diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a45f3d8530f6e6313ca4f80ed570078fe4700e1
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,185 @@
+# CMake script for C++ X!TandemPipeline
+# Author: Olivier Langella
+# Created: 05/06/2015
+
+# Global parameters
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+PROJECT(xtpcpp CXX)
+IF(NOT CMAKE_BUILD_TYPE)
+# SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
+# "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+# FORCE)
+ SET(CMAKE_BUILD_TYPE Debug CACHE STRING
+ "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+ FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+MESSAGE("CMAKE_BUILD_TYPE : ${CMAKE_BUILD_TYPE}")
+
+IF(CMAKE_BUILD_TYPE MATCHES "Release")
+ MESSAGE("compiling as release version")
+ ADD_DEFINITIONS("-DQT_NO_DEBUG_OUTPUT")
+ENDIF( CMAKE_BUILD_TYPE MATCHES "Release" )
+
+IF(CMAKE_BUILD_TYPE MATCHES "Debug")
+ MESSAGE("compiling as debug version")
+ENDIF( CMAKE_BUILD_TYPE MATCHES "Debug" )
+
+IF(CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo")
+ MESSAGE("compiling as release with debug info version")
+ENDIF( CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo" )
+
+#SET(CMAKE_CXX_FLAGS "-Wall -Weffc++ -Wshadow -Wconversion")
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+
+
+
+SET(SOFTWARE_NAME "XTPcpp")
+
+SET(XTPCPP_VERSION_MAJOR "0")
+SET(XTPCPP_VERSION_MINOR "2")
+SET(XTPCPP_VERSION_PATCH "0")
+SET(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}")
+
+# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
+# standard install location
+IF(CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+ENDIF(CMAKE_INSTALL_PREFIX)
+
+# Subdirectories
+ADD_SUBDIRECTORY(src)
+
+# Doxygen
+FIND_PACKAGE(Doxygen)
+IF (DOXYGEN_FOUND)
+ ADD_CUSTOM_TARGET (apidoc cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-build
+ COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-build
+ COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-build
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+ ADD_CUSTOM_TARGET (apidoc-stable cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND echo "HTML_HEADER=header.html" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-stable
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
+ENDIF (DOXYGEN_FOUND)
+
+# Packager
+SET(CPACK_PACKAGE_NAME "xtpcpp")
+SET(CPACK_PACKAGE_VENDOR "PAPPSO Development Team")
+SET(CPACK_PACKAGE_VERSION "${PAPPSOMSTOOLS_VERSION}")
+SET(CPACK_PACKAGE_VERSION_MAJOR "${PAPPSOMSTOOLS_VERSION_MAJOR}")
+SET(CPACK_PACKAGE_VERSION_MINOR "${PAPPSOMSTOOLS_VERSION_MINOR}")
+SET(CPACK_PACKAGE_VERSION_PATCH "${PAPPSOMSTOOLS_VERSION_PATCH}")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "various mass spectrometry and proteomics tools")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
+SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
+SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+SET(CPACK_SOURCE_IGNORE_FILES
+ "CMakeFiles"
+ "Makefile"
+ "_CPack_Packages"
+ "CMakeCache.txt"
+ ".*\\\\.git"
+ ".*\\\\.gz"
+ ".*\\\\.deb"
+ ".*\\\\.rpm"
+ ".*\\\\.dmg"
+ ".*\\\\..*\\\\.swp"
+ "src/\\\\..*"
+ "src/libbpp*"
+ "debian/tmp"
+ "debian/libbpp.*/"
+ "debian/libbpp.*\\\\.so.*"
+ "debian/libbpp.*\\\\.a"
+ "debian/libbpp.*\\\\.substvars"
+ "debian/libbpp.*\\\\.debhelper"
+ "debian/debhelper\\\\.log"
+ "build/"
+ "html"
+ "Core.tag"
+ "Testing"
+ "build-stamp"
+ "install_manifest.txt"
+ "DartConfiguration.tcl"
+ ${CPACK_SOURCE_IGNORE_FILES}
+)
+
+
+
+#dch -Djessie "message"
+#cmake ..
