From 7ea294d806f837a52938459786dfac4b6283d309 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 21 Jun 2018 15:42:16 +0200
Subject: [PATCH] xic extractor is now embedded in msrun
---
src/core/msrun.cpp | 210 +++++++++++++++++----------
src/core/msrun.h | 6 +
src/gui/xic_view/xicworkerthread.cpp | 141 +++++++++---------
3 files changed, 214 insertions(+), 143 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index d1a0ad8ce..3f577aa1e 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 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/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 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/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include "msrun.h"
@@ -36,92 +37,147 @@
#include <QDir>
#include <pappsomspp/msrun/msrunreaderfactory.h>
#include <pappsomspp/exception/exceptionnotfound.h>
+#include <pappsomspp/xicextractor/msrunxicextractorfactory.h>
-MsRun::MsRun(const QString & location):pappso::MsRunId(location) {
- QFileInfo fileinfo(location);
+MsRun::MsRun(const QString &location) : pappso::MsRunId(location)
+{
+ QFileInfo fileinfo(location);
}
-MsRun::MsRun(const MsRun& other):pappso::MsRunId(other) {
- _param_stats = other._param_stats;
+MsRun::MsRun(const MsRun &other) : pappso::MsRunId(other)
+{
+ _param_stats = other._param_stats;
}
-MsRun::~MsRun() {
+MsRun::~MsRun()
+{
}
-pappso::MsRunReaderSp & MsRun::getMsRunReaderSp() {
- return _msrun_reader_sp;
+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));
+void
+MsRun::setMsRunStatistics(MsRunStatistics param, const QVariant &value)
+{
+ _param_stats.insert(std::pair<MsRunStatistics, QVariant>(param, value));
}
-const std::map<MsRunStatistics, QVariant> & MsRun::getMsRunStatisticsMap() const {
- return _param_stats;
+const std::map<MsRunStatistics, QVariant> &
+MsRun::getMsRunStatisticsMap() const
+{
+ return _param_stats;
}
-const QVariant MsRun::getMsRunStatistics(MsRunStatistics param) const {
- try {
- return _param_stats.at(param);
+const QVariant
+MsRun::getMsRunStatistics(MsRunStatistics param) const
+{
+ try
+ {
+ return _param_stats.at(param);
}
- catch (std::out_of_range) {
- return QVariant();
+ catch(std::out_of_range)
+ {
+ return QVariant();
}
}
-bool MsRun::findMsRunFile() {
+bool
+MsRun::findMsRunFile()
+{
- QFileInfo file(this->getFilename());
- bool file_ok = false;
+ QFileInfo file(this->getFilename());
+ bool file_ok = false;
- if (file.exists()) {
- file_ok = true;
+ 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;
+ 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.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);
+ if(file_ok)
+ {
+ if(_msrun_reader_sp == nullptr)
+ {
+ _msrun_reader_sp =
+ pappso::MsRunReaderFactory::getInstance().buildPwizMsRunReaderSp(
+ *this);
}
}
- return file_ok;
+ 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));
+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
+ catch(pappso::ExceptionNotFound &error)
+ {
+ // no file found, no statistics
}
}
}
+
+pappso::MsRunXicExtractorSp
+MsRun::getMsRunXicExtractorSp()
+{
+ if(_xic_extractor_sp != nullptr)
+ {
+ return _xic_extractor_sp;
+ }
+ if(this->findMsRunFile())
+ {
+
+ pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
+ //_xic_extractor_sp = pappso::MsRunXicExtractorFactory::getInstance()
+ // .buildMsRunXicExtractorDiskBufferSp(*this);
+ _xic_extractor_sp = pappso::MsRunXicExtractorFactory::getInstance()
+ .buildMsRunXicExtractorPwizSp(*this);
+ }
+ return _xic_extractor_sp;
+}
diff --git a/src/core/msrun.h b/src/core/msrun.h
index fd711b1e0..08f04a853 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -37,6 +37,7 @@
#include <QVariant>
#include <pappsomspp/msrun/msrunid.h>
#include <pappsomspp/msrun/msrunreader.h>
+#include <pappsomspp/xicextractor/msrunxicextractor.h>
#include "../utils/types.h"
class MsRun;
@@ -69,11 +70,16 @@ public:
pappso::MsRunReaderSp & getMsRunReaderSp();
void checkMsRunStatistics();
+
+ pappso::MsRunXicExtractorSp getMsRunXicExtractorSp();
private :
std::map<MsRunStatistics, QVariant> _param_stats;
pappso::MsRunReaderSp _msrun_reader_sp;
+
+ pappso::MsRunXicExtractorSp _xic_extractor_sp;
+
};
#endif // MSRUN_H
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index f82119f59..98bc21116 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -5,92 +5,101 @@
* \brief XIC worker
*/
/*******************************************************************************
-* 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/>.
