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Commit 7ea294d8 authored by Langella Olivier's avatar Langella Olivier
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xic extractor is now embedded in msrun

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src/core/msrun.cpp
+ 133
− 77
View file @ 7ea294d8
......@@ -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;
}
src/core/msrun.h
+ 6
− 0
View file @ 7ea294d8
......@@ -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
src/gui/xic_view/xicworkerthread.cpp
+ 75
− 66
View file @ 7ea294d8
......@@ -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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