diff --git a/debian/control.cmake b/debian/control.cmake
index e54f68d519c1202e6ebd34a11f1d3d2056b8d431..d3f83a02400edae8c4a08565f20a6b5409f36b88 100644
--- a/debian/control.cmake
+++ b/debian/control.cmake
@@ -7,6 +7,7 @@ Build-Depends: debhelper (>= 9),
cmake (>= 2.6),
qtbase5-dev,
libpappsomspp-widget-qt5-dev (= @LIBPAPPSOMSPP_VERSION@),
+ libpwiz-dev,
libodsstream-qt5-dev,
libboost1.62-dev,
libqt5svg5-dev,
@@ -20,6 +21,7 @@ Multi-Arch: no
Depends: ${shlibs:Depends},
${misc:Depends},
libpappsomspp-widget-qt5-0 (= @LIBPAPPSOMSPP_VERSION@),
+ libpwiz3,
libodsstream-qt5-0,
libqt5gui5,
libqt5core5a,
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 76b83adf50be9ec63c244513e6eda552724d2113..a11e04512986f4189066da1ae8e0a6f1c851ef83 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -154,7 +154,6 @@ SET(CPP_FILES
utils/peptideevidencestore.cpp
utils/peptidestore.cpp
utils/proteinstore.cpp
- utils/readspectrum.cpp
utils/utils.cpp
)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index dfdfe885dc665934bcdac0242d76ec0033d35857..0f21750d3a4793713edd73a124d765b42693dfe5 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -24,8 +24,8 @@
#include "identificationdatasource.h"
#include "identificationxtandemfile.h"
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/exception/exceptionnotfound.h>
#include <QFileInfo>
-#include "../../utils/readspectrum.h"
#include "../peptideevidence.h"
IdentificationDataSource::IdentificationDataSource(const QString resource_name)
@@ -142,10 +142,17 @@ const QVariant IdentificationDataSource::getIdentificationEngineStatistics(Ident
}
pappso::SpectrumSp IdentificationDataSource::getSpectrumSp(unsigned int scan_number) const {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
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);
+ if (_ms_run_sp.get()->findMsRunFile() == false) {
+ throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(_ms_run_sp.get()->getFilename()));
+ }
+
+ //qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumListSize();
+ pappso::SpectrumSp spectrum_sp = _ms_run_sp.get()->getMsRunReaderSp().get()->getSpectrumSp(scan_number);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
return spectrum_sp;
}
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 6ff532309cf476e7599a6860e381b6fb031ad092..d1a0ad8ce93b49f2b35b0d73eeca3cb76d51218e 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -31,6 +31,11 @@
#include "msrun.h"
#include <QFileInfo>
+#include <QSettings>
+#include <QDebug>
+#include <QDir>
+#include <pappsomspp/msrun/msrunreaderfactory.h>
+#include <pappsomspp/exception/exceptionnotfound.h>
MsRun::MsRun(const QString & location):pappso::MsRunId(location) {
QFileInfo fileinfo(location);
@@ -42,6 +47,9 @@ MsRun::MsRun(const MsRun& other):pappso::MsRunId(other) {
MsRun::~MsRun() {
}
+pappso::MsRunReaderSp & MsRun::getMsRunReaderSp() {
+ return _msrun_reader_sp;
+}
void MsRun::setMsRunStatistics(MsRunStatistics param, const QVariant& value) {
_param_stats.insert(std::pair<MsRunStatistics, QVariant>(param, value));
@@ -59,3 +67,61 @@ const QVariant MsRun::getMsRunStatistics(MsRunStatistics param) const {
return QVariant();
}
}
+
+bool MsRun::findMsRunFile() {
+
+ QFileInfo file(this->getFilename());
+ bool file_ok = false;
+
+ if (file.exists()) {
+ file_ok = true;
+ }
+
+ QString basename = file.baseName();
+ QString onlyfilename = file.fileName();
+ QSettings settings;
+ QString path = settings.value("path/mzdatadir", "").toString();
+
