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Commit cd828929 authored by Langella Olivier's avatar Langella Olivier
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using new xic extractor API

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src/core/identification_sources/identificationdatasource.cpp
+ 1
− 1
View file @ cd828929
......@@ -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);
......
src/core/msrun.cpp
+ 2
− 52
View file @ cd828929
......@@ -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;
}
*/
src/core/msrun.h
+ 2
− 16
View file @ cd828929
......@@ -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;
};
......
src/gui/xic_view/xic_box/xicbox.cpp
+ 3
− 3
View file @ cd828929
......@@ -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";
}
......
src/gui/xic_view/xic_box/xicbox.h
+ 3
− 3
View file @ cd828929
......@@ -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();
......
src/gui/xic_view/xicworkerthread.cpp
+ 2
− 2
View file @ cd828929
......@@ -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);
......
src/gui/xic_view/xicworkerthread.h
+ 3
− 3
View file @ cd828929
......@@ -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);
......
src/main.cpp
+ 2
− 2
View file @ cd828929
......@@ -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>");
......
src/output/masschroqml.cpp
+ 1
− 1
View file @ cd828929
......@@ -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());
......
src/utils/readspectrum.cpp
+ 8
− 90
View file @ cd828929
......@@ -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);
}
src/utils/readspectrum.h
+ 2
− 2
View file @ cd828929
......@@ -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 *);
......
src/utils/types.h
+ 0
− 20
View file @ cd828929
......@@ -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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