+#make deb
+# scp pappsoms-tools* proteus.moulon.inra.fr:/var/www/apt/incoming
+# reprepro -Vb /var/www/apt processincoming default
+#
+# debuild -S -sa
+# dput -f olivier-langella *changes
+
+IF (MACOS)
+ SET(CPACK_GENERATOR "Bundle")
+ENDIF()
+
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
+INCLUDE(CPack)
+
+#This adds the 'dist' target
+ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
+# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
+IF("${CMAKE_GENERATOR}" MATCHES "Make")
+ ADD_CUSTOM_TARGET(make_clean
+ COMMAND ${CMAKE_MAKE_PROGRAM} clean
+ WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
+ )
+ ADD_DEPENDENCIES(dist make_clean)
+ENDIF()
+
+IF (UNIX)
+#This creates deb packages:
+
+
+
+ add_custom_target(targz
+ cpack -G TGZ --config CPackSourceConfig.cmake && tar xvfz ${CPACK_PACKAGE_NAME}-${PAPPSOMSTOOLS_VERSION}.tar.gz
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "Creating .tar.gz" VERBATIM
+ )
+
+
+ add_custom_target(deb
+ cd ${CPACK_PACKAGE_NAME}-${PAPPSOMSTOOLS_VERSION} && dpkg-buildpackage
+ DEPENDS targz
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "Creating Debian package" VERBATIM
+ )
+
+ file(GLOB changesdebs "${CMAKE_BINARY_DIR}/${CPACK_PACKAGE_NAME}_*.dsc")
+
+ foreach(libfile ${changesdebs})
+ SET(changesdeb "${libfile}")
+ endforeach(libfile)
+
+ message ("changes debian file : ${changesdeb}")
+ #lintian -IEi --pedantic tandem-mass_2013.06.15-1_amd64.changes
+ add_custom_target(lintian
+ lintian -IEi --pedantic ${changesdeb}
+ DEPENDS deb
+ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+ COMMENT "lintian check" VERBATIM
+ )
+
+ENDIF()
+
+SET(CTEST_UPDATE_TYPE git)
+SET(UPDATE_COMMAND "git")
+SET(UPDATE_OPTIONS "")
+
+#ENABLE_TESTING()
+#INCLUDE(CTest)
+#IF (BUILD_TESTING)
+# ADD_SUBDIRECTORY(test)
+#ENDIF(BUILD_TESTING)
+
+INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/src/xtpcpp DESTINATION bin)
\ No newline at end of file
diff --git a/cmake_modules/FindPwiz.cmake b/cmake_modules/FindPwiz.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..578ee5176d3353f373c970e445d787beddf77d9a
--- /dev/null
+++ b/cmake_modules/FindPwiz.cmake
@@ -0,0 +1,25 @@
+# Copyright : ETH Zurich
+# License : three-clause BSD license
+# Authors : Witold Wolski
+# for full text refer to files: LICENSE, AUTHORS and COPYRIGHT
+#FIND_PATH(Pwiz_INCLUDE_DIR pwiz/Version.hpp)
+ FIND_PATH( Pwiz_INCLUDE_DIR pwiz/Version.hpp
+ PATHS /usr/local/include /usr/include
+ PATH_SUFFIXES pwiz libpwiz ENV PATH)
+
+FIND_LIBRARY(Pwiz_LIBRARY NAMES pwiz)
+IF (Pwiz_INCLUDE_DIR AND Pwiz_LIBRARY)
+MESSAGE(STATUS "XXXXXXXXXXXXX ${Pwiz_LIBRARY} XXXXXXXXXXXXXXX")
+SET(Pwiz_FOUND TRUE)
+ENDIF (Pwiz_INCLUDE_DIR AND Pwiz_LIBRARY)
+IF (Pwiz_FOUND)
+# show which CppUnit was found only if not quiet
+IF (NOT Pwiz_FIND_QUIETLY)
+MESSAGE(STATUS "Found Pwiz: ${Pwiz_LIBRARY}")
+ENDIF (NOT Pwiz_FIND_QUIETLY)
+ELSE (Pwiz_FOUND)
+# fatal error if CppUnit is required but not found
+IF (Pwiz_FIND_REQUIRED)
+MESSAGE(FATAL_ERROR "Could not find Pwiz please do specify the Pwiz_INCLUDE_DIR and the Pwiz_LIBRARY variables using ccmake!")
