CMakeLists.txt

@@ -85,6 +85,11 @@ add_definitions(-Wall)
 message(STATUS "${BoldGreen}Setting definition -Wextra.${ColourReset}")
 add_definitions(-Wextra)
 
+if(WARN_AS_ERROR)
+  message(STATUS "${BoldYellow}Setting definition -Werror.${ColourReset}")
+  add_definitions(-Werror)
+endif()
+
 message(STATUS "${BoldRed}CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}${ColourReset}")
 
 
@@ -105,7 +110,8 @@ elseif(UNIX AND NOT APPLE)
   # Run the following cmake command line:
   # cmake -DBUILD_USER_MANUAL=1 -DCMAKE_BUILD_TYPE=Debug
 
-  include(${CMAKE_TOOLCHAINS_PATH}/unix-toolchain.cmake)
+  #include(${CMAKE_TOOLCHAINS_PATH}/unix-toolchain.cmake)
+  include(${CMAKE_TOOLCHAINS_PATH}/unix-toolchain-local.cmake)
 
 elseif(WIN32 OR _WIN32)
 
@@ -180,6 +186,13 @@ message(STATUS "Boost_INCLUDES: ${Boost_INCLUDE_DIRS}")
 message(STATUS "Boost_LIB_DIRS: ${Boost_LIBRARY_DIRS}")
 
 
+if(QCustomPlot_FOUND)
+else (QCustomPlot_FOUND)
+  set(QCustomPlot_DIR ${CMAKE_MODULE_PATH})
+  find_package(QCustomPlot REQUIRED)
+endif(QCustomPlot_FOUND)
+
+
 if(Alglib_FOUND)
 else (Alglib_FOUND)
   set(Alglib_DIR ${CMAKE_MODULE_PATH})

CMakeStuff/toolchains/unix-toolchain-local.cmake

+message("UNIX non APPLE environment")
+message("Please run the configuration like this:")
+message("cmake -G \"Unix Makefiles\" -DCMAKE_BUILD_TYPE=Debug ../development")
+
+set(CMAKE_C_IMPLICIT_INCLUDE_DIRECTORIES /usr/include)
+set(CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES /usr/include)
+
+set(LINKER_FLAGS "-Wl,--no-as-needed")
+
+find_package(PwizLite REQUIRED) 
+
+find_package(ZLIB REQUIRED)
+
+find_package(Zstd REQUIRED)
+
+find_package(liblzf REQUIRED)
+
+find_package(Qt6 COMPONENTS Widgets Core Gui PrintSupport Svg REQUIRED)
+
+#find_package(QCustomPlotQt6 REQUIRED)
+
+set(QCustomPlotQt6_FOUND 1)
+SET(QCustomPlotQt6_INCLUDE_DIR "/home/langella/developpement/git/qcustomplot-qt6")
+SET(QCustomPlotQt6_LIBRARIES "/home/langella/developpement/git/qcustomplot-qt6/build-qt6/libQCustomPlotQt6.so" )
+
+	add_library(QCustomPlotQt6::QCustomPlotQt6 UNKNOWN IMPORTED)
+	set_target_properties(QCustomPlotQt6::QCustomPlotQt6 PROPERTIES
+		IMPORTED_LOCATION             "${QCustomPlotQt6_LIBRARIES}"
+		INTERFACE_INCLUDE_DIRECTORIES "${QCustomPlotQt6_INCLUDE_DIR}"
+		INTERFACE_COMPILE_DEFINITIONS QCUSTOMPLOTQT6_USE_LIBRARY)
+
+# Per instructions of the lib author:
+# https://www.qcustomplot.com/index.php/tutorials/settingup
+message(STATUS "Setting definition -DQCUSTOMPLOT_USE_LIBRARY.")
+
+add_definitions(-fPIC)
+
+message("unix-toolchain.cmake - LOCAL_CMAKE_MODULE_PATH: ${LOCAL_CMAKE_MODULE_PATH}")
+
+# Install the cmake module
+message("LOCAL_CMAKE_MODULE_PATH: ${LOCAL_CMAKE_MODULE_PATH}")
+install(FILES ${LOCAL_CMAKE_MODULE_PATH}/FindPappsoMSpp.cmake 
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/pappsomspp)
+
+# Configure the cmake config
+configure_file (${LOCAL_CMAKE_MODULE_PATH}/PappsoMSppConfig.cmake.in
+  ${CMAKE_BINARY_DIR}/PappsoMSppConfig.cmake)
+# Install the cmake config
+install(FILES ${CMAKE_BINARY_DIR}/PappsoMSppConfig.cmake 
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/pappsomspp)
+
+

