src/pappsomspp/widget/xicwidget/qcpxic.cpp

@@ -103,13 +103,11 @@ QCPXic::keyReleaseEvent(QKeyEvent *event)
 void
 QCPXic::mousePressEvent(QMouseEvent *event)
 {
-  qDebug() << "QCPXic::mousePressEvent begin "
-           << xAxis->pixelToCoord(event->x()) << " "
-           << yAxis->pixelToCoord(event->y());
+  qDebug() << " begin ";
   _mouse_move = false;
   _click      = true;
-  _old_x      = event->x();
-  _old_y      = yAxis->pixelToCoord(event->y());
+  _old_x      = event->position().x();
+  _old_y      = yAxis->pixelToCoord(event->position().y());
   if(_old_y < 0)
     {
       _old_y = 0;
@@ -123,8 +121,8 @@ void
 QCPXic::mouseReleaseEvent(QMouseEvent *event)
 {
   qDebug() << "QCPXic::mouseReleaseEvent begin "
-           << xAxis->pixelToCoord(event->x()) << " "
-           << yAxis->pixelToCoord(event->y());
+           << xAxis->pixelToCoord(event->position().x()) << " "
+           << yAxis->pixelToCoord(event->position().y());
   _click = false;
   if(_mouse_move)
     {
@@ -140,13 +138,13 @@ void
 QCPXic::mouseMoveEvent(QMouseEvent *event)
 {
   _mouse_move             = true;
-  pappso::pappso_double x = xAxis->pixelToCoord(event->x());
+  pappso::pappso_double x = xAxis->pixelToCoord(event->position().x());
   if(_click)
     {
       qDebug() << "QCPXic::mouseMoveEvent begin "
-               << xAxis->pixelToCoord(event->x()) << " "
-               << yAxis->pixelToCoord(event->y());
-      pappso::pappso_double y = yAxis->pixelToCoord(event->y());
+               << xAxis->pixelToCoord(event->position().x()) << " "
+               << yAxis->pixelToCoord(event->position().y());
+      pappso::pappso_double y = yAxis->pixelToCoord(event->position().y());
       if(y < 0)
         {
           y = 0;
@@ -161,9 +159,9 @@ QCPXic::mouseMoveEvent(QMouseEvent *event)
       else
         {
           this->xAxis->moveRange(xAxis->pixelToCoord(_old_x) -
-                                 xAxis->pixelToCoord(event->x()));
+                                 xAxis->pixelToCoord(event->position().x()));
         }
-      _old_x = event->x();
+      _old_x = event->position().x();
       _old_y = y;
       replot();
       qDebug() << "QCPXic::mouseMoveEvent end";
@@ -179,7 +177,7 @@ QCPXic::mouseMoveEvent(QMouseEvent *event)
     }
 }
 
-void
+QCPGraph *
 QCPXic::addXicP(const Xic *xic_p)
 {
 
@@ -207,6 +205,8 @@ QCPXic::addXicP(const Xic *xic_p)
       if(_intensity_range.upper < xic_p->maxYDataPoint().y)
         _intensity_range.upper = xic_p->maxYDataPoint().y;
     }
+
+  return graph_xic;
 }
 
 

src/pappsomspp/widget/xicwidget/qcpxic.h

@@ -49,7 +49,7 @@ class QCPXic : public QCustomPlot
   protected:
   void clear();
   void rescale();
-  void addXicP(const Xic *xic_p);
+  QCPGraph *addXicP(const Xic *xic_p);
   void addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt);
   void
   addXicPeakList(const Xic *xic_p,

src/pappsomspp/widget/xicwidget/xicwidget.cpp

@@ -63,11 +63,11 @@ XicWidget::addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt)
   _qcp_xic->addMsMsEvent(xic_p, rt);
   _map_xic_msms_event[xic_p] = rt;
 }
-void
-XicWidget::addXicSp(XicCstSPtr &xic_sp)
+QCPGraph *
+XicWidget::addXicSp(XicCstSPtr xic_sp)
 {
   _xic_sp_list.push_back(xic_sp);
-  _qcp_xic->addXicP(xic_sp.get());
+  return _qcp_xic->addXicP(xic_sp.get());
 }
 
 const QString &

src/pappsomspp/widget/xicwidget/xicwidget.h

@@ -52,7 +52,7 @@ class PMSPP_LIB_DECL XicWidget : public GraphicDeviceWidget
   ~XicWidget();
 