+ENDIF (Pwiz_FIND_REQUIRED)
+ENDIF (Pwiz_FOUND)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dce53c9a5d40c88ddf999bb8875da1ab688894df
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,90 @@
+# CMake script for xtpcpp
+# Author: Olivier Langella
+# Created: 03/03/2015
+
+
+# Appeler automatique le moc quand nécessaire
+#SET(CMAKE_AUTOMOC ON)
+# Les fichiers générés par le moc sont générés dans le dossier bin, dire à CMake de toujours
+# inclure les entêtes de ce dossier
+#SET(CMAKE_INCLUDE_CURRENT_DIR ON)
+
+#FIND_PACKAGE(Boost REQUIRED)
+#INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS})
+
+FIND_PACKAGE( Qt4 COMPONENTS QTCORE QTGUI QTSVG REQUIRED )
+
+
+FIND_PACKAGE( Odsstream REQUIRED ) #ODSSTREAM_INCLUDE_DIR AND ODSSTREAM_LIBRARY
+#SET (ODSSTREAM_DIR "/home/olivier/eclipse/git/cpp_libodsstream")
+#SET (ODSSTREAM_INCLUDE_DIR "${ODSSTREAM_DIR}/src")
+#SET (ODSSTREAM_QT5_LIBRARY "${ODSSTREAM_DIR}/build/src/libodsstream-qt5.so")
+INCLUDE_DIRECTORIES(${ODSSTREAM_INCLUDE_DIR})
+
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5Gui_EXECUTABLE_COMPILE_FLAGS} ${Qt5Svg_EXECUTABLE_COMPILE_FLAGS}")
+
+
+#FIND_PACKAGE( Pappsomspp REQUIRED )
+SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+#SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/build/src/libpappsomspp-qt4.so")
+
+INCLUDE_DIRECTORIES( ${PAPPSOMSPP_INCLUDE_DIR} )
+
+set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake_modules)
+
+FIND_PACKAGE(Pwiz REQUIRED)
+INCLUDE_DIRECTORIES( ${Pwiz_INCLUDE_DIR})
+IF (Pwiz_FOUND)
+ INCLUDE_DIRECTORIES( ${Pwiz_INCLUDE_DIR})
+ #FIND_PACKAGE(Boost REQUIRED)
+ #INCLUDE_DIRECTORIES( ${Boost_INCLUDE_DIRS})
+ELSE (Pwiz_FOUND)
+ MESSAGE("Proteowizard library not found")
+ MESSAGE("did you apt-get install libpwiz-dev libboost-dev ?")
+ENDIF (Pwiz_FOUND)
+
+configure_file (${CMAKE_SOURCE_DIR}/src/config.h.cmake ${CMAKE_SOURCE_DIR}/src/config.h)
+
+# File list
+SET(CPP_FILES
+ utils/readspectrum.cpp
+)
+
+SET (GUI_UIS
+)
+
+SET(XTPCPP_MOC_HDRS
+)
+
+
+# this will run uic on .ui files:
+QT4_WRAP_UI( GUI_UI_HDRS ${GUI_UIS} )
+
+QT4_WRAP_CPP( XTPCPP_MOC_SRCS ${XTPCPP_MOC_HDRS} )
+
+
+
+set(QTLIBS ${Qt5Xml_LIBRARIES} ${Qt5Gui_LIBRARIES} ${Qt5Svg_LIBRARIES})
+
+# 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} )
+INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_SOURCE_DIR} )
+
+ADD_EXECUTABLE(xtpcpp ${CPP_FILES} ${GUI_UI_HDRS} ${XTPCPP_MOC_SRCS})
+target_include_directories (xtpcpp PUBLIC ${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR} ${QT_QTGUI_INCLUDE_DIR} ${QT_QTSVG_INCLUDE_DIR})
+ SET_TARGET_PROPERTIES(xtpcpp
+ PROPERTIES OUTPUT_NAME xtpcpp
+ CLEAN_DIRECT_OUTPUT 1
+ COMPILE_DEFINITIONS "${QT_DEFINITIONS}"
+ #INCLUDE_DIRECTORIES "${QT_INCLUDE_DIR} ${QT_QTCORE_INCLUDE_DIR}"
+ )
+TARGET_LINK_LIBRARIES(xtpcpp ${PAPPSOMSPP_QT4_LIBRARY} ${Pwiz_LIBRARY} ${ODSSTREAM_QT4_LIBRARY} ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY} ${QT_QTSVG_LIBRARY})
+
+INSTALL(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/xtpcpp DESTINATION bin)
+
+#configure_file (${CMAKE_SOURCE_DIR}/templates/share/applications/pt-peptideviewer.desktop.cmake ${CMAKE_BINARY_DIR}/templates/share/applications/pt-peptideviewer.desktop)
+
+
diff --git a/src/config.h.cmake b/src/config.h.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..02f0430420afff653cc5316049547f071271756d
--- /dev/null
+++ b/src/config.h.cmake
@@ -0,0 +1,13 @@
+#ifndef _CONFIG_H
+#define _CONFIG_H
+
+#cmakedefine XTPCPP_VERSION "@XTPCPP_VERSION@"
+
+#cmakedefine SOFTWARE_NAME "@SOFTWARE_NAME@"
+
+#include <QDebug>
+
+
+
+
+#endif /* _CONFIG_H */
diff --git a/src/main.cpp b/src/main.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d6375538653e730f6e2f794b1d34e9a56ca39b85
--- /dev/null
+++ b/src/main.cpp
@@ -0,0 +1,58 @@
+
+/*******************************************************************************
+* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+*
+* This file is part of PAPPSOms-tools.