debian/changelog

@@ -6,6 +6,52 @@ libpappsomspp (0.9.0-1) unstable; urgency=low
 
  -- Filippo Rusconi <lopippo@debian.org>  Thu, 22 Sep 2022 18:35:01 +0200
 
+libpappsomspp (0.8.60-1~bullseye+1) bullseye; urgency=medium
+
+  * bullseye backport
+
+ -- Olivier Langella <olivier.langella@u-psud.fr>  Mon, 31 Oct 2022 09:06:33 +0100
+
+libpappsomspp (0.8.60-1) unstable; urgency=low
+
+  * Fix the distribution... was working too late at night...
+
+ -- Filippo Rusconi <lopippo@debian.org>  Fri, 28 Oct 2022 10:20:12 +0200
+
+libpappsomspp (0.8.59-1) bullseye; urgency=low
+
+  * New upstream version.
+
+  * Incidentally, previous version was to fix a bug that was published in
+    betwwen the previous version and this one: (Closes: #1022934).
+
+ -- Filippo Rusconi <lopippo@debian.org>  Fri, 28 Oct 2022 03:30:29 +0200
+
+libpappsomspp (0.8.58-1) bullseye; urgency=low
+
+  * New upstream version (see 0.8.57-1~bullseye+1).
+
+  * Standards-Version: 4.6.1.
+
+  * d/rules: Fix by Adrian Bunk to work around the excess precision of the x87
+    FPU that causes
+    https://buildd.debian.org/status/logs.php?pkg=libpappsomspp&arch=i386.
+
+ -- Filippo Rusconi <lopippo@debian.org>  Thu, 27 Oct 2022 10:38:00 +0200
+
+libpappsomspp (0.8.57-1~bullseye+1) bullseye; urgency=medium
+
+  [ Olivier Langella ]
+  * avoid nullptr calls in custom plot widgets
+  * new tims frame widget color map
+  * better tdf handler
+  * new tests for protein , enzyme, psm, psmfeaures
+  * new psm feature API
+  [ Filippo Rusconi ]
+  * refactoring work to compile using Qt6
+
+ -- Olivier Langella <olivier.langella@u-psud.fr>  Tue, 04 Oct 2022 17:02:43 +0200
+
 libpappsomspp (0.8.56-1) unstable; urgency=low
 
   * New version that implements features in the dt|rt,m/z color map realms.

debian/rules

@@ -11,6 +11,11 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/buildflags.mk
 
+ifneq (,$(filter $(DEB_HOST_ARCH_CPU), i386))
+  export DEB_CXXFLAGS_MAINT_APPEND += -ffloat-store
+endif
+
+
 %:
 	dh $@ --buildsystem=cmake
 

src/CMakeLists.txt

@@ -57,7 +57,7 @@ set(CPP_FILES
   pappsomspp/processing/filters/filterceilingamplitudepercentage.cpp
   pappsomspp/processing/filters/filterlowintensitysignalremoval.cpp
 
-  #pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
+  pappsomspp/processing/tandemwrapper/tandemwrapperrun.cpp
   pappsomspp/processing/tandemwrapper/wraptandeminput.cpp
   pappsomspp/processing/tandemwrapper/wraptandemresults.cpp
   pappsomspp/processing/tandemwrapper/xtandempresetreader.cpp
@@ -90,7 +90,7 @@ set(CPP_FILES
   pappsomspp/msfile/msfilereader.cpp
   pappsomspp/msfile/mzformatenumstr.cpp
   pappsomspp/msfile/pwizmsfilereader.cpp
-  #pappsomspp/msfile/timsmsfilereader.cpp
+  pappsomspp/msfile/timsmsfilereader.cpp
   pappsomspp/msfile/xymsfilereader.cpp
 
