fix qt5 dependencies

debian/control.cmake

@@ -6,13 +6,13 @@ Homepage: http://pappso.inra.fr/bioinfo/gp/
 DM-Upload-Allowed: yes
 Uploaders: Olivier Langella <Olivier.Langella@moulon.inra.fr>
 Standards-Version: 1.0
-Build-Depends: debhelper (>= 7), dh-python, python, cmake (>= 2.6), libqt4-dev (>= 4.6.3), libpappsomspp-dev (= @LIBPAPPSOMSPP_VERSION@)
+Build-Depends: debhelper (>= 7), dh-python, python, cmake (>= 2.6), qt5-default, libpappsomspp-dev (= @LIBPAPPSOMSPP_VERSION@)
 Build-Conflicts: qt3-dev-tools
 
 
 
 Package: grouping-protein
 Architecture: linux-any
-Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends}, libqtcore4 (>= 4.6.3), denovopipeline-ng, libpappsomspp-qt4  (= @LIBPAPPSOMSPP_VERSION@)
+Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends}, libqt5concurrent5, libqt5core5a, libqt5xml5, denovopipeline-ng, libpappsomspp-qt5  (= @LIBPAPPSOMSPP_VERSION@)
 Description: Proteomics grouping algorithm
  Grouping-protein implements a fast algorithm that can filter thousands of peptides

src/cpp/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)
-FIND_PACKAGE( Qt4 REQUIRED )
+FIND_PACKAGE( Qt5 COMPONENTS Core Xml Concurrent REQUIRED )
 
 SET(GP_LIB_NAME "groupingprotein")
 SET(GP_LIB_VERSION ${GP_VERSION})
@@ -23,7 +18,7 @@ FIND_PACKAGE( Pappsomspp REQUIRED )
 
 #-std=c++11
 #SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Winline")
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+set(CMAKE_CXX_STANDARD 14)
 
 add_subdirectory(libgroupingprotein)
 add_subdirectory(bin)

src/cpp/bin/CMakeLists.txt

 
 INCLUDE_DIRECTORIES( ${CMAKE_SOURCE_DIR}/src/cpp/libgroupingprotein )
 
-
-# (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
-INCLUDE( ${QT_USE_FILE})
-
   
 SET(GP_GROUPING
   gp_grouping.cpp
@@ -19,18 +15,18 @@ SET(PG_FILTERPROTEINPEPTIDEORPHANS
 #TARGET_LINK_LIBRARIES(fastamanager ${PAPPSOMSPP_QT4_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTREAM_QT4_LIBRARY} ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY} ${QT_QTSVG_LIBRARY})
 
 ADD_EXECUTABLE(gp-grouping ${GP_GROUPING})
-target_include_directories (gp-grouping PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}  ${PAPPSOMSPP_INCLUDE_DIR})
-TARGET_LINK_LIBRARIES(gp-grouping ${GP_LIB_NAME} ${QT_LIBRARIES} ${PAPPSOMSPP_QT4_LIBRARY})
+target_include_directories (gp-grouping PUBLIC ${PAPPSOMSPP_INCLUDE_DIR} ${Qt5Core_INCLUDE_DIRS})
+TARGET_LINK_LIBRARIES(gp-grouping ${GP_LIB_NAME} Qt5::Core ${PAPPSOMSPP_QT5_LIBRARY})
 SET_TARGET_PROPERTIES(gp-grouping PROPERTIES OUTPUT_NAME gp-grouping)
 
 ADD_EXECUTABLE(pg-fastagrouper ${GP_FASTAGROUPER})
-target_include_directories (pg-fastagrouper PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}  ${PAPPSOMSPP_INCLUDE_DIR})
-TARGET_LINK_LIBRARIES(pg-fastagrouper ${GP_LIB_NAME} ${QT_LIBRARIES}  ${PAPPSOMSPP_QT4_LIBRARY})
+target_include_directories (pg-fastagrouper PUBLIC ${PAPPSOMSPP_INCLUDE_DIR} ${Qt5Core_INCLUDE_DIRS})
+TARGET_LINK_LIBRARIES(pg-fastagrouper ${GP_LIB_NAME} Qt5::Core ${PAPPSOMSPP_QT5_LIBRARY})
 SET_TARGET_PROPERTIES(pg-fastagrouper PROPERTIES OUTPUT_NAME pg-fastagrouper)
 
 ADD_EXECUTABLE(pg-filterproteinpeptideorphans ${PG_FILTERPROTEINPEPTIDEORPHANS} ${PAPPSOMSPP_QT4_LIBRARY})
-target_include_directories (pg-filterproteinpeptideorphans PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}  ${PAPPSOMSPP_INCLUDE_DIR})
-TARGET_LINK_LIBRARIES(pg-filterproteinpeptideorphans ${GP_LIB_NAME} ${QT_LIBRARIES} )
+target_include_directories (pg-filterproteinpeptideorphans PUBLIC ${PAPPSOMSPP_INCLUDE_DIR} ${Qt5Core_INCLUDE_DIRS})
+TARGET_LINK_LIBRARIES(pg-filterproteinpeptideorphans ${GP_LIB_NAME} Qt5::Core)
 SET_TARGET_PROPERTIES(pg-filterproteinpeptideorphans PROPERTIES OUTPUT_NAME pg-filterproteinpeptideorphans)
 
 INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/cpp/bin/gp-grouping DESTINATION bin)

src/cpp/libgroupingprotein/CMakeLists.txt

@@ -2,8 +2,6 @@
 MESSAGE("gp_lib_config.h.cmake gp_lib_config.h")
 configure_file (gp_lib_config.h.cmake ${CMAKE_SOURCE_DIR}/src/cpp/libgroupingprotein/gp_lib_config.h)
 
-# (QT_USE_FILE is a variable defined by FIND_PACKAGE( Qt4 ) that contains a path to CMake script)
-INCLUDE( ${QT_USE_FILE} )
 
 #SET(PG_LIB_MOC_HDRS
 #  pg_protseqengine.h
@@ -54,9 +52,10 @@ INCLUDE_DIRECTORIES( ${CMAKE_BINARY_DIR})
 
 
 
-  ADD_LIBRARY(${GP_LIB_NAME} SHARED ${GP_SRC_LIB} )
-target_include_directories (${GP_LIB_NAME} PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}  ${PAPPSOMSPP_INCLUDE_DIR})
-  TARGET_LINK_LIBRARIES(${GP_LIB_NAME} ${PAPPSOMSPP_QT4_LIBRARY} ${QT_QTCORE_LIBRARY})
+ADD_LIBRARY(${GP_LIB_NAME} SHARED ${GP_SRC_LIB} )
+
+target_include_directories (${GP_LIB_NAME} PUBLIC ${PAPPSOMSPP_INCLUDE_DIR} ${Qt5Core_INCLUDE_DIRS} ${Qt5Xml_INCLUDE_DIRS})
+TARGET_LINK_LIBRARIES(${GP_LIB_NAME} ${PAPPSOMSPP_QT5_LIBRARY} Qt5::Core Qt5::Xml Qt5::Concurrent)
 
   SET_TARGET_PROPERTIES(${GP_LIB_NAME} PROPERTIES 
     VERSION ${GP_LIB_VERSION}