+*
+* PAPPSOms-tools is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* PAPPSOms-tools is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+
+#include <QApplication>
+#include <iostream>
+#include "ptspectrumviewer.h"
+#include "qspectrumwidget.h"
+
+using namespace std;
+
+int main(int argc, char *argv[])
+{
+ QTextStream errorStream(stderr, QIODevice::WriteOnly);
+ QApplication app(argc, argv);
+
+ try {
+ QCoreApplication::setOrganizationName("PAPPSO");
+ QCoreApplication::setOrganizationDomain("pappso.inra.fr");
+ QCoreApplication::setApplicationName("xtpcpp");
+ PtSpectrumViewer window;
+ window.show();
+
+ return app.exec();
+ }
+ catch (pappso::PappsoException& error)
+ {
+ errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
+ errorStream << error.qwhat() << endl;
+ app.exit(1);
+ }
+
+ catch (std::exception& error)
+ {
+ errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
+ errorStream << error.what() << endl;
+ app.exit(1);
+ }
+}
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..37944bff5bd92835584230f03bef88ef3da05fd9
--- /dev/null
+++ b/src/utils/readspectrum.cpp
@@ -0,0 +1,218 @@
+
+/*******************************************************************************
+* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+*
+* This file is part of PAPPSOms-tools.
+*
+* PAPPSOms-tools is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* PAPPSOms-tools is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+
+#include "readspectrum.h"
+
+#include <QDebug>
+#include <pappsomspp/spectrum/spectrum.h>
+#include <pappsomspp/exception/exceptionnotfound.h>
+
+#include <pwiz/data/common/cv.hpp>
+#include <pwiz_tools/common/FullReaderList.hpp>
+//#include <pwiz/utility/misc/Std.hpp>
+#include <pwiz/data/msdata/SpectrumInfo.hpp>
+#include <pwiz/data/msdata/MSData.hpp>
+#include <locale>
+
+//http://sourceforge.net/p/proteowizard/mailman/message/28245157/
+
+using namespace pappso;
+
+
+pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
+ qDebug() << "getPwizMSDataFile opening file " << filename ;
+ std::string env;
+ env=setlocale(LC_ALL,"");
+ struct lconv * lc = localeconv ();
+ qDebug() << " env=" << env.c_str() << " lc->decimal_point " << lc->decimal_point;
+ setlocale(LC_ALL,"C");
+ //lc = localeconv ();
+ //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
+ pwiz::msdata::MSDataFile * dataFile = new pwiz::msdata::MSDataFile(filename.toStdString());
+
+ setlocale(LC_ALL,env.c_str());
+
+ return dataFile;
+}
+
+
+SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state) {
+
+ if (p_ms_data_file == nullptr) {
+ SpectrumSp empty;
+ return (empty);
+ }
+
+ const bool getBinaryData = true;
+ pwiz::msdata::SpectrumListPtr spectrum_list_ptr = p_ms_data_file->run.spectrumListPtr;
+ unsigned int spectrum_index = 0;
+ if (spectrum_list_ptr.get()->size() == 1) {
+ spectrum_index = 0;
+ }
+ else {
+ // turn our scan numbers into navtieId strings for pwiz
+ pwiz::msdata::CVID nativeIdFormat_ = pwiz::msdata::id::getDefaultNativeIDFormat(*p_ms_data_file);
+ string nativeScanId = pwiz::msdata::id::translateScanNumberToNativeID(nativeIdFormat_, QString("%1").arg(scan_num).toStdString());
+ spectrum_index = spectrum_list_ptr.get()->find(nativeScanId);
+ }
+ qDebug() << "spectrum_index " << spectrum_index;
+ if (spectrum_index == spectrum_list_ptr.get()->size()) {
+ //pwiz::msdata::SpectrumPtr simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(10, getBinaryData);
+ //qDebug() << "spectrum id 10 " << simple_spectrum_pwiz.get()->get;