   pappsomspp/msrun/alignment/msrunretentiontime.cpp
@@ -102,9 +102,9 @@ set(CPP_FILES
   pappsomspp/msrun/msrunid.cpp
   pappsomspp/msrun/msrunreader.cpp
   pappsomspp/msrun/private/pwizmsrunreader.cpp
-  #pappsomspp/msrun/private/timsmsrunreader.cpp
-  #pappsomspp/msrun/private/timsmsrunreaderms2.cpp
-  #pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp
+  pappsomspp/msrun/private/timsmsrunreader.cpp
+  pappsomspp/msrun/private/timsmsrunreaderms2.cpp
+  pappsomspp/msrun/private/timsmsrunreaderms2selected.cpp
   pappsomspp/msrun/xiccoord/xiccoord.cpp
   pappsomspp/msrun/xiccoord/xiccoordtims.cpp
   pappsomspp/msrun/xymsrunreader.cpp
@@ -159,18 +159,18 @@ set(CPP_FILES
   pappsomspp/trace/maptrace.cpp
   pappsomspp/trace/trace.cpp
 
-  #pappsomspp/vendors/tims/mzcalibration/mzcalibrationinterface.cpp
-  #pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp
-  #pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp
-  #pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
-  #pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp
-  #pappsomspp/vendors/tims/timsbindec.cpp
-  #pappsomspp/vendors/tims/timsdata.cpp
-  #pappsomspp/vendors/tims/timsframe.cpp
-  #pappsomspp/vendors/tims/timsframerawdatachunck.cpp
-  #pappsomspp/vendors/tims/timsframebase.cpp
-  #pappsomspp/vendors/tims/timsframetype1.cpp
-  #pappsomspp/vendors/tims/timsms2centroidfilter.cpp
+  pappsomspp/vendors/tims/mzcalibration/mzcalibrationinterface.cpp
+  pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp
+  pappsomspp/vendors/tims/mzcalibration/mzcalibrationstore.cpp
+  pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
+  pappsomspp/vendors/tims/xicextractor/timsxicextractorinterface.cpp
+  pappsomspp/vendors/tims/timsbindec.cpp
+  pappsomspp/vendors/tims/timsdata.cpp
+  pappsomspp/vendors/tims/timsframe.cpp
+  pappsomspp/vendors/tims/timsframerawdatachunck.cpp
+  pappsomspp/vendors/tims/timsframebase.cpp
+  pappsomspp/vendors/tims/timsframetype1.cpp
+  pappsomspp/vendors/tims/timsms2centroidfilter.cpp
 
   pappsomspp/xic/xic.cpp
   pappsomspp/xic/qualifiedxic.cpp

src/pappsomspp/msfile/msfileaccessor.cpp

@@ -7,7 +7,7 @@
 
 #include "msfileaccessor.h"
 #include "pwizmsfilereader.h"
-//#include "timsmsfilereader.h"
+#include "timsmsfilereader.h"
 #include "xymsfilereader.h"
 
 
@@ -16,8 +16,8 @@
 #include "../utils.h"
 #include "../msrun/msrunid.h"
 #include "../msrun/private/pwizmsrunreader.h"
-//#include "../msrun/private/timsmsrunreader.h"
-//#include "../msrun/private/timsmsrunreaderms2.h"
+#include "../msrun/private/timsmsrunreader.h"
+#include "../msrun/private/timsmsrunreaderms2.h"
 #include "../msrun/xymsrunreader.h"
 
 
@@ -260,8 +260,6 @@ MsFileAccessor::buildMsRunReaderSPtr(
         QObject::tr("unable to build a reader for %1 : unknown file format")
           .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
     }
-#if 0
-// Remove this section because it cripples my work on Qt6 build
   
   else if(file_format == MzFormat::brukerTims)
     {
@@ -278,7 +276,6 @@ MsFileAccessor::buildMsRunReaderSPtr(
       qDebug() << "by default, build a TimsMsRunReader.";
       return std::make_shared<TimsMsRunReader>(ms_run_id);
     }
-#endif
   else
     {
       qDebug() << "Returning a PwizMsRunReader .";

src/pappsomspp/obo/obopsimodterm.cpp

@@ -47,6 +47,43 @@ QRegularExpression OboPsiModTerm::m_findExactPsiModLabel(
 QRegularExpression OboPsiModTerm::m_findRelatedPsiMsLabel(
   "^(.*)\\sRELATED\\sPSI-MS-label\\s\\[\\]$");
 
