Commit 588a5e48 authored by Langella Olivier's avatar Langella Olivier
Browse files

bunch of warnings fixed

parent 735602b8
SET (QT_USE_QTXML true)
SET (QT_USE_QTXMLPATTERNS true)
set (QT_USE_QTXML true)
set (QT_USE_QTXMLPATTERNS true)
SET(masschroq_RCCS resources.qrc)
set(masschroq_RCCS resources.qrc)
FIND_PACKAGE( Qt5 COMPONENTS Core Gui Xml XmlPatterns Widgets Concurrent PrintSupport REQUIRED )
find_package( Qt5 COMPONENTS Core Gui Xml XmlPatterns Widgets Concurrent PrintSupport REQUIRED )
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/modules)
......@@ -17,46 +17,43 @@ set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/modules)
if (QCustomPlot_FOUND)
else (QCustomPlot_FOUND)
FIND_PACKAGE( QCustomPlot REQUIRED )
find_package( QCustomPlot REQUIRED )
endif (QCustomPlot_FOUND)
if (OdsStream_FOUND)
else (OdsStream_FOUND)
FIND_PACKAGE( OdsStream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
find_package( OdsStream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
endif (OdsStream_FOUND)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5Gui_EXECUTABLE_COMPILE_FLAGS} ${Qt5Svg_EXECUTABLE_COMPILE_FLAGS}")
#sudo apt-get install libpappsomspp-dev
if (PappsoMSpp_FOUND)
else (PappsoMSpp_FOUND)
MESSAGE("looking for PAPPSOms++ library")
FIND_PACKAGE( PappsoMSpp REQUIRED )
message("looking for PAPPSOms++ library")
find_package( PappsoMSpp REQUIRED )
endif (PappsoMSpp_FOUND)
IF (PappsoMSpp_FOUND)
ELSE (PappsoMSpp_FOUND)
MESSAGE("PAPPSOms++ library not found")
MESSAGE("did you apt-get install libpappsomspp-dev ?")
ENDIF (PappsoMSpp_FOUND)
if (PappsoMSpp_FOUND)
else (PappsoMSpp_FOUND)
message("PAPPSOms++ library not found")
message("did you apt-get install libpappsomspp-dev ?")
endif (PappsoMSpp_FOUND)
IF (PappsoMSppWidget_FOUND)
ELSE (PappsoMSppWidget_FOUND)
MESSAGE("PAPPSOms++ widget library not found")
MESSAGE("did you apt-get install libpappsomspp-widget-dev ?")
ENDIF (PappsoMSppWidget_FOUND)
if (PappsoMSppWidget_FOUND)
else (PappsoMSppWidget_FOUND)
message("PAPPSOms++ widget library not found")
message("did you apt-get install libpappsomspp-widget-dev ?")
endif (PappsoMSppWidget_FOUND)
SET (GUI_UIS
set (GUI_UIS
./gui/mcqgui/mcqgui.ui
)
SET(MASSCHROQ_LIB_SRCS
set(MASSCHROQ_LIB_SRCS
./masschroq_cli.cpp
./mcqsession.cpp
./lib/consoleout.cpp
......@@ -119,7 +116,7 @@ SET(MASSCHROQ_LIB_SRCS
)
SET(SAXLIB_SRCS
set(SAXLIB_SRCS
./encode/decodeBinary.cpp
./saxparsers/xmlSimpleParser.cpp
# ./saxparsers/mzxmlSimpleParser.cpp
......@@ -133,14 +130,14 @@ SET(SAXLIB_SRCS
./pepfileparser/pepParser.cpp
)
SET(OBIWARP_SRCS
set(OBIWARP_SRCS
./libobiwarp/lmat.cpp
./libobiwarp/vec.cpp
./libobiwarp/mat.cpp
./libobiwarp/dynprog.cpp
)
SET(GUI_SRCS
set(GUI_SRCS
./gui/mcqgui/guiworkerthread.cpp
./gui/mcqgui/launcherMainWindow.cpp
./gui/thread/mcqThread.cpp
......@@ -148,7 +145,7 @@ SET(GUI_SRCS
./gui/logQIODevice.cpp
)
SET(STUDIO_SRCS
set(STUDIO_SRCS
./gui/parameterMainWindow.cpp
./gui/logQIODevice.cpp
......@@ -187,21 +184,21 @@ SET(STUDIO_SRCS
QT5_ADD_RESOURCES(MASSCHROQ_RCC_SRCS_QT5 ${masschroq_RCCS})
qt5_add_resources(MASSCHROQ_RCC_SRCS_QT5 ${masschroq_RCCS})
