vec.cpp
  ./libobiwarp/mat.cpp
  ./libobiwarp/dynprog.cpp
  )

SET(GUI_SRCS
   ./gui/launcherMainWindow.cpp
   ./gui/thread/mcqThread.cpp
   ./gui/thread/masschroqRunningThread.cpp

   ./gui/logQIODevice.cpp
  )

SET(STUDIO_SRCS
   ./gui/parameterMainWindow.cpp

   ./gui/logQIODevice.cpp
   ./gui/masschroQWidget.cpp
   ./gui/runningQLabel.cpp
   ./gui/dom_methods/masschroqDomDocument.cpp
   ./gui/quantificationwidget/masschroqml_selection_widget.cpp
   ./gui/quantificationwidget/xicSelectionWidget.cpp
   ./gui/quantificationwidget/peptideSelectionWidget.cpp
   ./gui/quantificationwidget/filterBackgroundWidget.cpp
   ./gui/quantificationwidget/filterSpikeWidget.cpp
   ./gui/quantificationwidget/filterSmoothWidget.cpp
   ./gui/quantificationwidget/filterMinMaxWidget.cpp
   ./gui/quantificationwidget/filterMaxMinWidget.cpp
   ./gui/quantificationwidget/detectionZivyWidget.cpp
   ./gui/quantificationwidget/msrun_selection_widget.cpp
   ./gui/quantificationwidget/plot.cpp
   ./gui/alignementwidget/plot_aligned.cpp
   ./gui/alignementwidget/alignment_widget.cpp
   ./gui/alignementwidget/obiwarp_alignment_widget.cpp
   ./gui/alignementwidget/ms2_alignment_widget.cpp
   ./gui/thread/mcqThread.cpp
   ./gui/thread/msrunLoaderThread.cpp
   ./gui/thread/msrunSimpleLoaderThread.cpp
   ./gui/thread/masschroqmlLoaderThread.cpp
   ./gui/thread/masschroqml_gui_parser.cpp
   ./gui/thread/alignment_thread.cpp
   ./gui/engine/masschroq_gui_engin.cpp
   ./gui/engine/masschroq_gui_data.cpp
   ./gui/treatment/treatment_box.cpp
   ./gui/treatment/treatment_box_xic_extract.cpp
   ./gui/treatment/treatment_box_xic_filter.cpp
   ./gui/treatment/treatment_box_xic_detect.cpp
   ./gui/treatment/treatment_chain.cpp
   )

 # another list, this time it includes all header files that should be treated with moc
 SET(GUI_MOC_HDRS

   ./gui/logQIODevice.h
   ./gui/launcherMainWindow.h
   ./gui/thread/mcqThread.h
   ./gui/thread/masschroqRunningThread.h
  )

 SET(STUDIO_MOC_HDRS
   ./gui/parameterMainWindow.h
   ./gui/quantificationwidget/masschroqml_selection_widget.h
   ./gui/quantificationwidget/xicSelectionWidget.h
   ./gui/quantificationwidget/peptideSelectionWidget.h
   ./gui/quantificationwidget/filterBackgroundWidget.h
   ./gui/quantificationwidget/filterSpikeWidget.h
   ./gui/quantificationwidget/filterSmoothWidget.h
   ./gui/quantificationwidget/filterMinMaxWidget.h
   ./gui/quantificationwidget/filterMaxMinWidget.h
   ./gui/quantificationwidget/detectionZivyWidget.h
   ./gui/quantificationwidget/msrun_selection_widget.h
   ./gui/quantificationwidget/plot.h
   ./gui/alignementwidget/plot_aligned.h
   ./gui/alignementwidget/alignment_widget.h
   ./gui/alignementwidget/obiwarp_alignment_widget.h
   ./gui/alignementwidget/ms2_alignment_widget.h
   ./gui/thread/mcqThread.h
   ./gui/thread/msrunLoaderThread.h
   ./gui/thread/msrunSimpleLoaderThread.h
   ./gui/thread/masschroqmlLoaderThread.h
   ./gui/thread/alignment_thread.h

   ./gui/logQIODevice.h
   ./gui/runningQLabel.h
   ./gui/treatment/treatment_box.h
   ./gui/treatment/treatment_box_xic_extract.h
   ./gui/treatment/treatment_box_xic_filter.h
   ./gui/treatment/treatment_box_xic_detect.h
   )

set(CMAKE_MODULE_PATH ${masschroq_SOURCE_DIR}/modules)

QT4_WRAP_CPP( MASSCHROQ_LIB_MOC_SRCS ${MASSCHROQ_LIB_MOC_HDRS} )
QT4_ADD_RESOURCES(MASSCHROQ_RCC_SRCS_QT4 ${masschroq_RCCS})

IF (NOGUI)
ELSE (NOGUI)

	# this will run uic on .ui files:
	QT4_WRAP_UI( GUI_UI_HDRS ${GUI_UIS} )

	QT4_WRAP_CPP( GUI_MOC_SRCS ${GUI_MOC_HDRS} )