+
+OboPsiModTerm::OboPsiModTerm()
+{
+}
+
+OboPsiModTerm::~OboPsiModTerm()
+{
+}
+OboPsiModTerm::OboPsiModTerm(const OboPsiModTerm &other)
+{
+  m_accession   = other.m_accession;
+  m_name        = other.m_name;
+  m_definition  = other.m_definition;
+  m_psiModLabel = other.m_psiModLabel;
+  m_psiMsLabel  = other.m_psiMsLabel;
+  m_diffFormula = other.m_diffFormula;
+  m_origin      = other.m_origin;
+
+  m_diffMono = other.m_diffMono;
+}
+
+OboPsiModTerm &
+OboPsiModTerm::operator=(const OboPsiModTerm &other)
+{
+  m_accession   = other.m_accession;
+  m_name        = other.m_name;
+  m_definition  = other.m_definition;
+  m_psiModLabel = other.m_psiModLabel;
+  m_psiMsLabel  = other.m_psiMsLabel;
+  m_diffFormula = other.m_diffFormula;
+  m_origin      = other.m_origin;
+
+  m_diffMono = other.m_diffMono;
+  return *this;
+}
+
+
 bool
 OboPsiModTerm::isValid() const
 {

src/pappsomspp/obo/obopsimodterm.h

@@ -33,10 +33,10 @@ class PMSPP_LIB_DECL OboPsiModTerm
   friend OboPsiMod;
 
   public:
-  OboPsiModTerm()                      = default;
-  ~OboPsiModTerm()                     = default;
-  OboPsiModTerm(const OboPsiModTerm &) = default;
-  OboPsiModTerm &operator=(const OboPsiModTerm &) = default;
+  OboPsiModTerm();
+  virtual ~OboPsiModTerm();
+  OboPsiModTerm(const OboPsiModTerm &);
+  OboPsiModTerm &operator=(const OboPsiModTerm &);
 
   bool isValid() const;
 
@@ -49,7 +49,7 @@ class PMSPP_LIB_DECL OboPsiModTerm
   QString m_diffFormula;
   QString m_origin;
 
-  double m_diffMono;
+  double m_diffMono = 0;
 
   private:
   void parseLine(const QString &line);
@@ -63,5 +63,4 @@ class PMSPP_LIB_DECL OboPsiModTerm
 } // namespace pappso
 
 
-
 extern int oboPsiModTermMetaTypeId;

src/pappsomspp/peptide/peptide.cpp

@@ -39,6 +39,22 @@
 namespace pappso
 {
 
+bool
+peptideIonTypeIsComplement(PeptideIon ion_type_ref, PeptideIon ion_type)
+{
+  if(peptideIonIsNter(ion_type))
+    std::swap(ion_type_ref, ion_type);
+  if(peptideIonIsNter(ion_type))
+    return false;
+  if((ion_type_ref == PeptideIon::b) && (ion_type == PeptideIon::y))
+    return true;
+  if((ion_type_ref == PeptideIon::ao) && (ion_type == PeptideIon::yo))
+    return true;
+  if((ion_type_ref == PeptideIon::bstar) && (ion_type == PeptideIon::ystar))
+    return true;
+
+  return false;
+}
 
 bool
 peptideIonIsNter(PeptideIon ion_type)

src/pappsomspp/peptide/peptide.h

@@ -52,14 +52,21 @@ enum class PeptideDirection : std::int8_t
 /** \brief tells if an ion is Nter
  * \param ion_type the ion to test
  */
-bool peptideIonIsNter(PeptideIon ion_type);
+PMSPP_LIB_DECL bool peptideIonIsNter(PeptideIon ion_type);
+
+/** \brief tells if an ion type is the complement ion of the other
+ * \param ion_type_ref the ion type reference
+ * \param ion_type the ion to test
+ */
+PMSPP_LIB_DECL bool peptideIonTypeIsComplement(PeptideIon ion_type_ref,
+                                               PeptideIon ion_type);
 
