From bd1467f79e641cf3c28141c58b1ced634792e29b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 12 Jul 2018 21:47:48 +0200
Subject: [PATCH] compute TIC on spectrum ms levels
---
src/CMakeLists.txt | 1 +
src/core/msrun.cpp | 9 ++-
src/utils/msrunstatisticshandler.cpp | 92 ++++++++++++++++++++++++++++
src/utils/msrunstatisticshandler.h | 48 +++++++++++++++
src/utils/types.h | 3 +
5 files changed, 152 insertions(+), 1 deletion(-)
create mode 100644 src/utils/msrunstatisticshandler.cpp
create mode 100644 src/utils/msrunstatisticshandler.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 840bbd57b..e4de9a708 100644
--- a/src/CMakeLists.txt
+++ b/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
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 3f577aa1e..17723ee25 100644
--- a/src/core/msrun.cpp
+++ b/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)
{
diff --git a/src/utils/msrunstatisticshandler.cpp b/src/utils/msrunstatisticshandler.cpp
new file mode 100644
index 000000000..d61bed553
--- /dev/null
+++ b/src/utils/msrunstatisticshandler.cpp
@@ -0,0 +1,92 @@
+/**
+ * \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;
+}
diff --git a/src/utils/msrunstatisticshandler.h b/src/utils/msrunstatisticshandler.h
new file mode 100644
index 000000000..81645e296
--- /dev/null
+++ b/src/utils/msrunstatisticshandler.h
@@ -0,0 +1,48 @@
+/**
+ * \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;
+};
diff --git a/src/utils/types.h b/src/utils/types.h
index a7b2cd536..c80ad03cc 100644
--- a/src/utils/types.h
+++ b/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
};
--
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