diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index d1c701709fddb9d1dcf82dce52436972c51def85..cabdf57e8d80db59c02ea9aa61e1aa39e4afe32e 100644
--- a/src/core/identification_sources/identificationdatasource.cpp
+++ b/src/core/identification_sources/identificationdatasource.cpp
@@ -209,7 +209,7 @@ IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
{
throw pappso::ExceptionNotFound(
QObject::tr("mz data \"%1\" file not found")
- .arg(_ms_run_sp.get()->getFilename()));
+ .arg(_ms_run_sp.get()->getFileName()));
}
}
msrun_reader_sp = _ms_run_sp.get()->getMsRunReaderSp();
@@ -217,7 +217,7 @@ IdentificationDataSource::getMassSpectrumCstSPtr(unsigned int scan_number) const
{
throw pappso::ExceptionNotFound(
QObject::tr("mz data \"%1\" file not found")
- .arg(_ms_run_sp.get()->getFilename()));
+ .arg(_ms_run_sp.get()->getFileName()));
}
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index 5935f6058eed73c8e5efc3cbd020ad80cf365fcb..5347661218eff8d3f08a18a6b3e21a56e1ed5e3f 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -35,7 +35,6 @@
#include <QSettings>
#include <QDebug>
#include <QDir>
-#include <pappsomspp/msrun/msrunreaderfactory.h>
#include <pappsomspp/exception/exceptionnotfound.h>
#include <pappsomspp/xicextractor/msrunxicextractorfactory.h>
#include "../utils/msrunstatisticshandler.h"
@@ -55,17 +54,17 @@ MsRun::MsRun(const MsRun &other) : pappso::MsRunId(other)
MsRun::~MsRun()
{
}
-pappso::MsRunReaderSp &
-MsRun::getMsRunReaderSp()
+pappso::MsRunReaderSPtr &
+MsRun::getMsRunReaderSPtr()
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
- << " filename=" << getFilename();
+ << " filename=" << getFileName();
if(_msrun_reader_sp == nullptr)
{
try
{
- pappso::MsFileAccessor accessor(getFilename(), 0);
+ pappso::MsFileAccessor accessor(getFileName(), 0);
qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
auto msrunid_list = accessor.getMsRunIds();
if(msrunid_list.size() == 1)
@@ -126,10 +125,10 @@ bool
MsRun::findMsRunFile()
{
// first look at the file path :)
- _msrun_reader_sp = getMsRunReaderSp();
+ _msrun_reader_sp = getMsRunReaderSPtr();
if(_msrun_reader_sp != nullptr)
{
- QFileInfo real_file(this->getFilename());
+ QFileInfo real_file(this->getFileName());
if(real_file.exists())
{
return true;
@@ -139,7 +138,7 @@ MsRun::findMsRunFile()
_msrun_reader_sp = nullptr;
}
}
- QFileInfo file_original(this->getFilename());
+ QFileInfo file_original(this->getFileName());
QString basename = file_original.baseName();
QString onlyfilename = file_original.fileName();
QSettings settings;
@@ -165,7 +164,7 @@ MsRun::findMsRunFile()
if(_msrun_reader_sp == nullptr)
{
- pappso::MsFileAccessor accessor(getFilename(), 0);
+ pappso::MsFileAccessor accessor(getFileName(), 0);
qDebug()
<< __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
auto msrunid_list = accessor.getMsRunIds();
@@ -204,7 +203,7 @@ MsRun::findMsRunFile()
if(_msrun_reader_sp == nullptr)
{
- pappso::MsFileAccessor accessor(getFilename(), 0);
+ pappso::MsFileAccessor accessor(getFileName(), 0);
qDebug()
<< __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
auto msrunid_list = accessor.getMsRunIds();
@@ -294,8 +293,9 @@ MsRun::getMsRunXicExtractorInterfaceSp()
}
else
{
- _xic_extractor_sp = pappso::MsRunXicExtractorFactory::getInstance()
- .buildMsRunXicExtractorDiskBufferSp(_msrun_reader_sp);
+ _xic_extractor_sp =
+ pappso::MsRunXicExtractorFactory::getInstance()
+ .buildMsRunXicExtractorDiskBufferSp(_msrun_reader_sp);
}
//_xic_extractor_sp = pappso::MsRunXicExtractorFactory::getInstance()
// .buildMsRunXicExtractorDiskBufferSp(*this);
diff --git a/src/core/msrun.h b/src/core/msrun.h
index 81677f42e2645d000b5ad7152822ea8b0f458cb3..94b300cfaefb57aa5bf629f3f4c15ebf4c63f6d8 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -30,8 +30,7 @@
******************************************************************************/
-#ifndef MSRUN_H
-#define MSRUN_H
+#pragma once
#include <memory>
#include <QString>
@@ -69,7 +68,7 @@ class MsRun : public pappso::MsRunId
bool findMsRunFile();
- pappso::MsRunReaderSp &getMsRunReaderSp();
+ pappso::MsRunReaderSPtr &getMsRunReaderSPtr();
/** @brief release shared pointer on MSrun reader
*/
@@ -82,9 +81,7 @@ class MsRun : public pappso::MsRunId
private:
std::map<MsRunStatistics, QVariant> _param_stats;
- pappso::MsRunReaderSp _msrun_reader_sp;
+ pappso::MsRunReaderSPtr _msrun_reader_sp;
pappso::MsRunXicExtractorInterfaceSp _xic_extractor_sp;
};
-
-#endif // MSRUN_H
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index 589ae1fe84f65afced9adc2d401adf3babb25ab2..3f841cbe86afc33ab7241a9c1a444ff1692b1307 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -228,7 +228,7 @@ ExportMasschroqDialog::doCheckMsrunFilepath()
ui->warningDirectoryLabel->setText(
tr("%1 not found : Please choose the directory to look for this MS "
"run file.")