+ QDir dir_search(path);
+
+ QFileInfoList files = dir_search.entryInfoList();
+ foreach (QFileInfo file, files) {
+ if (file.isDir()) {
+ qDebug() << "DIR: " << file.fileName();
+ } else {
+ qDebug() << "FILE: " << file.fileName();
+ if (onlyfilename == file.fileName()) {
+ this->setFilename(file.absoluteFilePath());
+ file_ok = true;
+ }
+ if (file.fileName().contains(onlyfilename)) {
+ this->setFilename(file.absoluteFilePath());
+ file_ok = true;
+ }
+ }
+ }
+ if (file_ok) {
+ if (_msrun_reader_sp == nullptr) {
+ _msrun_reader_sp = pappso::MsRunReaderFactory::getInstance().buildPwizMsRunReaderSp(*this);
+ }
+ }
+ return file_ok;
+}
+
+void MsRun::checkMsRunStatistics() {
+ QVariant msrun_var = getMsRunStatistics(MsRunStatistics::total_spectra);
+ if (msrun_var.isNull()) {
+ try {
+ pappso::MsRunSimpleStatistics stats;
+ _msrun_reader_sp.get()->readSpectrumCollection(stats);
+
+ setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) stats.getTotalCount());
+ setMsRunStatistics(MsRunStatistics::total_spectra_ms1, (unsigned int) stats.getMsLevelCount(1));
+ setMsRunStatistics(MsRunStatistics::total_spectra_ms2, (unsigned int) stats.getMsLevelCount(2));
+ setMsRunStatistics(MsRunStatistics::total_spectra_ms3, (unsigned int) stats.getMsLevelCount(3));
+ }
+ catch (pappso::ExceptionNotFound& error) {
+ //no file found, no statistics
+ }
+ }
+}
diff --git a/src/core/msrun.h b/src/core/msrun.h
index f6429edb0d873bf3ac99551d5bbeb4b4661a17b3..fd711b1e0ca90df8b6b43348c3a65755c36483e2 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -36,6 +36,7 @@
#include <QString>
#include <QVariant>
#include <pappsomspp/msrun/msrunid.h>
+#include <pappsomspp/msrun/msrunreader.h>
#include "../utils/types.h"
class MsRun;
@@ -62,9 +63,17 @@ public:
/** \brief get MS run statistics map
*/
virtual const std::map<MsRunStatistics, QVariant> & getMsRunStatisticsMap() const;
+
+ bool findMsRunFile();
+
+ pappso::MsRunReaderSp & getMsRunReaderSp();
+
+ void checkMsRunStatistics();
private :
std::map<MsRunStatistics, QVariant> _param_stats;
+
+ pappso::MsRunReaderSp _msrun_reader_sp;
};
#endif // MSRUN_H
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index dd71b7fb1a1605e35721dc1c6671712c1418f2a8..3aed2e9b0eefc7f8c6f3eb8f23467cbafca51314 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -31,8 +31,6 @@
#include <pappsomspp/types.h>
#include <pappsomspp/peptide/peptide.h>
#include <pappsomspp/spectrum/spectrum.h>
-#include <pwiz/data/msdata/MSDataFile.hpp>
-#include "../utils/readspectrum.h"
#include "core/project.h"
#include "project_view/projectwindow.h"
#include "load_results_dialog/loadresultsdialog.h"
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index cfda3d450d2438589fcca0694a35e25d5fa580e3..9e8591291ce5fdc56aa8add50c3e7bb9a4556d6e 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -23,7 +23,6 @@
#include "peptidewindow.h"
#include "../project_view/projectwindow.h"
-#include "../../utils/readspectrum.h"
#include "../../config.h"
#include "ui_peptide_detail_view.h"
#include <pappsomspp/exception/exceptionnotfound.h>
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index 63858aa38b3456f41ef1cdc660ca6b17ac2f2658..3f83a25d6076e3af508b0fcf3f5a85fe73958fa5 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -28,9 +28,11 @@
#include <tuple>
#include "xicworkerthread.h"
-#include "../../utils/readspectrum.h"
#include <pappsomspp/peptide/peptidenaturalisotopelist.h>
#include <pappsomspp/pappsoexception.h>