 
-  void addXicSp(XicCstSPtr &xic_sp);
+  QCPGraph *addXicSp(XicCstSPtr xic_sp);
   void addMsMsEvent(const Xic *xic_p, pappso::pappso_double rt);
   void
   addXicPeakList(const Xic *xic_p,

src/pappsomspp/xic/xic.cpp

@@ -40,6 +40,10 @@ Xic::Xic()
   qDebug() << "Xic::Xic end";
 }
 
+Xic::Xic(const Trace &other) : Trace(other)
+{
+}
+
 Xic::~Xic()
 {
 }

src/pappsomspp/xic/xic.h

@@ -44,6 +44,7 @@ class PMSPP_LIB_DECL Xic : public Trace
 {
   public:
   Xic();
+  Xic(const Trace & other);
   virtual ~Xic();
 
 

src/pappsomspp/xicextractor/msrunxicextractorfactory.cpp

@@ -72,8 +72,6 @@ MsRunXicExtractorInterfaceSp
 MsRunXicExtractorFactory::buildMsRunXicExtractorSp(
   MsRunReaderSPtr &msrun_reader) const
 {
-#if 0
-// Remove this section because it cripples my work on Qt6 build
 
   pappso::TimsMsRunReaderMs2 *tims2_reader =
     dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
@@ -116,7 +114,6 @@ MsRunXicExtractorFactory::buildMsRunXicExtractorSp(
       return (msrun_xic_extractor_sp);
     }
   return nullptr;
-#endif
 }
 
 

tests/CMakeLists.txt

@@ -32,6 +32,7 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
 
   find_package(Catch2 REQUIRED)
 
+
   if(OdsStream_FOUND)
   else (OdsStream_FOUND)
     find_package(OdsStream REQUIRED)
@@ -150,17 +151,17 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
   target_link_libraries(test_fasta_reader Qt6::Core pappsomspp-shared)
   add_test(test_fasta_reader "test_fasta_reader")
 
-  add_executable(test_protein test_protein.cpp)
-  target_link_libraries(test_protein Qt6::Core pappsomspp-shared)
-  add_test(test_protein "test_protein")
+  #add_executable(test_protein test_protein.cpp)
+  #target_link_libraries(test_protein Qt6::Core pappsomspp-shared)
+  #add_test(test_protein "test_protein")
 
   add_executable(test_massrange test_massrange.cpp)
   target_link_libraries(test_massrange Qt6::Core pappsomspp-shared)
   add_test(test_massrange "test_massrange")
 
-  add_executable(test_peptide test_peptide.cpp)
-  target_link_libraries(test_peptide Qt6::Core Qt6::Gui pappsomspp-shared)
-  add_test(test_peptide "test_peptide")
+  #add_executable(test_peptide test_peptide.cpp)
+  #target_link_libraries(test_peptide Qt6::Core Qt6::Gui pappsomspp-shared)
+  #add_test(test_peptide "test_peptide")
 
   add_executable(test_peptidenaturalisotopelist test_peptidenaturalisotopelist.cpp)
   target_link_libraries(test_peptidenaturalisotopelist Qt6::Core Qt6::Gui pappsomspp-shared)
@@ -179,9 +180,9 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
   add_test(test_fragmentationcid "test_fragmentationcid")
 
   #IF (FALSE) 
-  add_executable(test_big_hyperscore test_big_hyperscore.cpp ${CPP_TEST_FILES})
-  target_link_libraries(test_big_hyperscore Qt6::Core Qt6::Gui Qt6::Xml pappsomspp-shared)
-  add_test(test_big_hyperscore "test_big_hyperscore")
+  #add_executable(test_big_hyperscore test_big_hyperscore.cpp ${CPP_TEST_FILES})
+  #target_link_libraries(test_big_hyperscore Qt6::Core Qt6::Gui Qt6::Xml pappsomspp-shared)
+  #add_test(test_big_hyperscore "test_big_hyperscore")
   #ENDIF(FALSE)
 
   add_executable(test_rawmasslist test_rawmasslist.cpp)
@@ -189,32 +190,35 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
   add_test(test_rawmasslist "test_rawmasslist")
 
