From cd82892964354d4d56db7615d7fc0e7337f379df Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Tue, 8 May 2018 07:50:47 +0200
Subject: [PATCH] using new xic extractor API
---
.../identificationdatasource.cpp | 2 +-
src/core/msrun.cpp | 54 +---------
src/core/msrun.h | 18 +---
src/gui/xic_view/xic_box/xicbox.cpp | 6 +-
src/gui/xic_view/xic_box/xicbox.h | 6 +-
src/gui/xic_view/xicworkerthread.cpp | 4 +-
src/gui/xic_view/xicworkerthread.h | 6 +-
src/main.cpp | 4 +-
src/output/masschroqml.cpp | 2 +-
src/utils/readspectrum.cpp | 98 ++-----------------
src/utils/readspectrum.h | 4 +-
src/utils/types.h | 20 ----
12 files changed, 29 insertions(+), 195 deletions(-)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index 4ae412c97..dfdfe885d 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -142,7 +142,7 @@ const QVariant IdentificationDataSource::getIdentificationEngineStatistics(Ident
}
pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
- if (_ms_run_sp.get()->getMzFormat() == MzFormat::MGF) {
+ if (_ms_run_sp.get()->getMzFormat() == pappso::MzFormat::MGF) {
scan_number = scan_number-1;
}
pappso::SpectrumSp spectrum_sp = SpectrumStore::getSpectrumSpFromMsRunSp(_ms_run_sp.get(), scan_number);
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 79fe42606..6ff532309 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -32,61 +32,17 @@
#include "msrun.h"
#include <QFileInfo>
-MsRun::MsRun(const QString & location) {
- _xml_id = location;
- _location = location;
+MsRun::MsRun(const QString & location):pappso::MsRunId(location) {
QFileInfo fileinfo(location);
- _name = fileinfo.baseName();
}
-MsRun::MsRun(const MsRun& other) {
- _xml_id = other._xml_id;
- _location = other._location;
- _name = other._name;
- _mz_format=other._mz_format;
+MsRun::MsRun(const MsRun& other):pappso::MsRunId(other) {
_param_stats = other._param_stats;
}
MsRun::~MsRun() {
}
-
-void MsRun::setSampleName(const QString & name) {
- _name = name;
-}
-const QString & MsRun::getSampleName() const {
- return _name;
-}
-
-void MsRun::setFilename(const QString filename) {
- _location = filename;
- QFileInfo file_info(filename);
- QString extension = file_info.suffix();
- _mz_format = MzFormat::unknown;
- if (extension.toLower() == "mzxml") {
- _mz_format = MzFormat::mzXML;
- }
- else if (extension.toLower() == "mgf") {
- _mz_format = MzFormat::MGF;
- }
- else if (extension.toLower() == "mzml") {
- _mz_format = MzFormat::mzML;
- }
-}
-void MsRun::setXmlId(const QString xmlid) {
- _xml_id = xmlid;
-}
-const QString & MsRun::getXmlId() const {
- return _xml_id;
-}
-const QString & MsRun::getFilename() const {
- return _location;
-}
-
-MzFormat MsRun::getMzFormat() const {
- return _mz_format;
-}
-
void MsRun::setMsRunStatistics(MsRunStatistics param, const QVariant& value) {
_param_stats.insert(std::pair<MsRunStatistics, QVariant>(param, value));
}
@@ -103,9 +59,3 @@ const QVariant MsRun::getMsRunStatistics(MsRunStatistics param) const {
return QVariant();
}
}
-
-/*
-void MsRun::setMzFormat(MzFormat mz_format) {
- _mz_format = mz_format;
-}
-*/
diff --git a/src/core/msrun.h b/src/core/msrun.h
index e56bbc469..f6429edb0 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -35,29 +35,19 @@
#include <memory>
#include <QString>
#include <QVariant>
+#include <pappsomspp/msrun/msrunid.h>
#include "../utils/types.h"
class MsRun;
typedef std::shared_ptr<MsRun> MsRunSp;
-class MsRun
+class MsRun:public pappso::MsRunId
{
public:
MsRun(const QString & location);
MsRun(const MsRun& other);
~MsRun();
- void setFilename(const QString filename);
- void setSampleName(const QString & name);
- void setXmlId(const QString xmlid);
-
- const QString & getFilename() const;
- const QString & getSampleName() const;
- const QString & getXmlId() const;
-
- MzFormat getMzFormat() const;
- //void setMzFormat(MzFormat mz_format);
-
/** \brief set MS run statistics
* any statistics on this MS run file
@@ -74,10 +64,6 @@ public:
virtual const std::map<MsRunStatistics, QVariant> & getMsRunStatisticsMap() const;
private :