+#include <pappsomspp/xicextractor/msrunxicextractorfactory.h>
+#include <pappsomspp/exception/exceptionnotfound.h>
+#include <QDebug>
void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list, pappso::PrecisionP precision, pappso::XicExtractMethod method) {
@@ -39,9 +41,35 @@ void XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_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::XicSp> xic_sp_list = SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
- emit xicLoaded(xic_sp_list);
+ if (p_msrun.get()->findMsRunFile()) {
+ pappso::MsRunId msrun_id = * (p_msrun.get());
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " " << msrun_id.getFilename();
+ auto it = std::find_if(_extractor_list.begin(), _extractor_list.end(), [msrun_id](const pappso::MsRunXicExtractorSp & extractor_sp) {
+ return extractor_sp.get()->getMsRunId().getXmlId() == msrun_id.getXmlId();
+ });
+
+ pappso::MsRunXicExtractorSp extractor;
+ if (it == _extractor_list.end()) {
+
+ pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
+ extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorPwizSp(msrun_id);
+ _extractor_list.push_back(extractor);
+ }
+ else {
+ extractor = *it;
+ }
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
+ extractor.get()->setXicExtractMethod(method);
+
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
+ std::vector<pappso::XicSp> xic_sp_list = extractor.get()->getXicSpList(mass_list);
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
+ emit xicLoaded(xic_sp_list);
+ }
}
catch (pappso::PappsoException & error) {
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index a59b86c58d45fd84a7e7af4ea136f1ea7dc61db1..36f4cce343057365ba16b01e7425fe9d8b9b07f6 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -33,6 +33,7 @@
#include<QObject>
#include "../../core/msrun.h"
#include <pappsomspp/xic/xic.h>
+#include <pappsomspp/xicextractor/msrunxicextractor.h>
class XicWorkerThread : public QObject
{
@@ -47,6 +48,9 @@ signals:
void xicLoaded(std::vector<pappso::XicSp> xic_sp_list);
void isotopeMassListComputed(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list);
void operationFailed(QString error);
+
+private:
+ std::vector<pappso::MsRunXicExtractorSp> _extractor_list;
};
#endif // XICWORKERTHREAD_H
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index bd14cf75a786c54ffbfa0d660800af7b9e8d455c..a9f2665a6e2e92641758dcd2c484fc5bb4635ed4 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -28,7 +28,6 @@
******************************************************************************/
#include "samplesheet.h"
-#include "../../utils/readspectrum.h"
SampleSheet::SampleSheet (OdsExport * p_ods_export, CalcWriterInterface * p_writer, const Project * p_project): _p_project(p_project) {
_p_writer = p_writer;
@@ -109,7 +108,7 @@ void SampleSheet::writeIdentificationDataSource(IdentificationDataSource * p_ide
_p_writer->writeLine();
MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
if (_msrun_statistics) {
- SpectrumStore::checkMsRunStatistics(msrun_sp.get());
+ if (msrun_sp->findMsRunFile()) msrun_sp->checkMsRunStatistics();
}
_p_writer->writeCell(msrun_sp.get()->getXmlId());
diff --git a/src/utils/readspectrum.cpp b/src/utils/readspectrum.cpp
deleted file mode 100644
index 935d916003701d595b20cbfe3272dc02def1f01b..0000000000000000000000000000000000000000
--- a/src/utils/readspectrum.cpp
+++ /dev/null
@@ -1,359 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools 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.