   add_executable(test_isotope_with_spectrum common.cpp test_isotope_with_spectrum.cpp)
-  target_link_libraries(test_isotope_with_spectrum Qt6::Core Qt6::Gui pappsomspp-shared  ${Boost_LIBRARIES})
+  target_link_libraries(test_isotope_with_spectrum Qt6::Core Qt6::Gui
+    QuaZip::QuaZip pappsomspp-shared  ${Boost_LIBRARIES})
   add_test(test_isotope_with_spectrum "test_isotope_with_spectrum")
   set(TEST_LIST ${TEST_LIST} test_isotope_with_spectrum)
 
   add_executable(test_hyperscore common.cpp test_hyperscore.cpp)
-  target_link_libraries(test_hyperscore Qt6::Core pappsomspp-shared Qt6::Gui  ${Boost_LIBRARIES})
+  target_link_libraries(test_hyperscore Qt6::Core pappsomspp-shared Qt6::Gui
+    QuaZip::QuaZip ${Boost_LIBRARIES})
   add_test(test_hyperscore "test_hyperscore")
   set(TEST_LIST ${TEST_LIST} test_hyperscore)
 
   add_executable(test_xtandem_spectrum common.cpp test_xtandem_spectrum.cpp)
-  target_link_libraries(test_xtandem_spectrum Qt6::Core pappsomspp-shared Qt6::Gui  ${Boost_LIBRARIES})
+  target_link_libraries(test_xtandem_spectrum Qt6::Core pappsomspp-shared
+    Qt6::Gui QuaZip::QuaZip ${Boost_LIBRARIES})
   add_test(test_xtandem_spectrum "test_xtandem_spectrum")
   set(TEST_LIST ${TEST_LIST} test_xtandem_spectrum)
 
   add_executable(test_scan_15968  common.cpp test_scan_15968.cpp)
-  target_link_libraries(test_scan_15968 Qt6::Core Qt6::Gui pappsomspp-shared  ${Boost_LIBRARIES})
+  target_link_libraries(test_scan_15968 Qt6::Core Qt6::Gui pappsomspp-shared QuaZip::QuaZip ${Boost_LIBRARIES})
   add_test(test_scan_15968 "test_scan_15968")
   set(TEST_LIST ${TEST_LIST} test_scan_15968)
 
   add_executable(test_psm common.cpp test_psm.cpp)
-  target_link_libraries(test_psm Qt6::Core pappsomspp-shared Qt6::Gui Qt6::Concurrent  ${Boost_LIBRARIES})
+  target_link_libraries(test_psm Qt6::Core pappsomspp-shared Qt6::Gui Qt6::Concurrent QuaZip::QuaZip ${Boost_LIBRARIES})
   add_test(test_psm "test_psm")
   set(TEST_LIST ${TEST_LIST} test_psm)
 
   add_executable(test_xicextractor test_xicextractor.cpp)
-  target_link_libraries(test_xicextractor Qt6::Core Qt6::Gui pappsomspp-shared  ${Boost_LIBRARIES} OdsStream::Core)
+  target_link_libraries(test_xicextractor Qt6::Core Qt6::Gui pappsomspp-shared  ${Boost_LIBRARIES} QuaZip::QuaZip OdsStream::Core)
   add_test(test_xicextractor "test_xicextractor")
   set(TEST_LIST ${TEST_LIST} test_xicextractor)
 
@@ -224,14 +228,14 @@ if(MAKE_TESTS AND (WIN64 OR (UNIX AND NOT APPLE)))
   set(TEST_LIST ${TEST_LIST} test_msrunoutput)
 
 
-  if(UNIX)
+  #if(UNIX)
 
-    set_property(TEST catch2-only-tests test_big_hyperscore test_fasta_reader 
-      test_massrange test_peptidenaturalisotopelist test_peptidefragment 
-      test_fragmentationcid ${TEST_LIST} test_natural_isotope_average test_rawmasslist 
-      PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
+  #set_property(TEST catch2-only-tests test_big_hyperscore test_fasta_reader 
+  #test_massrange test_peptidenaturalisotopelist test_peptidefragment 
+  #test_fragmentationcid ${TEST_LIST} test_natural_isotope_average test_rawmasslist 
+  #PROPERTY ENVIRONMENT "LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH}:../src")
 