IF (NOGUI)
ELSE (NOGUI)
if (NOGUI)
else (NOGUI)
# this will run uic on .ui files:
QT5_WRAP_UI( GUI_UI_HDRS ${GUI_UIS} )
qt5_wrap_ui( GUI_UI_HDRS ${GUI_UIS} )
ENDIF (NOGUI)
endif (NOGUI)
ADD_LIBRARY(${MASSCHROQ_LIB_NAME} SHARED ${MASSCHROQ_LIB_SRCS} ${MASSCHROQ_LIB_MOC_SRCS}
add_library(${MASSCHROQ_LIB_NAME} SHARED ${MASSCHROQ_LIB_SRCS} ${MASSCHROQ_LIB_MOC_SRCS}
${SAXLIB_SRCS} ${OBIWARP_SRCS} ${MASSCHROQ_RCC_SRCS_QT5})
TARGET_LINK_LIBRARIES(${MASSCHROQ_LIB_NAME}
target_link_libraries(${MASSCHROQ_LIB_NAME}
PappsoMSpp::Core
PappsoMSpp::Widget
OdsStream::Core
......@@ -215,13 +212,13 @@ target_include_directories (${MASSCHROQ_LIB_NAME} PUBLIC
${QCustomPlot_INCLUDES}
${QUAZIP_INCLUDE_DIR}
)
SET_TARGET_PROPERTIES(${MASSCHROQ_LIB_NAME} PROPERTIES
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}
add_executable(masschroq_main main.cpp)
target_link_libraries(masschroq_main ${MASSCHROQ_LIB_NAME}
PappsoMSpp::Core
PappsoMSpp::Widget
OdsStream::Core
......@@ -234,16 +231,16 @@ TARGET_LINK_LIBRARIES(masschroq_main ${MASSCHROQ_LIB_NAME}
${Boost_thread_LIBRARY}
Qt5::Core
)
SET_TARGET_PROPERTIES(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
set_target_properties(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
target_include_directories (masschroq_main PUBLIC
${QUAZIP_INCLUDE_DIR}
)
IF (NOGUI)
ELSE (NOGUI)
ADD_EXECUTABLE(masschroq_gui gui/mcqgui/launcherGui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS} ${GUI_UI_HDRS})
TARGET_LINK_LIBRARIES(masschroq_gui ${MASSCHROQ_LIB_NAME}
if (NOGUI)
else (NOGUI)
add_executable(masschroq_gui gui/mcqgui/launcherGui.cpp ${GUI_SRCS} ${GUI_MOC_SRCS} ${GUI_UI_HDRS})
target_link_libraries(masschroq_gui ${MASSCHROQ_LIB_NAME}
PappsoMSpp::Core
PappsoMSpp::Widget
OdsStream::Core
......@@ -259,8 +256,8 @@ ELSE (NOGUI)
${Boost_thread_LIBRARY}
)
ADD_EXECUTABLE(masschroq_studio gui/parameterGui.cpp ${STUDIO_SRCS} ${STUDIO_MOC_SRCS})
TARGET_LINK_LIBRARIES(masschroq_studio ${MASSCHROQ_LIB_NAME}
add_executable(masschroq_studio gui/parameterGui.cpp ${STUDIO_SRCS} ${STUDIO_MOC_SRCS})
target_link_libraries(masschroq_studio ${MASSCHROQ_LIB_NAME}
PappsoMSpp::Core
PappsoMSpp::Widget
OdsStream::Core
......@@ -277,30 +274,30 @@ ELSE (NOGUI)
${Boost_system_LIBRARY}
${Boost_thread_LIBRARY}
)
ENDIF (NOGUI)
endif (NOGUI)
IF (MXE)
SET_TARGET_PROPERTIES(masschroq_main PROPERTIES LINK_FLAGS "-Wl,--subsystem,console ${CMAKE_EXE_LINKER_FLAGS}")
if (MXE)
set_target_properties(masschroq_main PROPERTIES LINK_FLAGS "-Wl,--subsystem,console ${CMAKE_EXE_LINKER_FLAGS}")
target_compile_options(
masschroq_gui PRIVATE -mwindows
)
SET_TARGET_PROPERTIES(masschroq_gui PROPERTIES LINK_FLAGS "-Wl,--subsystem,windows ${CMAKE_EXE_LINKER_FLAGS}")
set_target_properties(masschroq_gui PROPERTIES LINK_FLAGS "-Wl,--subsystem,windows ${CMAKE_EXE_LINKER_FLAGS}")
target_compile_options(
masschroq_studio PRIVATE -mwindows
)
SET_TARGET_PROPERTIES(masschroq_studio PROPERTIES LINK_FLAGS "-Wl,--enable-auto-import -Wl,--subsystem,windows ${CMAKE_EXE_LINKER_FLAGS}")
set_target_properties(masschroq_studio PROPERTIES LINK_FLAGS "-Wl,--enable-auto-import -Wl,--subsystem,windows ${CMAKE_EXE_LINKER_FLAGS}")