-*
-* PAPPSOms-tools 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 PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-
-#include "readspectrum.h"
-
-#include <QDebug>
-#include <QSettings>
-#include <QFileInfo>
-#include <QDir>
-#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>
-//#include <pwiz/utility/misc/Std.hpp>
-#include <pwiz/data/msdata/SpectrumInfo.hpp>
-#include <pwiz/data/msdata/MSData.hpp>
-#include <locale>
-
-#include <pwiz/data/msdata/MSDataFile.hpp>
-//http://sourceforge.net/p/proteowizard/mailman/message/28245157/
-
-using namespace pappso;
-
-pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename);
-
-pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num);
-
-
-pwiz::msdata::MSDataFile * getPwizMSDataFile(const QString & filename) {
- qDebug() << "getPwizMSDataFile opening file " << filename ;
- std::string env;
- env=setlocale(LC_ALL,"");
- struct lconv * lc = localeconv ();
- qDebug() << " env=" << env.c_str() << " lc->decimal_point " << lc->decimal_point;
- setlocale(LC_ALL,"C");
- //lc = localeconv ();
- //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
- pwiz::msdata::MSDataFile * dataFile;
- try {
- QByteArray byte_array = filename.toUtf8();
- std::string res = "";
- for (char c : byte_array) {
- res += c;
- }
- dataFile = new pwiz::msdata::MSDataFile(res);
- }
- catch (std::exception& error)
- {
- qDebug() << "getPwizMSDataFile std error ";
- throw pappso::PappsoException(QObject::tr("Error reading file (%1) using proteowizard library : %2").arg(filename).arg(error.what()));
- }
- setlocale(LC_ALL,env.c_str());
-
- return dataFile;
-}
-
-pappso::QualifiedSpectrum getQualifiedSpectrumFromPwizMSDataFile(pwiz::msdata::MSDataFile * p_ms_data_file, unsigned int scan_num) {
- unsigned int precursor_charge_state=0;
-
- pappso::QualifiedSpectrum qspectrum;
-
- vector< pwiz::msdata::SourceFilePtr >::iterator source_file_it = p_ms_data_file->fileDescription.sourceFilePtrs.begin();
- if (source_file_it != p_ms_data_file->fileDescription.sourceFilePtrs.end()) {
- qspectrum.setSpectrumId(SpectrumId(MsRunId((*source_file_it)->name.c_str()), scan_num));
- }
- else {
- qspectrum.setSpectrumId(SpectrumId(MsRunId("no msrun id"), scan_num));
- }
- if (p_ms_data_file == nullptr) {
- return (qspectrum);
- }
- std::string env;
- env=setlocale(LC_ALL,"");
- setlocale(LC_ALL,"C");
- const bool getBinaryData = true;
- pwiz::msdata::SpectrumListPtr spectrum_list_ptr = p_ms_data_file->run.spectrumListPtr;
- pwiz::msdata::CVID native_id_format;
- unsigned int spectrum_index = 0;
- if (spectrum_list_ptr.get()->size() == 1) {
- spectrum_index = 0;
- }
- else {
- // turn our scan numbers into navtieId strings for pwiz
- native_id_format = pwiz::msdata::id::getDefaultNativeIDFormat(*p_ms_data_file);
- string nativeScanId = pwiz::msdata::id::translateScanNumberToNativeID(native_id_format, QString("%1").arg(scan_num).toStdString());
- spectrum_index = spectrum_list_ptr.get()->find(nativeScanId);
- }
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile spectrum_index " << spectrum_index;
- if (spectrum_index == spectrum_list_ptr.get()->size()) {
- //pwiz::msdata::SpectrumPtr simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(10, getBinaryData);
- //qDebug() << "spectrum id 10 " << simple_spectrum_pwiz.get()->get;
- throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file").arg(scan_num));
- }
- pwiz::msdata::SpectrumPtr simple_spectrum_pwiz;
- try {
- simple_spectrum_pwiz = spectrum_list_ptr.get()->spectrum(spectrum_index, getBinaryData);
- } catch (std::runtime_error & error) {