- QString _xml_id;
- QString _location;
- QString _name;
- MzFormat _mz_format=MzFormat::mzXML;
std::map<MsRunStatistics, QVariant> _param_stats;
};
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 2dbb52512..8180f0dd8 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -230,7 +230,7 @@ void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidenc
}
-void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
+void XicBox::setXic(std::vector< pappso::MsRunXicSp> xic_sp_list) {
qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
ui->xic_widget->clear();
for (int i=0; i < xic_sp_list.size(); i++) {
@@ -361,7 +361,7 @@ void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverage
_natural_isotope_list.push_back({nullptr, natural_isotope_average, nullptr, nullptr});
}
- emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
+ emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), pappso::XicExtractMethod::max);
//histogram
QCPBars * theoretical_ratio = new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis);
@@ -417,7 +417,7 @@ void XicBox::reExtractXic() {
for (const XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
mass_list.push_back(xic_isotope.peptide_natural_isotope_sp.get()->getMz());
}
- emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
+ emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), pappso::XicExtractMethod::max);
qDebug() << "XicBox::reExtractXic end";
}
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 91eac5074..f16ed3333 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -35,7 +35,7 @@
#include "../../../utils/types.h"
#include "../../../core/peptideevidence.h"
#include "../xicwindow.h"
-#include <pappsomspp/xic/xic.h>
+#include <pappsomspp/xicextractor/msrunxic.h>
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include <qcustomplot.h>
@@ -66,12 +66,12 @@ public:
void setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidence, MsRunSp msrun_sp);
signals :
- void loadXic(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method);
+ void loadXic(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, pappso::XicExtractMethod method);
void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
private slots:
void remove();
void reExtractXic();
- void setXic(std::vector< pappso::XicSp> xic_sp_list);
+ void setXic(std::vector< pappso::MsRunXicSp> xic_sp_list);
void setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void error(QString error_message);
void extractXicInOtherMsRun();
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index 32ac2202f..db6b3593e 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -32,14 +32,14 @@
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include <pappsomspp/pappsoexception.h>
-void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method) {
+void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, pappso::XicExtractMethod method) {
try {
std::vector<pappso::MassRange> mass_list;
for (pappso::mz mass:mz_list) {
mass_list.push_back(pappso::MassRange(mass, precision));
}
- std::vector<pappso::XicSp> xic_sp_list = SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
+ std::vector<pappso::MsRunXicSp> xic_sp_list = SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
emit xicLoaded(xic_sp_list);
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index 6d4c294af..cdc6e7fa6 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -29,7 +29,7 @@
#ifndef XICWORKERTHREAD_H
#define XICWORKERTHREAD_H
-#include <pappsomspp/xic/xic.h>
+#include <pappsomspp/xicextractor/msrunxic.h>
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include<QObject>
#include "../../core/msrun.h"
@@ -40,11 +40,11 @@ class XicWorkerThread : public QObject
public:
public slots:
- void doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, XicExtractMethod method);
+ void doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, pappso::XicExtractMethod method);
void doComputeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio);
signals:
- void xicLoaded(std::vector<pappso::XicSp> xic_sp_list);