ELSE (MXE)
else (MXE)
#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} LIBRARY DESTINATION lib)
install(TARGETS ${MASSCHROQ_LIB_NAME} LIBRARY DESTINATION lib)
ENDIF(MXE)
endif(MXE)
#if lib quanti is graphical
#TARGET_LINK_LIBRARIES(masschroq libmasschroq ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
......@@ -16,6 +16,7 @@ MasschroQWidget::~MasschroQWidget()
}
void
MasschroQWidget::writeElement(MasschroqDomDocument *domDocument) const
MasschroQWidget::writeElement(MasschroqDomDocument *domDocument
[[maybe_unused]]) const
{
}
......@@ -30,7 +30,7 @@
#include "guiworkerthread.h"
GuiWorkerThread::GuiWorkerThread(LauncherMainWindow *parent)
GuiWorkerThread::GuiWorkerThread(LauncherMainWindow *parent [[maybe_unused]])
{
}
GuiWorkerThread::~GuiWorkerThread()
......@@ -38,11 +38,11 @@ GuiWorkerThread::~GuiWorkerThread()
}
void
GuiWorkerThread::doRunningMassChroQ(MassChroqRun mcq_run)
GuiWorkerThread::doRunningMassChroQ(MassChroqRun mcq_run [[maybe_unused]])
{
}
void
GuiWorkerThread::doCheckMassChroQ(MassChroqRun mcq_run)
GuiWorkerThread::doCheckMassChroQ(MassChroqRun mcq_run [[maybe_unused]])
{
}
......@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
#ifndef GUIWORKERTHREAD_H
#define GUIWORKERTHREAD_H
#pragma once
#include <QObject>
......@@ -54,5 +53,3 @@ class GuiWorkerThread : public QObject
void doRunningMassChroQ(MassChroqRun mcq_run);
void doCheckMassChroQ(MassChroqRun mcq_run);
};
#endif // GUIWORKERTHREAD_H
......@@ -182,7 +182,7 @@ PepParser::whatSeparator() const
return ret;
}
const bool
bool
PepParser::isHeader(const QString &line)
{
QRegExp header("scan.+sequence.+mh.+z.+protein", Qt::CaseInsensitive);
......@@ -273,7 +273,7 @@ PepParser::processProtOrMods(QString &prot_token)
return prot_token;
}
const int
int
PepParser::processScan(QString &scan_token)
{
QString error_token(scan_token);
......@@ -294,7 +294,7 @@ PepParser::processScan(QString &scan_token)
}
}
const int
int
PepParser::processCharge(QString &charge_token)
{
QString error_token(charge_token);
......
......@@ -23,8 +23,7 @@
* \author Edlira Nano
*/
#ifndef PEP_PARSER_H_
#define PEP_PARSER_H_ 1
#pragma once
#include <QFileInfo>
#include <QTextStream>
......@@ -75,7 +74,7 @@ class PepParser
void processLine(QString &line);
/// verifies if the given line is a header line or not
const bool isHeader(const QString &header_line);
bool isHeader(const QString &header_line);
/// get the separator for the peptide file using header line;
/// the other lines will be expected to use the same separator.
......@@ -91,10 +90,10 @@ class PepParser
const QString processProtOrMods(QString &prot_token);
/// parses a scan number field
const int processScan(QString &scan_token);
int processScan(QString &scan_token);
/// parses a peptide charge field
const int processCharge(QString &charge_token);
int processCharge(QString &charge_token);
private:
const QString whatSeparator() const;
......@@ -119,4 +118,3 @@ class PepParser
int _current_z;
QString _current_mods;
};
#endif /* PEP_PARSER_H_ */
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