 
 /** \brief get the direction of a peptide ion
  * \param ion_type the ion to test
  * \return the peptide direction
  */
-PeptideDirection getPeptideIonDirection(PeptideIon ion_type);
+PMSPP_LIB_DECL PeptideDirection getPeptideIonDirection(PeptideIon ion_type);
 
 enum class PeptideIonNter
 {

src/pappsomspp/peptide/peptidenaturalisotope.h

@@ -48,7 +48,7 @@ class PMSPP_LIB_DECL PeptideNaturalIsotope : public PeptideInterface
   PeptideNaturalIsotope(const PeptideInterfaceSp &peptide,
                         const std::map<Isotope, int> &map_isotope);
   PeptideNaturalIsotope(const PeptideNaturalIsotope &other);
-  ~PeptideNaturalIsotope();
+  virtual ~PeptideNaturalIsotope();
 
   virtual unsigned int size() const override;
   virtual const QString getSequence() const override;

src/pappsomspp/peptide/peptidenaturalisotopeaverage.cpp

@@ -29,6 +29,28 @@
 
 namespace pappso
 {
+
+
+PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
+  const PeptideInterfaceSp &peptide,
+  unsigned int isotopeNumber,
+  unsigned int charge,
+  PrecisionPtr precision)
+  : mcsp_peptideSp(peptide),
+    m_isotopeLevel(isotopeNumber),
+    m_isotopeRank(1),
+    m_z(charge),
+    mp_precision(precision)
+{
+
+  m_peptideNaturalIsotopeSpList.clear();
+
+  double diffC13 = ((double)isotopeNumber * DIFFC12C13) / (double)charge;
+
+  m_averageMz      = peptide.get()->getMz(charge) + diffC13;
+  m_abundanceRatio = 0;
+}
+
 PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
   const PeptideInterfaceSp &peptide,
   unsigned int askedIsotopeRank,
@@ -161,6 +183,7 @@ PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
   : mcsp_peptideSp(other.mcsp_peptideSp), mp_precision(other.mp_precision)
 {
 
+  qDebug();
   m_peptideNaturalIsotopeSpList = other.m_peptideNaturalIsotopeSpList;
 
   m_averageMz      = other.m_averageMz;
@@ -168,6 +191,7 @@ PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(
   m_isotopeLevel   = other.m_isotopeLevel;
   m_isotopeRank    = other.m_isotopeRank;
   m_z              = other.m_z;
+  qDebug();
 }
 
 PeptideNaturalIsotopeAverage::~PeptideNaturalIsotopeAverage()
@@ -237,4 +261,14 @@ PeptideNaturalIsotopeAverage::isEmpty() const
   return (m_peptideNaturalIsotopeSpList.size() == 0);
 }
 
+QString
+PeptideNaturalIsotopeAverage::toString() const
+{
+  return QString("%1 l%2 mz%3 z%4 N%5")
+    .arg(getPeptideInterfaceSp().get()->getSequence())
+    .arg(getPeptideInterfaceSp().get()->size())
+    .arg(getMz())
+    .arg(getCharge())
+    .arg(getIsotopeNumber());
+}
 } // namespace pappso

src/pappsomspp/peptide/peptidenaturalisotopeaverage.h

@@ -42,6 +42,14 @@ typedef std::shared_ptr<const PeptideNaturalIsotopeAverage>
 class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
 {
   public:
+  /** @brief fast constructor
+   * simple isotope build, not computing isotope ratio
+   */
+  PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide,
+                               unsigned int isotopeNumber,
+                               unsigned int charge,
+                               PrecisionPtr precision);
+
   PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide,
                                unsigned int askedIsotopeRank,
                                unsigned int isotopeLevel,
@@ -54,7 +62,7 @@ class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
                                PrecisionPtr precision);
 
   PeptideNaturalIsotopeAverage(const PeptideNaturalIsotopeAverage &other);
-  ~PeptideNaturalIsotopeAverage();
+  virtual ~PeptideNaturalIsotopeAverage();
 
   PeptideNaturalIsotopeAverageSp makePeptideNaturalIsotopeAverageSp() const;
   pappso_double getMz() const;
@@ -67,6 +75,7 @@ class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
   PrecisionPtr getPrecision() const;
   virtual bool matchPeak(pappso_double peak_mz) const final;
   bool isEmpty() const;
+  virtual QString toString() const;
 
   private:
   void recursiveDepletion(std::vector<PeptideNaturalIsotopeSp> &v_isotope_list,

src/pappsomspp/processing/detection/tracedetectioninterface.h

@@ -43,8 +43,15 @@ class TraceDetectionSinkInterface
 class TraceDetectionInterface
 {
   public:
-  virtual void detect(const Trace &xic,
-                      TraceDetectionSinkInterface &sink) const = 0;
+  /** @brief detect peaks on a trace
+   * @param trace the trace to detect peaks on
+   * @param sink the object to store peaks or stream it
+   * @param remove_peak_base if true, removes the area under the base of the
+   * peak
+   */
+  virtual void detect(const Trace &trace,
+                      TraceDetectionSinkInterface &sink,
+                      bool remove_peak_base) const = 0;
 };
 