-  endif()
+  #endif()
 
   if(WIN32)
     set(ENV{PATH} "$ENV{PATH};..\\src")

tests/test_psm.cpp

@@ -27,11 +27,16 @@
  ******************************************************************************/
 
 // make test ARGS="-V -I 18,18"
+// ./tests/catch2-only-tests [psm] -s
+// ./tests/catch2-only-tests [psmfeature] -s
 
 #define CATCH_CONFIG_MAIN
+
+#include <algorithm>
 #include <catch2/catch.hpp>
 #include <pappsomspp/mzrange.h>
 #include <pappsomspp/psm/peptidespectrummatch.h>
+#include <pappsomspp/psm/features/psmfeatures.h>
 #include <iostream>
 #include <iomanip>
 #include <set>
@@ -83,5 +88,242 @@ TEST_CASE("psm test suite.", "[psm]")
       spectrum_simple, peptide_sp, 2, precision, ion_list);
     test_count = psmb.countTotalMatchedIons();
     REQUIRE(test_count == 0);
+
+
+    precision = PrecisionFactory::getDaltonInstance(0.02);
+    PeptideIsotopeSpectrumMatch psm_iso(
+      spectrum_simple, peptide_sp, 2, precision, ion_list, 2, 0);
+
+    std::list<PeakIonIsotopeMatch> peak_ion_isotope_match_list =
+      psm_iso.getPeakIonIsotopeMatchList();
+
+    for(auto peak : peak_ion_isotope_match_list)
+      {
+        qDebug() << peak.toString() << " "
+                 << peak.getPeptideNaturalIsotopeAverageSp().get();
+      }
+    REQUIRE(peak_ion_isotope_match_list.size() == 19);
+
+    psm_iso.dropPeaksLackingMonoisotope();
+    peak_ion_isotope_match_list = psm_iso.getPeakIonIsotopeMatchList();
+    for(auto peak : peak_ion_isotope_match_list)
+      {
+        qDebug() << peak.toString() << " "
+                 << peak.getPeptideNaturalIsotopeAverageSp().get();
+      }
+    REQUIRE(peak_ion_isotope_match_list.size() == 19);
+
+    qDebug() << peak_ion_isotope_match_list.size();
+    peak_ion_isotope_match_list.sort(
+      [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+        qDebug() << a.getPeak().y << " > ";
+        qDebug() << b.getPeak().y << " . ";
+        return (a.getPeak().y > b.getPeak().y);
+      });
+
+
+    spectrum_simple = readMgf(
+      QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
+
+    peptide_sp = Peptide("AIADGSLLDLLR").makePeptideSp();
+
+
+    precision = PrecisionFactory::getDaltonInstance(0.02);
+    qDebug();
+    PeptideIsotopeSpectrumMatch psm_iso_check(
+      spectrum_simple, peptide_sp, 2, precision, ion_list, 2, 0);
+
+    qDebug();
+    peak_ion_isotope_match_list = psm_iso_check.getPeakIonIsotopeMatchList();
+
+    REQUIRE(peak_ion_isotope_match_list.size() == 39);
+    qDebug();
+
+    for(auto &peak : peak_ion_isotope_match_list)
+      {
+        qDebug() << peak.toString() << " "
+                 << peak.getPeptideNaturalIsotopeAverageSp().get();
+      }
+
+
+    peak_ion_isotope_match_list.sort(
+      [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
+        if(a.getPeptideIonType() < b.getPeptideIonType())
+          return true;
+        if(a.getPeptideFragmentIonSp().get()->size() <
+           b.getPeptideFragmentIonSp().get()->size())
+          return true;
+        if(a.getCharge() < b.getCharge())
+          return true;
+        if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() <
+           b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
+          return true;
+        return false;
+      });
+
+
+    auto it = peak_ion_isotope_match_list.begin();
+    REQUIRE(it->toString().toStdString() == "b2+isotope0r1mz185.128");
+    it++;
+    REQUIRE(it->toString().toStdString() == "b3+isotope0r1mz256.165");
+
+    for(auto peak : peak_ion_isotope_match_list)
+      {
+        qDebug() << peak.toString() << " "
+                 << peak.getPeptideNaturalIsotopeAverageSp().get();
+      }
+
+    psm_iso_check.dropPeaksLackingMonoisotope();
+    peak_ion_isotope_match_list = psm_iso_check.getPeakIonIsotopeMatchList();
+
+    for(auto peak : peak_ion_isotope_match_list)
+      {
+        qDebug() << peak.toString() << " "
+                 << peak.getPeptideNaturalIsotopeAverageSp().get();
+      }
+    REQUIRE(peak_ion_isotope_match_list.size() == 39);
+  }
+}
+
+
+TEST_CASE("psm features test suite.", "[psmfeature]")
+{
+  // Set the debugging message formatting pattern.
+  qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
+
+  SECTION("..:: readMgf ::..", "[psm]")
+  {
+    cout << std::endl << "..:: readMgf ::.." << std::endl;
+    // bool refine_spectrum_synthesis = false;
+
+    MassSpectrum spectrum_simple =
+      readMgf(QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_2016.mgf"));
+    //.applyCutOff(150).takeNmostIntense(100).applyDynamicRange(100);
+
+
+    Peptide peptide("EDKPQPPPEGR");
+    PeptideSp peptide_sp(peptide.makePeptideSp());
+    // peptide_sp.get()->addAaModification(AaModification::getInstance("MOD:00397"),
+    // 0);
+
+    PsmFeatures features(PrecisionFactory::getDaltonInstance(0.02), 150);
+
+    features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 3);
+