	IF (NOQWT)
		INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR})
  	ELSE (NOQWT)
 		set(Qwt5_DIR ${masschroq_SOURCE_DIR}/Modules)
 		FIND_PACKAGE(Qwt5 REQUIRED)
 		# and finally this will run moc:
 		QT4_WRAP_CPP( STUDIO_MOC_SRCS ${STUDIO_MOC_HDRS} )
		# we need this to be able to include headers produced by uic in our code
		# (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
		INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR} ${Qwt5_INCLUDE_DIR})
  	ENDIF (NOQWT)

  # this command will generate rules that will run rcc on all files from SAMPLE_RCS
  # in result SAMPLE_RC_SRCS variable will contain paths to files produced by rcc
  #QT4_ADD_RESOURCES( SAMPLE_RC_SRCS ${SAMPLE_RCS} )

 
ENDIF (NOGUI)


# we need this to be able to include headers produced by uic in our code
  # (CMAKE_BINARY_DIR holds a path to the build directory, while INCLUDE_DIRECTORIES() works just like INCLUDEPATH from qmake)
  INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_BINARY_DIR} )

IF (MINGW32)
  ADD_EXECUTABLE(masschroq main.cpp  ${MASSCHROQ_LIB_SRCS} ${MASSCHROQ_LIB_MOC_SRCS}
      ${SAXLIB_SRCS} ${OBIWARP_SRCS} ${MASSCHROQ_RCC_SRCS_QT4})
  TARGET_LINK_LIBRARIES(masschroq ${QT_LIBRARIES}  )
  SET_TARGET_PROPERTIES(masschroq PROPERTIES LINK_FLAGS "-Wl,--subsystem,console ${ADD_MINGW_EXE_LINKER_FLAGS}")

  IF (NOGUI)

  ELSE (NOGUI)

    ADD_EXECUTABLE(masschroq_gui gui/launcherGui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS} ${MASSCHROQ_LIB_SRCS}  
    ${MASSCHROQ_LIB_MOC_SRCS} ${SAXLIB_SRCS} ${OBIWARP_SRCS} ${GUI_UI_HDRS} ${MASSCHROQ_RCC_SRCS_QT4})
    TARGET_LINK_LIBRARIES(masschroq_gui ${QT_LIBRARIES})
    SET_TARGET_PROPERTIES(masschroq_gui PROPERTIES LINK_FLAGS "-Wl,--subsystem,windows ${ADD_MINGW_EXE_LINKER_FLAGS}")

	IF (NOQWT)
  	ELSE (NOQWT)
  	    ADD_EXECUTABLE(masschroq_studio gui/parameterGui.cpp ${STUDIO_SRCS} ${STUDIO_MOC_SRCS} ${MASSCHROQ_LIB_SRCS}  ${MASSCHROQ_LIB_MOC_SRCS} ${SAXLIB_SRCS} ${OBIWARP_SRCS})
    	TARGET_LINK_LIBRARIES(masschroq_studio ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
    	SET_TARGET_PROPERTIES(masschroq_studio PROPERTIES LINK_FLAGS "-Wl,--enable-auto-import  -Wl,--subsystem,windows ${ADD_MINGW_EXE_LINKER_FLAGS}")
  	ENDIF (NOQWT)

 ENDIF (NOGUI)

ELSE (MINGW32)

  ADD_LIBRARY(${MASSCHROQ_LIB_NAME} SHARED ${MASSCHROQ_LIB_SRCS}  ${MASSCHROQ_LIB_MOC_SRCS}
    ${SAXLIB_SRCS} ${OBIWARP_SRCS} ${MASSCHROQ_RCC_SRCS_QT4})

  SET_TARGET_PROPERTIES(${MASSCHROQ_LIB_NAME} PROPERTIES
    VERSION ${MASSCHROQ_LIB_VERSION}
    SOVERSION ${MASSCHROQ_LIB_SOVERSION}
    )

  ADD_EXECUTABLE(masschroq_main main.cpp)
  TARGET_LINK_LIBRARIES(masschroq_main ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${PAPPSOMSPP_QT4_LIBRARY} ${ODSSTREAM_QT4_LIBRARY})
  SET_TARGET_PROPERTIES(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
  #add new executable called new_parseur
  #ADD_EXECUTABLE(new_parseur parseur.cpp)
  #TARGET_LINK_LIBRARIES(new_parseur ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES})

  INSTALL(TARGETS ${MASSCHROQ_LIB_NAME}  DESTINATION lib)

  IF (NOGUI)
  ELSE (NOGUI)


    ADD_EXECUTABLE(masschroq_gui gui/launcherGui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS} ${GUI_UI_HDRS})
    TARGET_LINK_LIBRARIES(masschroq_gui ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY}  ${PAPPSOMSPP_QT4_LIBRARY} ${ODSSTREAM_QT4_LIBRARY})

    IF (NOQWT)
  	ELSE (NOQWT)
		ADD_EXECUTABLE(masschroq_studio gui/parameterGui.cpp ${STUDIO_SRCS} ${STUDIO_MOC_SRCS})
		TARGET_LINK_LIBRARIES(masschroq_studio ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY}  ${PAPPSOMSPP_QT4_LIBRARY} ${ODSSTREAM_QT4_LIBRARY})
 	ENDIF (NOQWT)

  ENDIF (NOGUI)
ENDIF(MINGW32)

#if lib quanti is graphical
#TARGET_LINK_LIBRARIES(masschroq libmasschroq ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})