+ throw ExceptionNotFound(QObject::tr("scan number %1 not found MS file").arg(scan_num));
+ }
+ pwiz::msdata::SpectrumPtr simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(spectrum_index, getBinaryData);
+ if (simple_spectrum_pwiz.get()->precursors.size() > 0) {
+ pwiz::msdata::Precursor & precursor = *(simple_spectrum_pwiz.get()->precursors.begin());
+ if (precursor.selectedIons.size() > 0) {
+ pwiz::msdata::SelectedIon & ion = *(precursor.selectedIons.begin());
+
+ //selected ion m/z
+ mz selected_ion_mz = QString(ion.cvParam(pwiz::cv::MS_selected_ion_m_z).value.c_str()).toDouble();
+ //peak intensity
+ pappso_double peak_intensity = QString(ion.cvParam(pwiz::cv::MS_peak_intensity).value.c_str()).toDouble();
+
+ // unsigned int test = QString(ion.cvParam(pwiz::cv::MS_1200_series_LC_MSD_SL).value.c_str()).toUInt();
+ // qDebug() << " tes "<< test;
+ //charge state
+ unsigned int charge_state = QString(ion.cvParam(pwiz::cv::MS_charge_state).value.c_str()).toUInt();
+
+ qDebug() << " selected_ion_mz "<< selected_ion_mz ;
+ qDebug() << " peak_intensity "<< peak_intensity;
+ qDebug() << " charge_state "<< charge_state;
+ if (charge_state > 0) {
+ precursor_charge_state = charge_state;
+ }
+ }
+ }
+
+ /* for (pwiz::data::CVParam cv_param :ion.cvParams) {
+ pwiz::msdata::CVID param_id = cv_param.cvid;
+ qDebug() << param_id ;
+ //qDebug() << cv_param.cvid.c_str();
+ qDebug() << cv_param.name().c_str();
+ qDebug() << cv_param.value.c_str();
+ }*/
+ // fill in MZIntensityPair vector for convenient access to binary data
+ vector<pwiz::msdata::MZIntensityPair> pairs;
+ simple_spectrum_pwiz->getMZIntensityPairs(pairs);
+ // cout << "spectrum_simple size:" << pairs.size() << endl;
+
+ Spectrum spectrum;
+
+ // iterate through the m/z-intensity pairs
+ for (vector<pwiz::msdata::MZIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
+ {
+ //qDebug() << "it->mz " << it->mz << " it->intensity" << it->intensity;
+ spectrum.push_back(Peak(it->mz, it->intensity));
+ }
+ qDebug() << "spectrum size " << spectrum.size();
+ //cout << "spectrum_simple size " << spectrum_simple.getSpectrumSize()<< endl;
+
+ // lc = localeconv ();
+ //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
+ return spectrum.makeSpectrumSp();
+}
+
+Spectrum readSpectrum(const QString & filename, unsigned int scan_num, unsigned int & precursor_charge_state) {
+ qDebug() << "opening file " << filename << " scan " << scan_num;
+ std::string env;
+ env=setlocale(LC_ALL,"");
+ struct lconv * lc = localeconv ();
+ qDebug() << " env=" << env.c_str() << " lc->decimal_point " << lc->decimal_point;
+ setlocale(LC_ALL,"C");
+ //lc = localeconv ();
+ //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
+ pwiz::msdata::MSDataFile dataFile(filename.toStdString());
+
+ const bool getBinaryData = true;
+ pwiz::msdata::SpectrumListPtr spectrum_list_ptr = dataFile.run.spectrumListPtr;
+ unsigned int spectrum_index = 0;
+ if (spectrum_list_ptr.get()->size() == 1) {
+ spectrum_index = 0;
+ }
+ else {
+ // turn our scan numbers into navtieId strings for pwiz
+ pwiz::msdata::CVID nativeIdFormat_ = pwiz::msdata::id::getDefaultNativeIDFormat(dataFile);
+ string nativeScanId = pwiz::msdata::id::translateScanNumberToNativeID(nativeIdFormat_, QString("%1").arg(scan_num).toStdString());
+ spectrum_index = spectrum_list_ptr.get()->find(nativeScanId);
+ }
+ qDebug() << "spectrum_index " << spectrum_index;
+ if (spectrum_index == spectrum_list_ptr.get()->size()) {
+ //pwiz::msdata::SpectrumPtr simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(10, getBinaryData);