+    REQUIRE(features.getTotalIntensity() == Approx(248641.8659667977));
+    REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::b) ==
+            Approx(1751.5864257813).epsilon(0.001));
+    REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::y) ==
+            Approx(57112.2947998047).epsilon(0.001));
+
+
+    REQUIRE(features.countMatchedIonComplementPairs() == 0);
+
+
+    /*
+    <group id="15968" mh="1275.731419" z="2" rt="PT2843.58S" expect="1.7e-04"
+  label="GRMZM5G815453_P01 P00874 Ribulose bisphosphate carboxylase large chain
+  Precursor..." type="model" sumI="6.08" maxI="111642" fI="1116.42" act="0" >
+  <protein expect="-191.8" id="15968.1" uid="49237" label="GRMZM5G815453_P01
+  P00874 Ribulose bisphosphate carboxylase large chain Precursor..." sumI="8.97"
+  > <note label="description">GRMZM5G815453_P01 P00874 Ribulose bisphosphate
+  carboxylase large chain Precursor (RuBisCO large subunit)(EC 4.1.1.39)
+  seq=translation; coord=Pt:56824..58323:1; parent_transcript=GRMZM5G815453_T01;
+  parent_gene=GRMZM5G815453</note> <file type="peptide"
+  URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/> <peptide
+  start="1" end="483"> <domain id="15968.1.1" start="347" end="357"
+  expect="1.7e-04" mh="1275.7311" delta="0.0003" hyperscore="29.0"
+  nextscore="10.8" y_score="10.5" y_ions="8" b_score="3.8" b_ions="1" pre="EGER"
+  post="DDFI" seq="EITLGFVDLLR" missed_cleavages="0">
+  </domain>
+  </peptide>
+  */
+    spectrum_simple =
+      readMgf(QString(CMAKE_SOURCE_DIR).append("/tests/data/scan_15968.mgf"));
+
+
+    peptide_sp = Peptide("EITLGFVDLLR").makePeptideSp();
+
+    features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 2);
+
+
+    REQUIRE(
+      features.getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() ==
+      Approx(-0.0036778069).epsilon(0.00001));
+    REQUIRE(features.countMatchedIonComplementPairs() == 3);
+
+    REQUIRE(features.getPeakIonPairs().size() == 3);
+
+    REQUIRE(features.getPeakIonPairs()[0].first.toString().toStdString() ==
+            "b2+isotope0r1mz243.134");
+    REQUIRE(features.getPeakIonPairs()[0].second.toString().toStdString() ==
+            "y9+isotope0r1mz1033.61");
+
+    REQUIRE(features.getPeakIonPairs()[1].first.toString().toStdString() ==
+            "b6+isotope0r1mz661.367");
+    REQUIRE(features.getPeakIonPairs()[1].second.toString().toStdString() ==
+            "y5+isotope0r1mz615.383");
+
+    REQUIRE(features.getPeakIonPairs()[2].first.toString().toStdString() ==
+            "b7+isotope0r1mz760.435");
+    REQUIRE(features.getPeakIonPairs()[2].second.toString().toStdString() ==
+            "y4+isotope0r1mz516.315");
+
+
+    REQUIRE(
+      features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[0]) ==
+      Approx(-0.0036778069).epsilon(0.001));
+    REQUIRE(
+      features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[1]) ==
+      Approx(-0.0118262069).epsilon(0.001));
+    REQUIRE(
+      features.getIonPairPrecursorMassDelta(features.getPeakIonPairs()[2]) ==
+      Approx(-0.0114600069).epsilon(0.001));
+
+
+    REQUIRE(features.getMaxConsecutiveIon(PeptideIon::y) == 9);
+    REQUIRE(features.getMaxConsecutiveIon(PeptideIon::b) == 2);
+    REQUIRE(features.getMaxConsecutiveIon(PeptideIon::a) == 0);
+
+
+    spectrum_simple = readMgf(
+      QString(CMAKE_SOURCE_DIR).append("/tests/data/peaklist_15046.mgf"));
+
+    peptide_sp = Peptide("AIADGSLLDLLR").makePeptideSp();
+
+    features.setPeptideSpectrumCharge(peptide_sp, &spectrum_simple, 2);
+    REQUIRE(features.getMaxConsecutiveIon(PeptideIon::y) == 10);
+    REQUIRE(features.getMaxConsecutiveIon(PeptideIon::b) == 3);
+    REQUIRE(features.getAaSequenceCoverage(PeptideIon::y) == 10);
+    REQUIRE(features.getAaSequenceCoverage(PeptideIon::b) == 5);
+
+
+    REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::y) ==
+            Approx(863068.6967769999));
+    REQUIRE(features.getMaxIntensityPeakIonMatch(PeptideIon::y) ==
+            Approx(114514.0625));
+
+    REQUIRE(features.getIntensityOfMatchedIon(PeptideIon::b) ==
+            Approx(254791.342651));
+    REQUIRE(features.getMaxIntensityPeakIonMatch(PeptideIon::b) ==
+            Approx(161016.984375));
+
+
+    // SeqCoverComplementPeaks
+    REQUIRE(features.getComplementPairsAaSequenceCoverage() == 5);
+    REQUIRE(((double)features.getComplementPairsAaSequenceCoverage() /
+             (double)peptide_sp.get()->size()) == Approx(5.0 / 12.0));
+    REQUIRE(((double)0 / (double)peptide_sp.get()->size()) == Approx(0));
+
+
+    REQUIRE((features.getTotalIntensityOfMatchedIonComplementPairs() /
+             features.getTotalIntensity()) == Approx(0.1727291768));
+
+    REQUIRE((features.getTotalIntensityOfMatchedIonComplementPairs() <
+             features.getTotalIntensity()));
+
+    REQUIRE(
+      features.getMaxIntensityMatchedIonComplementPairPrecursorMassDelta() ==
+      Approx(0.0008592852).epsilon(0.00001));
   }
 }