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile error " << error.what() << " " << typeid(error).name();
- throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file std::runtime_error :\n%2").arg(scan_num).arg(error.what()));
- }
- catch (std::exception & error) {
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile error " << error.what() << " " << typeid(error).name();
- throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file :\n%2").arg(scan_num).arg(error.what()));
- }
- if (simple_spectrum_pwiz.get() == nullptr) {
- throw ExceptionNotFound(QObject::tr("scan number %1 not found in MS file : null pointer").arg(scan_num));
- }
-
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile precursors.size() " << simple_spectrum_pwiz.get()->precursors.size();
- if (simple_spectrum_pwiz.get()->precursors.size() > 0) {
- pwiz::msdata::Precursor & precursor = *(simple_spectrum_pwiz.get()->precursors.begin());
- if (precursor.selectedIons.size() > 0) {
- pwiz::msdata::SelectedIon & ion = *(precursor.selectedIons.begin());
-
- //selected ion m/z
- mz selected_ion_mz = QString(ion.cvParam(pwiz::cv::MS_selected_ion_m_z).value.c_str()).toDouble();
- //peak intensity
- pappso_double peak_intensity = QString(ion.cvParam(pwiz::cv::MS_peak_intensity).value.c_str()).toDouble();
-
- // unsigned int test = QString(ion.cvParam(pwiz::cv::MS_1200_series_LC_MSD_SL).value.c_str()).toUInt();
- // qDebug() << " tes "<< test;
- //charge state
- unsigned int charge_state = QString(ion.cvParam(pwiz::cv::MS_charge_state).value.c_str()).toUInt();
-
-
- qspectrum.setPrecursorMz(selected_ion_mz);
- qDebug() << " selected_ion_mz "<< selected_ion_mz ;
- qDebug() << " peak_intensity "<< peak_intensity;
- qDebug() << " charge_state "<< charge_state;
- if (charge_state > 0) {
- precursor_charge_state = charge_state;
- qspectrum.setPrecursorCharge(charge_state);
-
- }
- }
- }
-
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile msLevel" ;
- unsigned int msLevel(QString(simple_spectrum_pwiz->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
-
- pappso_double retentionTime = QString(simple_spectrum_pwiz->scanList.scans[0].cvParam(pwiz::msdata::MS_scan_start_time).value.c_str()).toDouble();
- qspectrum.setRtInSeconds(retentionTime);
- qspectrum.setMsLevel(msLevel);
-
- /* for (pwiz::data::CVParam cv_param :ion.cvParams) {
- pwiz::msdata::CVID param_id = cv_param.cvid;
- qDebug() << param_id ;
- //qDebug() << cv_param.cvid.c_str();
- qDebug() << cv_param.name().c_str();
- qDebug() << cv_param.value.c_str();
- }*/
- // fill in MZIntensityPair vector for convenient access to binary data
- vector<pwiz::msdata::MZIntensityPair> pairs;
- simple_spectrum_pwiz->getMZIntensityPairs(pairs);
- // cout << "spectrum_simple size:" << pairs.size() << endl;
- setlocale(LC_ALL,env.c_str());
-
- Spectrum spectrum;
-
- // iterate through the m/z-intensity pairs
- for (vector<pwiz::msdata::MZIntensityPair>::const_iterator it=pairs.begin(), end=pairs.end(); it!=end; ++it)
- {
- //qDebug() << "it->mz " << it->mz << " it->intensity" << it->intensity;
- spectrum.push_back(Peak(it->mz, it->intensity));
- }
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile spectrum size " << spectrum.size();
- if (native_id_format == pwiz::cv::CVID::MS_Mascot_MGF_format) {
- //sort peaks by mz
- spectrum = spectrum.takeNmostIntense(1000);
- //spectrum.sortMz();
- }
- //cout << "spectrum_simple size " << spectrum_simple.getSpectrumSize()<< endl;
-
- // lc = localeconv ();
- //qDebug() << " env=" << localeconv () << " lc->decimal_point " << lc->decimal_point;
- SpectrumSp spectrum_sp = spectrum.makeSpectrumSp();