 

src/pappsomspp/processing/detection/tracedetectionmoulon.cpp

@@ -84,7 +84,8 @@ TraceDetectionMoulon::getTicStop() const
 
 void
 TraceDetectionMoulon::detect(const Trace &xic,
-                             TraceDetectionSinkInterface &sink) const
+                             TraceDetectionSinkInterface &sink,
+                             bool remove_peak_base) const
 {
 
   Trace xic_smoothed(xic);
@@ -138,7 +139,7 @@ TraceDetectionMoulon::detect(const Trace &xic,
 
               if(banked)
                 {
-                  TracePeak peak(it_begin, it + 1);
+                  TracePeak peak(it_begin, it + 1, remove_peak_base);
                   sink.setTracePeak(peak);
                 }
               banked = false;

src/pappsomspp/processing/detection/tracedetectionmoulon.h

@@ -56,7 +56,8 @@ class PMSPP_LIB_DECL TraceDetectionMoulon : public TraceDetectionInterface
 
 
   void detect(const Trace &xic,
-              TraceDetectionSinkInterface &sink) const override;
+              TraceDetectionSinkInterface &sink,
+              bool remove_peak_base) const override;
 };
 
 

src/pappsomspp/processing/detection/tracedetectionzivy.cpp

@@ -107,7 +107,8 @@ TraceDetectionZivy::getDetectionThresholdOnMaxmin() const
 
 void
 TraceDetectionZivy::detect(const Trace &xic,
-                           TraceDetectionSinkInterface &sink) const
+                           TraceDetectionSinkInterface &sink,
+                           bool remove_peak_base) const
 {
 
   // detect peak positions on close curve : a peak is an intensity value
@@ -214,7 +215,7 @@ TraceDetectionZivy::detect(const Trace &xic,
               // peak.setMaxXicElement(*maxYDataPoint(it, xic_position));
 
               // areaTrace()
-              TracePeak peak(it, xic_position);
+              TracePeak peak(it, xic_position, remove_peak_base);
               sink.setTracePeak(peak);
               // }
               //++i;

src/pappsomspp/processing/detection/tracedetectionzivy.h

@@ -35,12 +35,6 @@ namespace pappso
 
 class PMSPP_LIB_DECL TraceDetectionZivy : public TraceDetectionInterface
 {
-  private:
-  FilterMorphoMean m_smooth;
-  FilterMorphoMinMax m_minMax;
-  FilterMorphoMaxMin m_maxMin;
-  pappso_double m_detectionThresholdOnMinMax;
-  pappso_double m_detectionThresholdOnMaxMin;
 
   public:
   TraceDetectionZivy(unsigned int smoothing_half_window_length,
@@ -65,7 +59,16 @@ class PMSPP_LIB_DECL TraceDetectionZivy : public TraceDetectionInterface
   pappso_double getDetectionThresholdOnMaxmin() const;
 
   void detect(const Trace &xic,
-              TraceDetectionSinkInterface &sink) const override;
+              TraceDetectionSinkInterface &sink,
+              bool remove_peak_base) const override;
+
+
+  private:
+  FilterMorphoMean m_smooth;
+  FilterMorphoMinMax m_minMax;
+  FilterMorphoMaxMin m_maxMin;
+  pappso_double m_detectionThresholdOnMinMax;
+  pappso_double m_detectionThresholdOnMaxMin;
 };
 
 } // namespace pappso

src/pappsomspp/processing/detection/tracepeak.cpp

@@ -31,6 +31,7 @@ namespace pappso
 TracePeak::TracePeak()
 {
 }
+
 TracePeak::TracePeak(std::vector<DataPoint>::const_iterator it_begin,
                      std::vector<DataPoint>::const_iterator it_end)
 {
@@ -41,6 +42,24 @@ TracePeak::TracePeak(std::vector<DataPoint>::const_iterator it_begin,
   m_area  = areaTrace(it_begin, it_end);
 }
 