tests/test_xic.cpp

@@ -313,15 +313,15 @@ TEST_CASE("XIC test suite.", "[XIC]")
                xicprm_test);
 
     INFO("readOdsXic OK");
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     TraceDetectionZivy _zivy(2, 3, 3, 5000, 6000);
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     TraceDetectionMaxSink max_peak_tic;
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     try
       {
-        _zivy.detect(xicprm_test, max_peak_tic);
-        qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+        _zivy.detect(xicprm_test, max_peak_tic, true);
+        qDebug();
       }
     catch(PappsoException &error)
       {
@@ -339,41 +339,41 @@ TEST_CASE("XIC test suite.", "[XIC]")
     OdsDocWriter writer(&fileods);
     TracePeakOdsWriterSink ods_sink(writer);
 
-    _zivy.detect(xicprm_test, ods_sink);
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    _zivy.detect(xicprm_test, ods_sink, true);
+    qDebug();
     writer.close();
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     fileods.close();
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
 
     Xic realxic_test;
     readOdsXic(QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic.ods"),
                realxic_test);
     INFO("readOdsXic OK");
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     QFile realfileods(
       QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic_detect.ods"));
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     OdsDocWriter realwriter(&realfileods);
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     TracePeakOdsWriterSink real_ods_sink(realwriter);
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     //_zivy.setSink(&max_peak_tic);
     TraceDetectionZivy _zivyb(2, 4, 3, 30000, 50000);
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     try
       {
-        _zivyb.detect(realxic_test, real_ods_sink);
+        _zivyb.detect(realxic_test, real_ods_sink, true);
       }
     catch(PappsoException &error)
       {
         INFO("error TraceDetectionZivy : " << error.qwhat().toStdString());
         throw error;
       }
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
     realwriter.close();
     realfileods.close();
-    qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+    qDebug();
 