+ void xicLoaded(std::vector<pappso::MsRunXicSp> xic_sp_list);
void isotopeMassListComputed(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void operationFailed(QString error);
diff --git a/src/main.cpp b/src/main.cpp
index 0ccd5ce68..52d22fcce 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -39,9 +39,9 @@ int main(int argc, char *argv[])
qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
- qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
+ qRegisterMetaType<std::vector<pappso::MsRunXicSp>>("std::vector<pappso::MsRunXicSp>");
qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
- qRegisterMetaType<XicExtractMethod>("XicExtractMethod");
+ qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
qRegisterMetaType<MsRunSp>("MsRunSp");
qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>("std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index a5a4e3f50..ac070fda9 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -126,7 +126,7 @@ void MassChroQml::write(ProjectSp sp_project) {
//<data_file id="samp0" format="mzxml" path="bsa1.mzXML" type="centroid" />
_output_stream->writeStartElement("data_file");
_output_stream->writeAttribute("id",msrun.get()->getXmlId());
- if(msrun.get()->getMzFormat() == MzFormat::mzXML) {
+ if(msrun.get()->getMzFormat() == pappso::MzFormat::mzXML) {
_output_stream->writeAttribute("format","mzxml");
}
_output_stream->writeAttribute("path",msrun.get()->getFilename());
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
index 0bc49b518..6c8e03314 100644
--- a/src/utils/readspectrum.cpp
+++ b/src/utils/readspectrum.cpp
@@ -30,6 +30,7 @@
#include <QString>
#include <pappsomspp/spectrum/spectrum.h>
#include <pappsomspp/exception/exceptionnotfound.h>
+#include <pappsomspp/xicextractor/msrunxicextractorfactory.h>
#include <pwiz/data/common/cv.hpp>
#include <pwiz_tools/common/FullReaderList.hpp>
@@ -78,85 +79,6 @@ pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
return dataFile;
}
-void getXicFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, std::vector< pappso::Xic> & xic_list, const std::vector<pappso::MassRange> & mass_range_list, XicExtractMethod method) {
- qDebug() << "getXicFromPwizMSDataFile begin mass_range_list.size()=" << mass_range_list.size() << " xic_list.size()=" << xic_list.size();
- std::string env;
- env=setlocale(LC_ALL,"");
- setlocale(LC_ALL,"C");
-
-
-
-
- const pwiz::msdata::SpectrumList * p_spectrum_list = p_ms_data_file->run.spectrumListPtr.get();
- std::size_t spectrum_list_size = p_spectrum_list->size();
- pwiz::msdata::SpectrumPtr spectrum;
-
- std::vector<XicElement> peak_for_mass;
- for (const pappso::MassRange & mass_range: mass_range_list) {
- peak_for_mass.push_back(XicElement());
- qDebug() << "getXicFromPwizMSDataFile begin mass_range=" << mass_range.getMz();
- }
-
- bool ms1 = false;
-
- for (std::size_t i=0; i < spectrum_list_size; i++) {
- spectrum = p_spectrum_list->spectrum(i, false);
- unsigned int ms_level(QString(spectrum->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
-//qDebug() << "getXicFromPwizMSDataFile ms_level" << ms_level;
- if (ms_level == 1) {
- ms1 = true;
- spectrum = p_spectrum_list->spectrum(i, true);
- for (XicElement & peak: peak_for_mass) {
- peak.rt = QString(spectrum->scanList.scans[0].cvParam(pwiz::msdata::MS_scan_start_time).value.c_str()).toDouble();
- peak.intensity = 0;
- }
-
- vector<pwiz::msdata::MZIntensityPair> pairs;
- spectrum->getMZIntensityPairs(pairs);
-
- // iterate through the m/z-intensity pairs
- for (vector<pwiz::msdata::MZIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
- {
- //qDebug() << "getXicFromPwizMSDataFile it->mz " << it->mz << " it->intensity" << it->intensity;
- for (int i=0; i < mass_range_list.size(); i++) {
- if (mass_range_list[i].contains(it->mz)) {
- if (method == XicExtractMethod::max) {
- if (peak_for_mass[i].intensity < it->intensity) {
- peak_for_mass[i].intensity = it->intensity;
- }
- }
- else {
- peak_for_mass[i].intensity += it->intensity;
- }
- }
- }
- }
-