+ //qDebug() << "spectrum id 10 " << simple_spectrum_pwiz.get()->get;
+ throw ExceptionNotFound(QObject::tr("scan number %1 not found in %2").arg(scan_num).arg(filename));
+ }
+ pwiz::msdata::SpectrumPtr simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(spectrum_index, getBinaryData);
+ if (simple_spectrum_pwiz.get()->precursors.size() > 0) {
+ pwiz::msdata::Precursor & precursor = *(simple_spectrum_pwiz.get()->precursors.begin());
+ if (precursor.selectedIons.size() > 0) {
+ pwiz::msdata::SelectedIon & ion = *(precursor.selectedIons.begin());
+
+ //selected ion m/z
+ mz selected_ion_mz = QString(ion.cvParam(pwiz::cv::MS_selected_ion_m_z).value.c_str()).toDouble();
+ //peak intensity
+ pappso_double peak_intensity = QString(ion.cvParam(pwiz::cv::MS_peak_intensity).value.c_str()).toDouble();
+
+ // unsigned int test = QString(ion.cvParam(pwiz::cv::MS_1200_series_LC_MSD_SL).value.c_str()).toUInt();
+ // qDebug() << " tes "<< test;
+ //charge state
+ unsigned int charge_state = QString(ion.cvParam(pwiz::cv::MS_charge_state).value.c_str()).toUInt();
+
+ qDebug() << " selected_ion_mz "<< selected_ion_mz ;
+ qDebug() << " peak_intensity "<< peak_intensity;
+ qDebug() << " charge_state "<< charge_state;
+ if (charge_state > 0) {
+ precursor_charge_state = charge_state;
+ }
+ }
+ }
+
+ /* for (pwiz::data::CVParam cv_param :ion.cvParams) {
+ pwiz::msdata::CVID param_id = cv_param.cvid;
+ qDebug() << param_id ;
+ //qDebug() << cv_param.cvid.c_str();
+ qDebug() << cv_param.name().c_str();
+ qDebug() << cv_param.value.c_str();
+ }*/
+ // fill in MZIntensityPair vector for convenient access to binary data
+ vector<pwiz::msdata::MZIntensityPair> pairs;
+ simple_spectrum_pwiz->getMZIntensityPairs(pairs);
+ // cout << "spectrum_simple size:" << pairs.size() << endl;
+
+ Spectrum spectrum;
+
+ // iterate through the m/z-intensity pairs
+ for (vector<pwiz::msdata::MZIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
+ {
+ //qDebug() << "it->mz " << it->mz << " it->intensity" << it->intensity;
+ spectrum.push_back(Peak(it->mz, it->intensity));
+ }
+ qDebug() << "spectrum size " << spectrum.size();
+ //cout << "spectrum_simple size " << spectrum_simple.getSpectrumSize()<< endl;
+
+ setlocale(LC_ALL,env.c_str());
+ // lc = localeconv ();
+ //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
+ return spectrum;
+}
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
new file mode 100644
index 0000000000000000000000000000000000000000..da0cfeb53aa89c0abf063cf774a9024b4b0f00c1
--- /dev/null
+++ b/src/utils/readspectrum.h
@@ -0,0 +1,40 @@
+
+/*******************************************************************************
+* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+*
+* This file is part of PAPPSOms-tools.
+*
+* PAPPSOms-tools is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* PAPPSOms-tools is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
+*
+* Contributors:
+* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef READSPECTRUM_H
+#define READSPECTRUM_H
+
+#include <QString>
+#include <pappsomspp/spectrum/spectrum.h>
+
+#include <pwiz/data/msdata/MSDataFile.hpp>
+
+using namespace pappso;
+
+Spectrum readSpectrum(const QString & filename, unsigned int scan_num,unsigned int & precursor_charge_state);
+
+pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename);
+
+SpectrumSp getSpectrumSpFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num, unsigned int & precursor_charge_state);
+
+#endif // READSPECTRUM_H