- .arg(msrun_sp.get()->getFilename()));
+ .arg(msrun_sp.get()->getFileName()));
ui->directorySelectWidget->setHidden(false);
break;
}
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 33d21dad54bf3ac853b22a80251891304424c2b2..78da5131ffe72e9b46f91b8f35135ebef17ba110 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -306,7 +306,7 @@ PeptideWindow::openInPeptideViewer()
QStringList arguments;
arguments << _p_peptide_evidence->getPeptideXtpSp().get()->toString()
<< QString("%1").arg(_p_peptide_evidence->getCharge())
- << _p_peptide_evidence->getMsRunP()->getFilename()
+ << _p_peptide_evidence->getMsRunP()->getFileName()
<< QString("%1").arg(_p_peptide_evidence->getScanNumber());
qDebug() << "PeptideWindow::openInPeptideViewer " << program << " "
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index d9553771896bc077da40ffe1bfacdc05acf5c9a6..a56f7145ba7f58b76bfd3a4a13b02e3df54e1be6 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -215,9 +215,9 @@ PeptideListWindow::setProteinMatch(IdentificationGroup *p_identification_group,
QStringList msrun_list;
for(MsRunSp msrun_sp : _p_identification_group->getMsRunSpList())
{
- msrun_list << msrun_sp.get()->getFilename();
+ msrun_list << msrun_sp.get()->getFileName();
qDebug() << "PeptideListWindow::setIdentificationGroup "
- << msrun_sp.get()->getFilename();
+ << msrun_sp.get()->getFileName();
}
QCompleter *completer = new QCompleter(msrun_list, this);
completer->setCaseSensitivity(Qt::CaseInsensitive);
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index c07b7aa67508f56c04814bfe1637ce96298d205b..4a0f1551a15913ff21e9e55d26d5e4f636f9c1ff 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -384,9 +384,9 @@ ProteinListWindow::setIdentificationGroup(
QStringList msrun_list;
for(MsRunSp msrun_sp : _p_identification_group->getMsRunSpList())
{
- msrun_list << msrun_sp.get()->getFilename();
+ msrun_list << msrun_sp.get()->getFileName();
qDebug() << "ProteinListWindow::setIdentificationGroup "
- << msrun_sp.get()->getFilename();
+ << msrun_sp.get()->getFileName();
}
QCompleter *completer = new QCompleter(msrun_list, this);
completer->setCaseSensitivity(Qt::CaseInsensitive);
diff --git a/src/gui/protein_list_view/proteintableproxymodel.cpp b/src/gui/protein_list_view/proteintableproxymodel.cpp
index 7ebb39c35d7ecbfcc7ba173c75f88cfc7942d744..a0d2ff59418ff82b93da5d6373550347ad347ace 100644
--- a/src/gui/protein_list_view/proteintableproxymodel.cpp
+++ b/src/gui/protein_list_view/proteintableproxymodel.cpp
@@ -143,7 +143,7 @@ ProteinTableProxyModel::filterAcceptsRow(int source_row,
msrun_ok = false;
if(p_peptide_match.getPeptideEvidence()
->getMsRunP()
- ->getFilename()
+ ->getFileName()
.toLower()
.contains(file_search_string))
{
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index f5354fcbcee2efa01898fa84e5b9e64d965266c0..9cb7b2265e1cdda70e6bc7109c15ed0f6e9fb4da 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -175,9 +175,9 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
->getMsRunStore()
.getMsRunList())
{
- msrun_list << msrun_sp.get()->getFilename();
+ msrun_list << msrun_sp.get()->getFileName();
qDebug() << "ProteinListWindow::setIdentificationGroup "
- << msrun_sp.get()->getFilename();
+ << msrun_sp.get()->getFileName();
}
QCompleter *completer = new QCompleter(msrun_list, this);
completer->setCaseSensitivity(Qt::CaseInsensitive);