-*
-* Contributors:
-* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * 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/>.
+ *
+ * Contributors:
+ * Olivier Langella <olivier.langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#include <tuple>
#include "xicworkerthread.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) {
+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));
+ 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::XicSp> xic_sp_list =
+ // SpectrumStore::getXicSpFromMsRunSp(p_msrun.get(), mass_list, method);
- 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 =
+ p_msrun.get()->getMsRunXicExtractorSp();
+ if(extractor != nullptr)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ extractor.get()->setXicExtractMethod(method);
- pappso::MsRunXicExtractorSp extractor;
- if (it == _extractor_list.end()) {
- pappso::MsRunXicExtractorFactory::getInstance().setTmpDir("/tmp");
- extractor = pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorDiskBufferSp(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__ ;
- std::vector<pappso::XicSp> xic_sp_list = extractor.get()->getXicSpList(mass_list);
-
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ ;
- emit xicLoaded(xic_sp_list);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ emit xicLoaded(xic_sp_list);
}
-
}
- catch (pappso::PappsoException & error) {
- emit operationFailed(tr("Error extracting XIC for MSrun %1:\n%2").arg(p_msrun->getFilename()).arg(error.qwhat()));
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(tr("Error extracting XIC for MSrun %1:\n%2")
+ .arg(p_msrun->getFilename())
+ .arg(error.qwhat()));
}
}
-void XicWorkerThread::doComputeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge, pappso::PrecisionP precision, double minimum_isotope_pattern_ratio) {
- qDebug() << "XicWorkerThread::doComputeIsotopeMassList " << precision->toString();
- std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list;
- //compute isotope masses :
- if (peptide_sp != nullptr) {
- pappso::PeptideNaturalIsotopeList isotope_list(peptide_sp);
- isotope_mass_list = isotope_list.getByIntensityRatio(charge, precision, minimum_isotope_pattern_ratio);
+void
+XicWorkerThread::doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
+ unsigned int charge,
+ pappso::PrecisionP precision,
+ double minimum_isotope_pattern_ratio)
+{
+ qDebug() << "XicWorkerThread::doComputeIsotopeMassList "
+ << precision->toString();
+ std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list;
+ // compute isotope masses :
+ if(peptide_sp != nullptr)
+ {
+ pappso::PeptideNaturalIsotopeList isotope_list(peptide_sp);
+ isotope_mass_list = isotope_list.getByIntensityRatio(
+ charge, precision, minimum_isotope_pattern_ratio);
- std::sort (isotope_mass_list.begin(), isotope_mass_list.end(), [](const pappso::PeptideNaturalIsotopeAverageSp & m,const pappso::PeptideNaturalIsotopeAverageSp & n)-> bool {
- unsigned int mn(m.get()->getIsotopeNumber()), nn(n.get()->getIsotopeNumber());
- unsigned int mr(m.get()->getIsotopeRank()), nr(n.get()->getIsotopeRank());
- return (std::tie(mn, mr) < std::tie(nn, nr));
- });
- emit isotopeMassListComputed(isotope_mass_list);
+ std::sort(isotope_mass_list.begin(), isotope_mass_list.end(),
+ [](const pappso::PeptideNaturalIsotopeAverageSp &m,
+ const pappso::PeptideNaturalIsotopeAverageSp &n) -> bool {
+ unsigned int mn(m.get()->getIsotopeNumber()),
+ nn(n.get()->getIsotopeNumber());
+ unsigned int mr(m.get()->getIsotopeRank()),
+ nr(n.get()->getIsotopeRank());
+ return (std::tie(mn, mr) < std::tie(nn, nr));
+ });
+ emit isotopeMassListComputed(isotope_mass_list);
}
}
--
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