- qspectrum.setOriginalSpectrumSp(spectrum_sp);
- qDebug() << "getQualifiedSpectrumFromPwizMSDataFile end ";
- return qspectrum;
-}
-
-std::map<const MsRun *, pwiz::msdata::MSDataFile *> create_map()
-{
- std::map<const MsRun *, pwiz::msdata::MSDataFile *> m;
- return m;
-}
-
-std::map<const MsRun *, pwiz::msdata::MSDataFile *> SpectrumStore::_map_msrun_msdatafile = create_map();
-
-std::map<const MsRun *, pappso::MsRunXicExtractorSp> create_xicmap()
-{
- std::map<const MsRun *, pappso::MsRunXicExtractorSp> m;
- return m;
-}
-
-std::map<const MsRun *, pappso::MsRunXicExtractorSp> SpectrumStore::_map_msrun_msrunxicextractor = create_xicmap();
-
-
-const QString SpectrumStore::findMzFile(const QString &filename) {
-
- QFileInfo file(filename);
-
- if (file.exists()) {
- return file.absoluteFilePath();
- }
-
- QString basename = file.baseName();
- QString onlyfilename = file.fileName();
- QSettings settings;
- QString path = settings.value("path/mzdatadir", "").toString();
-
- QDir dir_search(path);
-
- QFileInfoList files = dir_search.entryInfoList();
- foreach (QFileInfo file, files) {
- if (file.isDir()) {
- qDebug() << "DIR: " << file.fileName();
- } else {
- qDebug() << "FILE: " << file.fileName();
- if (onlyfilename == file.fileName()) {
- return file.absoluteFilePath();
- }
- if (file.fileName().contains(onlyfilename)) {
- return file.absoluteFilePath();
- }
- }
- }
- return QString();
-}
-
-void SpectrumStore::checkMsRunStatistics(MsRun * msrun) {
- QVariant msrun_var = msrun->getMsRunStatistics(MsRunStatistics::total_spectra);
- if (msrun_var.isNull()) {
- try {
- pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
- const pwiz::msdata::SpectrumList * p_spectrum_list = p_msdatafile->run.spectrumListPtr.get();
- std::size_t spectrum_list_size = p_spectrum_list->size();
- msrun->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
-
- unsigned int count_mslevel[50] = {0};
- for (std::size_t i=0; i < spectrum_list_size; i++) {
- pwiz::msdata::SpectrumPtr spectrum = p_spectrum_list->spectrum(i, false);
- unsigned int msLevel(QString(spectrum->cvParam(pwiz::msdata::MS_ms_level).value.c_str()).toUInt());
- count_mslevel[msLevel]++;
- }
-
- msrun->setMsRunStatistics(MsRunStatistics::total_spectra, (unsigned int) spectrum_list_size);
- msrun->setMsRunStatistics(MsRunStatistics::total_spectra_ms1, (unsigned int) count_mslevel[1]);
- msrun->setMsRunStatistics(MsRunStatistics::total_spectra_ms2, (unsigned int) count_mslevel[2]);
- msrun->setMsRunStatistics(MsRunStatistics::total_spectra_ms3, (unsigned int) count_mslevel[3]);
- }
- catch (pappso::ExceptionNotFound& error) {
- //no file found, no statistics
- }
- }
-}
-
-pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(const MsRun * p_msrun) {
- pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
- std::map<const MsRun *, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(p_msrun);
- if (it_msdata == _map_msrun_msdatafile.end()) {
- //not found
- throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(p_msrun->getFilename()));
- }
- else {
- p_msdatafile =it_msdata->second;
- }
- return p_msdatafile;
-}
-
-pwiz::msdata::MSDataFile * SpectrumStore::findPwizMSDataFile(MsRun * p_msrun) {
- pwiz::msdata::MSDataFile * p_msdatafile = nullptr;
- std::map<const MsRun *, pwiz::msdata::MSDataFile *>::iterator it_msdata = _map_msrun_msdatafile.find(p_msrun);
- if (it_msdata == _map_msrun_msdatafile.end()) {
- //not found
-
- QString mz_file = findMzFile(p_msrun->getFilename());
- if (mz_file.isEmpty()) {
- qDebug() << "SpectrumStore::getSpectrumSpFromMsRunIdSp ERROR file not found " << p_msrun->getFilename();