     QFile realfilemoulondetectods(
       QString(CMAKE_SOURCE_DIR)
@@ -383,7 +383,7 @@ TEST_CASE("XIC test suite.", "[XIC]")
 
     TraceDetectionMoulon moulon(4, 60000, 40000);
 
-    moulon.detect(realxic_test, real_detect_moulonods_sink);
+    moulon.detect(realxic_test, real_detect_moulonods_sink, true);
 
     realdetectmoulonwriter.close();
     realfilemoulondetectods.close();
@@ -453,25 +453,25 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
     Xic empty_xic;
     TraceDetectionZivy _zivy(2, 3, 3, 5000, 6000);
     TracePeakList peak_list;
-    _zivy.detect(empty_xic, peak_list);
+    _zivy.detect(empty_xic, peak_list, true);
     REQUIRE(peak_list.size() == 0);
 
     empty_xic.resize(2);
     fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1));
 
-    _zivy.detect(empty_xic, peak_list);
+    _zivy.detect(empty_xic, peak_list, true);
     REQUIRE(peak_list.size() == 0);
 
     empty_xic.resize(3);
     fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1));
 
-    _zivy.detect(empty_xic, peak_list);
+    _zivy.detect(empty_xic, peak_list, true);
     REQUIRE(peak_list.size() == 0);
 
     empty_xic.resize(4);
     fill(empty_xic.begin(), empty_xic.end(), DataPoint(1, 1));
 
-    _zivy.detect(empty_xic, peak_list);
+    _zivy.detect(empty_xic, peak_list, true);
     REQUIRE(peak_list.size() == 0);
 
 
@@ -484,7 +484,7 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
         i++;
       }
 
-    _zivy.detect(empty_xic, peak_list);
+    _zivy.detect(empty_xic, peak_list, true);
     REQUIRE(peak_list.size() == 0);
 
 
@@ -497,7 +497,7 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
         i++;
       }
 
-    _zivy.detect(empty_xic, peak_list);
+    _zivy.detect(empty_xic, peak_list, true);
     REQUIRE(peak_list.size() == 0);
   }
   SECTION("test for masschroq issue#15", "[tracepeaklist]")
@@ -512,7 +512,7 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
     TraceDetectionZivy zivy15(2, 4, 3, 5000, 3000);
     TracePeakList peak_list;
     qDebug();
-    zivy15.detect(xic, peak_list);
+    zivy15.detect(xic, peak_list, true);
     qDebug();
     REQUIRE(peak_list.size() == 0);
   }
@@ -528,8 +528,23 @@ TEST_CASE("test operations on tracepeaklist", "[tracepeaklist]")
     readOdsXic(QString(CMAKE_SOURCE_DIR).append("/tests/data/xic/real_xic.ods"),
                xicprm_test);
 
+    TracePeak peak(
+      xicprm_test.begin() + 9079, xicprm_test.begin() + 9142, false);
+
+    REQUIRE(peak.getArea() == Approx(96163224.06));
+
+    TracePeak peak_nobase(
+      xicprm_test.begin() + 9079, xicprm_test.begin() + 9142, true);
+
+    REQUIRE(peak_nobase.getArea() == Approx(76281621.60));
+
+    REQUIRE(
+      peak_nobase.getLeftBoundary().y *
+        (peak_nobase.getRightBoundary().x - peak_nobase.getLeftBoundary().x) ==
+      Approx(peak.getArea() - peak_nobase.getArea()));
+
     INFO("readOdsXic OK");
-    REQUIRE_NOTHROW(_zivy.detect(xicprm_test, peak_list));
+    REQUIRE_NOTHROW(_zivy.detect(xicprm_test, peak_list, true));
 
     REQUIRE(peak_list.size() == 64);
 

tests/widget/main.cpp

@@ -28,6 +28,7 @@
  ******************************************************************************/
 
 #include <QApplication>
+#include <QIODevice>
 #include <pappsomspp/pappsoexception.h>
 #include "testwidgetgui.h"