compute TIC on spectrum ms levels

src/CMakeLists.txt

@@ -152,6 +152,7 @@ SET(CPP_FILES
   utils/fastafilestore.cpp
   utils/identificationdatasourcestore.cpp
   utils/groupstore.cpp
+  utils/msrunstatisticshandler.cpp
   utils/msrunstore.cpp
   utils/peptideevidencestore.cpp
   utils/peptidestore.cpp

src/core/msrun.cpp

@@ -38,6 +38,7 @@
 #include <pappsomspp/msrun/msrunreaderfactory.h>
 #include <pappsomspp/exception/exceptionnotfound.h>
 #include <pappsomspp/xicextractor/msrunxicextractorfactory.h>
+#include "../utils/msrunstatisticshandler.h"
 
 MsRun::MsRun(const QString &location) : pappso::MsRunId(location)
 {
@@ -144,7 +145,7 @@ MsRun::checkMsRunStatistics()
     {
       try
         {
-          pappso::MsRunSimpleStatistics stats;
+          MsRunStatisticsHandler stats;
           _msrun_reader_sp.get()->readSpectrumCollection(stats);
 
           setMsRunStatistics(MsRunStatistics::total_spectra,
@@ -155,6 +156,12 @@ MsRun::checkMsRunStatistics()
                              (unsigned int)stats.getMsLevelCount(2));
           setMsRunStatistics(MsRunStatistics::total_spectra_ms3,
                              (unsigned int)stats.getMsLevelCount(3));
+          setMsRunStatistics(MsRunStatistics::tic_spectra_ms1,
+                             (unsigned int)stats.getMsLevelTic(1));
+          setMsRunStatistics(MsRunStatistics::tic_spectra_ms2,
+                             (unsigned int)stats.getMsLevelTic(2));
+          setMsRunStatistics(MsRunStatistics::tic_spectra_ms3,
+                             (unsigned int)stats.getMsLevelTic(3));
         }
       catch(pappso::ExceptionNotFound &error)
         {

src/utils/msrunstatisticshandler.cpp

+/**
+ * \file utils/msrunstatisticshandler.cpp
+ * \date 12/08/2018
+ * \author Olivier Langella
+ * \brief handler on MZ data file to read all spectrums and make basic
+ * statistics
+ */
+
+
+/*******************************************************************************
+ * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ *     XTPcpp 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.
+ *
+ *     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+ ******************************************************************************/
+
+#include "msrunstatisticshandler.h"
+#include <pappsomspp/msrun/msrunreader.h>
+
+
+bool
+MsRunStatisticsHandler::needPeakList() const
+{
+  return true;
+}
+void
+MsRunStatisticsHandler::setQualifiedSpectrum(
+  const pappso::QualifiedSpectrum &qspectrum)
+{
+  unsigned int ms_level = qspectrum.getMsLevel();
+  if(ms_level == 0)
+    return;
+  if(ms_level > _count_ms_level_spectrum.size())
+    {
+      _count_ms_level_spectrum.resize(ms_level);
+      _tic_ms_level_spectrum.resize(ms_level);
+    }
+  _count_ms_level_spectrum[ms_level - 1]++;
+
+  pappso::SpectrumSp spectrum_sp = qspectrum.getOriginalSpectrumSp();
+  if(spectrum_sp != nullptr)
+    {
+      for(auto &&peak : *(spectrum_sp.get()))
+        {
+
+          _tic_ms_level_spectrum[ms_level - 1] += peak.intensity;
+        }
+    }
+}
+
+unsigned long
+MsRunStatisticsHandler::getMsLevelCount(unsigned int ms_level) const
+{
+  if(ms_level == 0)
+    return 0;
+  if(ms_level > _count_ms_level_spectrum.size())
+    return 0;
+  return (_count_ms_level_spectrum[ms_level - 1]);
+}
+
+pappso::pappso_double
+MsRunStatisticsHandler::getMsLevelTic(unsigned int ms_level) const
+{
+  if(ms_level == 0)
+    return 0;
+  if(ms_level > _tic_ms_level_spectrum.size())
+    return 0;
+  return (_tic_ms_level_spectrum[ms_level - 1]);
+}
+
+unsigned long
+MsRunStatisticsHandler::getTotalCount() const
+{
+  unsigned long total = 0;
+  for(unsigned long count : _count_ms_level_spectrum)
+    {
+      total += count;
+    }
+  return total;
+}

src/utils/msrunstatisticshandler.h

+/**
+ * \file utils/msrunstatisticshandler.h
+ * \date 12/08/2018
+ * \author Olivier Langella
+ * \brief handler on MZ data file to read all spectrums and make basic statistics
+ */
+
+
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+*     XTPcpp 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.
+*
+*     XTPcpp 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 XTPcpp.  If not, see <http://www.gnu.org/licenses/>.
+******************************************************************************/
+
+#pragma once
+
+#include <pappsomspp/msrun/msrunreader.h>
+
+
+class MsRunStatisticsHandler : public pappso::SpectrumCollectionHandlerInterface
+{
+public:
+    virtual void setQualifiedSpectrum (const pappso::QualifiedSpectrum & qspectrum) override;
+    virtual bool needPeakList () const override ;
+    
+    unsigned long getMsLevelCount(unsigned int ms_level) const;
+    pappso::pappso_double getMsLevelTic(unsigned int ms_level) const;
+    
+    
+    unsigned long getTotalCount() const;
+    
+private:
+    std::vector<unsigned long> _count_ms_level_spectrum;
+    std::vector<pappso::pappso_double> _tic_ms_level_spectrum;
+};

src/utils/types.h

@@ -124,6 +124,9 @@ enum class MsRunStatistics : std::int8_t
   total_spectra_ms1 = 2, ///< total number of MS1 spectra
   total_spectra_ms2 = 3, ///< total number of MS2 spectra
   total_spectra_ms3 = 4, ///< total number of MS3 spectra
+  tic_spectra_ms1 = 5, ///< total ion current in MS1 spectra
+  tic_spectra_ms2 = 6, ///< total ion current in MS2 spectra
+  tic_spectra_ms3 = 7, ///< total ion current in MS3 spectra
 };