- throw pappso::ExceptionNotFound(QObject::tr("mz data \"%1\" file not found").arg(p_msrun->getFilename()));
- //return spectrum;
- }
- p_msrun->setFilename(mz_file);
- p_msdatafile = getPwizMSDataFile(mz_file);
- //msrun.get()->setMzFormat(getPwizMSDataFileFormat(p_msdatafile));
- _map_msrun_msdatafile.insert(std::pair<const MsRun *, pwiz::msdata::MSDataFile *>(p_msrun, p_msdatafile));
- }
- else {
- p_msdatafile =it_msdata->second;
- }
- return p_msdatafile;
-}
-
-pappso::SpectrumSp SpectrumStore::getSpectrumSpFromMsRunSp(MsRun * msrun, unsigned int scan_num) {
- pappso::QualifiedSpectrum spectrum;
- pwiz::msdata::MSDataFile * p_msdatafile = findPwizMSDataFile(msrun);
-
- if (p_msdatafile == nullptr) {
- return spectrum.getOriginalSpectrumSp();
- }
- spectrum = getQualifiedSpectrumFromPwizMSDataFile(p_msdatafile, scan_num);
- if (msrun->getMzFormat() == pappso::MzFormat::MGF) {
- if (spectrum.getRtInSeconds() == 0) {
- spectrum = getQualifiedSpectrumFromPwizMSDataFile(p_msdatafile, scan_num-1);
- }
- }
- return spectrum.getOriginalSpectrumSp();
-
-}
-
-std::vector<pappso::XicSp> SpectrumStore::getXicSpFromMsRunSp(MsRun * p_msrun, const std::vector<pappso::MassRange> & mass_range_list, pappso::XicExtractMethod method) {
- qDebug() << "SpectrumStore::getXicSpFromMsRunSp begin" ;
- pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
- std::vector<pappso::XicSp> 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) {
- auto it = _map_msrun_msrunxicextractor.find(p_msrun);
- if (it == _map_msrun_msrunxicextractor.end()) {
- pappso::MsRunXicExtractorSp extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorPwizSp(*p_msrun);
-
- _map_msrun_msrunxicextractor.insert(std::pair<MsRun *, pappso::MsRunXicExtractorSp>(p_msrun, extractor));
- extractor->setXicExtractMethod(method);
- return extractor.get()->getXicSpList(mass_range_list);
- }
- it->second.get()->setXicExtractMethod(method);
- return it->second.get()->getXicSpList(mass_range_list);
- }
- return (xic_sp_list);
-}
diff --git a/src/utils/readspectrum.h b/src/utils/readspectrum.h
deleted file mode 100644
index 1f5c916eae2c7aac971ea6b21656ac01d2a11369..0000000000000000000000000000000000000000
--- a/src/utils/readspectrum.h
+++ /dev/null
@@ -1,58 +0,0 @@
-
-/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools 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.
-*
-* PAPPSOms-tools 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 PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
-
-#ifndef READSPECTRUM_H
-#define READSPECTRUM_H
-
-#include <QString>
-#include <pappsomspp/spectrum/qualifiedspectrum.h>
-#include <pappsomspp/xicextractor/msrunxicextractor.h>
-#include <map>
-#include "../core/msrun.h"
-
-pappso::Spectrum readSpectrum(const QString & filename, unsigned int scan_num,unsigned int & precursor_charge_state);
-
-
-namespace pwiz {
-namespace msdata {
-class MSDataFile;
-}
-}
-//MzFormat getPwizMSDataFileFormat(pwiz::msdata::MSDataFile * p_ms_data_file);
-
-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, pappso::XicExtractMethod method);
- /** @brief try to find MS run statistics
- */
- static void checkMsRunStatistics(MsRun *);
-private:
- static const QString findMzFile(const QString &filename);
- static pwiz::msdata::MSDataFile * findPwizMSDataFile(MsRun * p_msrun) ;
- static pwiz::msdata::MSDataFile * findPwizMSDataFile(const MsRun * p_msrun) ;
-private:
- static std::map<const MsRun *, pwiz::msdata::MSDataFile *> _map_msrun_msdatafile;
- static std::map<const MsRun *, pappso::MsRunXicExtractorSp> _map_msrun_msrunxicextractor;
-};
-#endif // READSPECTRUM_H