+TracePeak::TracePeak(std::vector<DataPoint>::const_iterator it_begin,
+                     std::vector<DataPoint>::const_iterator it_end,
+                     bool remove_base)
+{
+
+  m_left  = *it_begin;
+  m_right = *(it_end - 1);
+  m_max   = *maxYDataPoint(it_begin, it_end);
+  m_area  = areaTrace(it_begin, it_end);
+  if(remove_base)
+    {
+      // remove the base of this peak
+      m_area -= std::min(m_left.y, m_right.y) * (m_right.x - m_left.x);
+      if(m_area < 0)
+        m_area = 0;
+    }
+}
+
 TracePeak::TracePeak(const TracePeak &other)
 {
   m_area  = other.m_area;
@@ -117,4 +136,38 @@ TracePeak::containsRt(pappso::pappso_double rt) const
   return (false);
 }
 
+
+const DataPoint &
+TracePeak::getMaxXicElement() const
+{
+  return m_max;
+}
+
+const DataPoint &
+TracePeak::getLeftBoundary() const
+{
+  return m_left;
+}
+
+
+bool
+TracePeak::operator==(const TracePeak &other) const
+{
+  return ((m_area == other.m_area) && (m_max == other.m_max) &&
+          (m_left == other.m_left) && (m_right == other.m_right));
+}
+
+TracePeak &
+TracePeak::operator=(const TracePeak &other)
+{
+  if(this == &other)
+    return *this;
+
+  m_area  = other.m_area;
+  m_max   = other.m_max;
+  m_left  = other.m_left;
+  m_right = other.m_right;
+
+  return *this;
+}
 } // namespace pappso

src/pappsomspp/processing/detection/tracepeak.h

@@ -38,18 +38,22 @@ typedef std::shared_ptr<const TracePeak> TracePeakCstSPtr;
  * */
 class PMSPP_LIB_DECL TracePeak
 {
-  protected:
-  pappso_double m_area = 0;
-  DataPoint m_max;
-  DataPoint m_left;
-  DataPoint m_right;
-
   public:
   TracePeak();
   /** @brief construct a peak given a trace, begin and end x coordinate
    */
   TracePeak(std::vector<DataPoint>::const_iterator it_begin,
             std::vector<DataPoint>::const_iterator it_end);
+
+  /** @brief construct a peak given a trace, begin and end x coordinate
+   *
+   * @param it_begin begining of trace
+   * @param it_end end of trace
+   * @param remove_base if true, remove the base peak signal
+   */
+  TracePeak(std::vector<DataPoint>::const_iterator it_begin,
+            std::vector<DataPoint>::const_iterator it_end,
+            bool remove_base);
   TracePeak(const TracePeak &other);
   ~TracePeak();
 
@@ -57,50 +61,34 @@ class PMSPP_LIB_DECL TracePeak
   TracePeakCstSPtr makeTracePeakCstSPtr() const;
 
   DataPoint &getMaxXicElement();
-  const DataPoint &
-  getMaxXicElement() const
-  {
-    return m_max;
-  };
+  const DataPoint &getMaxXicElement() const;
   void setMaxXicElement(const DataPoint &max);
 
   DataPoint &getLeftBoundary();
-  const DataPoint &
-  getLeftBoundary() const
-  {
-    return m_left;
-  };
+  const DataPoint &getLeftBoundary() const;
   void setLeftBoundary(const DataPoint &left);
 
   DataPoint &getRightBoundary();
   const DataPoint &getRightBoundary() const;
   void setRightBoundary(const DataPoint &right);
   pappso_double getArea() const;
+
+
   void setArea(pappso_double area);
 
   bool containsRt(pappso::pappso_double rt) const;
 
 
-  bool
-  operator==(const TracePeak &other) const
-  {
-    return ((m_area == other.m_area) && (m_max == other.m_max) &&
-            (m_left == other.m_left) && (m_right == other.m_right));
-  };
+  bool operator==(const TracePeak &other) const;
 
-  TracePeak &
-  operator=(const TracePeak &other)
-  {
-    if(this == &other)
-      return *this;
+  TracePeak &operator=(const TracePeak &other);
 
-    m_area  = other.m_area;
-    m_max   = other.m_max;
-    m_left  = other.m_left;
-    m_right = other.m_right;
 
-    return *this;
-  }
+  protected:
+  pappso_double m_area = 0;
+  DataPoint m_max;
+  DataPoint m_left;
+  DataPoint m_right;
 };