- for (int i=0; i < mass_range_list.size(); i++) {
- //qDebug() << "getXicFromPwizMSDataFile push_back " << peak_for_mass[i].rt;
- xic_list[i].push_back(peak_for_mass[i]);
- }
- }
-
- }
-
-
- if (ms1 == false) {
- throw pappso::PappsoException(QObject::tr("error extracting XIC: no MS level 1 in data file"));
- }
-
- for (int i=0; i < xic_list.size(); i++) {
- xic_list[i] .sortByRetentionTime();
-
- //qDebug() << "getXicFromPwizMSDataFile end " << xic_list[i].size();
- }
- qDebug() << "getXicFromPwizMSDataFile end";
-
-
- setlocale(LC_ALL,env.c_str());
-
-}
-
pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num) {
unsigned int precursor_charge_state=0;
@@ -394,7 +316,7 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsign
return spectrum.getOriginalSpectrumSp();
}
spectrum = getQualifiedSpectrumFromPwizMSDataFile(p_msdatafile, scan_num);
- if (msrun->getMzFormat() == MzFormat::MGF) {
+ if (msrun->getMzFormat() == pappso::MzFormat::MGF) {
if (spectrum.getRtInSeconds() == 0) {
spectrum = getQualifiedSpectrumFromPwizMSDataFile(p_msdatafile, scan_num-1);
}
@@ -403,25 +325,21 @@ pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsign
}
-std::vector<pappso::XicSp> SpectrumStore::getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, XicExtractMethod method) {
+std::vector<pappso::MsRunXicSp> SpectrumStore::getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method) {
qDebug() << "SpectrumStore::getXicSpFromMsRunSp begin" ;
- std::vector<pappso::XicSp> xic_sp_list;
+ std::vector<pappso::MsRunXicSp> xic_sp_list;
if (p_msrun == nullptr) {
qDebug() << "SpectrumStore::getXicSpFromMsRunSp ERROR p_msrun == nullptr " ;
throw pappso::ExceptionNotFound(QObject::tr("SpectrumStore::getXicSpFromMsRunSp ERROR p_msrun == nullptr"));
//return spectrum;
}
+
pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(p_msrun);
if (p_msdatafile != nullptr) {
- std::vector<Xic> xic_list;
- xic_list.resize(mass_range_list.size());
- getXicFromPwizMSDataFile(p_msdatafile, xic_list, mass_range_list, method);
-
- for (const Xic & xic:xic_list) {
- xic_sp_list.push_back( xic.makeXicSp());
- }
- //qDebug() << "SpectrumStore::getXicSpFromMsRunSp end" << xic_sp.get()->size();
+ pappso::MsRunXicExtractorSp extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorPwizSp(*p_msrun);
+ extractor->setXicExtractMethod(method);
+ return extractor.get()->getMsRunXicSpList(mass_range_list);
}
return (xic_sp_list);
}
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
index 84c1752c0..3680a0729 100644
--- a/src/utils/readspectrum.h
+++ b/src/utils/readspectrum.h
@@ -26,7 +26,7 @@
#include <QString>
#include <pappsomspp/spectrum/qualifiedspectrum.h>
-#include <pappsomspp/xic/xic.h>
+#include <pappsomspp/xicextractor/msrunxic.h>
#include <map>
#include "../core/msrun.h"
@@ -43,7 +43,7 @@ class MSDataFile;
class SpectrumStore {
public:
static pappso::SpectrumSp getSpectrumSpFromMsRunSp(MsRun * p_msrun, unsigned int scan_num);
- static std::vector<pappso::XicSp> getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, XicExtractMethod method);
+ static std::vector<pappso::MsRunXicSp> getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method);
/** @brief try to find MS run statistics
*/
static void checkMsRunStatistics(MsRun *);
diff --git a/src/utils/types.h b/src/utils/types.h
index a4c17d75f..0809820b3 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -91,15 +91,6 @@ enum class MsRunStatistics: std::int8_t {
-/** \def XixExtactMethod method to extract Xic
- *
- */
-enum class XicExtractMethod: std::int8_t {
- sum=1, ///< sum of intensities
- max=2 ///< maximum of intensities
-};
-
-
/** \def ProjectMode separate each samples or combine all
*
*/
@@ -119,17 +110,6 @@ enum class GroupingType {
};
-/** \def MzFormat mz data file format types
- *
- */
-
-enum class MzFormat: std::int8_t {
- unknown=0, ///< unknown format
- mzML=1, ///< mzML
- mzXML=2, ///< mzXML
- MGF=3, ///< Mascot format
-};
-
/** \def ValidationState
*
*/
--
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