include added to compile with mingw64

CMakeLists.txt

@@ -36,10 +36,10 @@ SET (MASSCHROQ_SCHEMA_VERSION "${MASSCHROQ_MAJOR_VERSION}.2")
 
 #SET (CMAKE_INSTALL_SO_NO_EXE "0")
 
-IF (MINGW32)
-ELSE (MINGW32)
+#IF (MINGW32)
+#ELSE (MINGW32)
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-ENDIF(MINGW32)
+#ENDIF(MINGW32)
 
 
 IF (CMAKE_SYSTEM_NAME MATCHES "Windows")

masschroq.kdev4

 [Project]
+CreatedFrom=masschroq
 Manager=KDevCMakeManager
 Name=masschroq

src/CMakeLists.txt

@@ -13,7 +13,9 @@ 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})
 
@@ -22,13 +24,15 @@ INCLUDE_DIRECTORIES(${ODSSTREAM_INCLUDE_DIR})
 INCLUDE( ${QT_USE_FILE} )
 
 #sudo apt-get install libpappsomspp-dev
-FIND_PACKAGE( Pappsomspp REQUIRED )
+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} )
+INCLUDE_DIRECTORIES( ${PAPPSOMSPP_INCLUDE_DIR})
 
 
 SET (GUI_UIS
@@ -291,7 +295,7 @@ ELSE (MINGW32)
   #ADD_EXECUTABLE(new_parseur parseur.cpp)
   #TARGET_LINK_LIBRARIES(new_parseur ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES})
 
-  INSTALL(TARGETS ${MASSCHROQ_LIB_NAME} LIBRARY DESTINATION lib)
+  INSTALL(TARGETS ${MASSCHROQ_LIB_NAME}  DESTINATION lib)
 
   IF (NOGUI)
   ELSE (NOGUI)

src/lib/peptides/peptidert.cpp

@@ -24,6 +24,8 @@
 #include "peptidert.h"
 #include <QDebug>
 #include <pappsomspp/xic/xicpeak.h>
+#include <cmath>
+#include <numeric>
 #include "../mcq_error.h"
 
 PeptideRt::PeptideRt()

src/lib/quantifications/mapquanti.cpp

@@ -27,6 +27,7 @@
 #include "../xic/xic_base.h"
 #include "../xic/xictracebase.h"
 #include "../consoleout.h"
+#include <cmath>
 
 MapQuanti::MapQuanti(MonitorSpeedInterface & monitor, Msrun * current_msrun, McqXicType xic_type, Quantificator * quantificator,
                      const pappso::XicFilterInterface * p_xic_filter,const pappso::XicDetectionInterface * p_detection)

src/lib/xic/xicfilterdetectmatch.cpp

@@ -25,6 +25,7 @@
 #include <pappsomspp/xic/detection/xicdetectioninterface.h>
 #include <pappsomspp/xic/xicpeak.h>
 #include "../consoleout.h"
+#include <cmath>
 
 XicFilterDetectMatch::XicFilterDetectMatch(XicTraceBase * p_trace, MonitorSpeedInterface & monitor, const pappso::XicFilterInterface * p_xic_filter,const pappso::XicDetectionInterface * p_detection, McqMatchingMode matching_mode)
     :_monitor(monitor)

src/masschroq_cli.cpp

@@ -38,10 +38,10 @@ masschroqCli::masschroqCli(QObject *parent) :
 void
 masschroqCli::windaube_exit()
 {
-#  if (WIN32)
+//#if (WIN32)
 //    mcqout() << "Press any key then enter to exit" << endl;
 //    getchar();
-#endif
+//#endif
 }
 
 void

win64/Toolchain-mingw64.cmake

@@ -5,10 +5,10 @@
 # cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=../win64/Toolchain-mingw64.cmake ..
 
 SET (NOGUI 0)
-SET (NOQWT 0)
+SET (NOQWT 1)
 # scp index.html tryphon@bioinformatics.org:~/public_html/populations
 #
-SET (MINGW32 1)
+#SET (MINGW32 1)
 #SET (WIN32 1)
 
 # this one is important
@@ -16,7 +16,7 @@ SET(CMAKE_SYSTEM_NAME Windows)
 #this one not so much
 SET(CMAKE_SYSTEM_VERSION 1)
 
-SET (WINDAUBE_ENV_PATH /opt/win64)
+SET (WINDAUBE_ENV_PATH /home/langella/opt)
 # it worked on 27 nov 2013 :
 # download and install from http://download.qt-project.org/archive/qt/4.8/4.8.2/ the mingw32 version
 
@@ -28,6 +28,20 @@ SET(QT_PREFIX    ${WINDAUBE_ENV_PATH}/Qt64-4.8.6)
 #SET(QWT_PREFIX  /usr/local/src/mingw32_f15/qwt-5.2.1/i686-pc-mingw32/sys-root/mingw)
 #SET(QWT_PREFIX  /usr/local/src/mingw_qwt/usr/i686-pc-mingw32/sys-root/mingw)
 SET(QWT_PREFIX  ${WINDAUBE_ENV_PATH}/qwt-5.2.2)
+SET(QT_PREFIX    ${WINDAUBE_ENV_PATH}/qt-4.8.7)
+SET(QT5_PREFIX    ${WINDAUBE_ENV_PATH}/qt-5.6.0)
+
+SET (ZLIB_INCLUDE_DIR "/home/langella/opt/zlib-1.2.8/include")
+SET (QUAZIP_INCLUDE_DIR "/home/langella/opt/quazip-0.7.2")
+
+SET (ODSSTREAM_DIR "/home/langella/developpement/git/libodsstream")
+SET (ODSSTREAM_INCLUDE_DIR "${ODSSTREAM_DIR}/src")
+SET (ODSSTREAM_QT4_LIBRARY "${ODSSTREAM_DIR}/buildw64/src/libodsstream-qt4.dll.a")
+
+  SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+  SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+  SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/buildw64/src/libpappsomspp-qt4.dll.a")
+
 
 #SET(QT_MOC_EXECUTABLE      /usr/local/src/QtSDK/Desktop/Qt/4.8.1/gcc/bin/moc)
 #SET(QMAKE_UIC      /usr/local/src/QtSDK/Desktop/Qt/4.8.1/gcc/bin/uic)
@@ -42,9 +56,11 @@ SET(CMAKE_C_COMPILER   /usr/bin/x86_64-w64-mingw32-gcc)
 SET(CMAKE_CXX_COMPILER /usr/bin/x86_64-w64-mingw32-g++)
 SET(CMAKE_RC_COMPILER /usr/bin/x86_64-w64-mingw32-windres)
 
+INCLUDE_DIRECTORIES( ${QUAZIP_INCLUDE_DIR} ${ZLIB_INCLUDE_DIR})
+
 # where is the target environment
 #http://qt.nokia.com/downloads/windows-cpp
-SET(CMAKE_FIND_ROOT_PATH  /usr/i586-mingw32msvc ${QT_PREFIX} ${QWT_PREFIX})
+SET(CMAKE_FIND_ROOT_PATH  /usr/i586-mingw32msvc ${QT_PREFIX} ${QWT_PREFIX} )
 #SET(CMAKE_FIND_ROOT_PATH  /usr/local/src/mingw32_f15/glibc-2.13 /usr/local/src/mingw32_f15/gcc-4.5.3/i686-pc-mingw32/sys-root/mingw ${QT_PREFIX} ${QWT_PREFIX})
 
 # search for programs in the build host directories