@@ -258,7 +258,7 @@ XicBox::setPeptideEvidence(const PeptideEvidence *p_peptide_evidence)
ui->peptide_label->setText(
_p_peptide_evidence->getPeptideXtpSp().get()->toString());
- ui->msrun_label->setText(_p_peptide_evidence->getMsRunP()->getFilename());
+ ui->msrun_label->setText(_p_peptide_evidence->getMsRunP()->getFileName());
ui->charge_label->setText(
QString("%1").arg(_p_peptide_evidence->getCharge()));
ui->mz_label->setText(
@@ -290,7 +290,7 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
ui->peptide_label->setText(
_p_peptide_evidence->getPeptideXtpSp().get()->toString());
- ui->msrun_label->setText(msrun_sp->getFilename());
+ ui->msrun_label->setText(msrun_sp->getFileName());
ui->charge_label->setText(
QString("%1").arg(_p_peptide_evidence->getCharge()));
ui->mz_label->setText(
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index 8b9e2386e2bc157bf8f48ee19533153e6d6d9fdb..e038f058889cab4dee9be321119b7158fce333d8 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -76,7 +76,7 @@ XicWorkerThread::doXicLoad(MsRunSp p_msrun,
catch(pappso::PappsoException &error)
{
emit operationFailed(tr("Error extracting XIC for MSrun %1:\n%2")
- .arg(p_msrun->getFilename())
+ .arg(p_msrun->getFileName())
.arg(error.qwhat()));
}
}
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index dd2df33799b0b24d2c706aadb64a889b7c42b96b..1baa9b397ae62eeea40de3ae7659fd39a517de14 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -150,7 +150,7 @@ MassChroQml::write(ProjectSp sp_project)
{
_output_stream->writeAttribute("format", "mzxml");
}
- _output_stream->writeAttribute("path", msrun.get()->getFilename());
+ _output_stream->writeAttribute("path", msrun.get()->getFileName());
_output_stream->writeAttribute("type", "centroid");
// <data_file id="samp1" format="mzxml" path="bsa2.mzXML" type="profile"
// />
diff --git a/src/output/mcqrspectralcount.cpp b/src/output/mcqrspectralcount.cpp
index 5f0346f4975e38205aab3bd6f1c7fdda2f771bac..60c8e45c0f532e9d1be664f40c39d4ab069fb5a2 100644
--- a/src/output/mcqrspectralcount.cpp
+++ b/src/output/mcqrspectralcount.cpp
@@ -175,7 +175,7 @@ McqrSpectralCount::writeOneProteinLabel(const pappso::GrpProtein *p_grp_protein,
_p_writer->writeCell(p_grp_protein->getGroupingId());
_p_writer->writeCell(p_msrun->getXmlId());
- _p_writer->writeCell(p_msrun->getFilename());
+ _p_writer->writeCell(p_msrun->getFileName());
if(p_label != nullptr)
{
diff --git a/src/output/ods/samplesheet.cpp b/src/output/ods/samplesheet.cpp
index 5fe39259fef811b24b10052bfca30773d09984b2..7f4f1570564cb42ef14f8fc4c1580e9ec0a0909f 100644
--- a/src/output/ods/samplesheet.cpp
+++ b/src/output/ods/samplesheet.cpp
@@ -156,7 +156,7 @@ SampleSheet::writeIdentificationDataSource(
_p_writer->writeCell(msrun_sp.get()->getXmlId());
_p_writer->writeCell(msrun_sp.get()->getSampleName());
- _p_writer->writeCell(msrun_sp.get()->getFilename());
+ _p_writer->writeCell(msrun_sp.get()->getFileName());
_p_writer->writeCell(p_ident_data_source->getIdentificationEngineName());
_p_writer->writeCell(p_ident_data_source->getIdentificationEngineVersion());
_p_writer->writeCell(p_ident_data_source->getResourceName());
diff --git a/src/output/proticdbml.cpp b/src/output/proticdbml.cpp
index ada23f214b992d21b5e31559d0e885707b9f46e7..527fc88b981e206ab81fa0dae166e3291e2f9182 100644
--- a/src/output/proticdbml.cpp
+++ b/src/output/proticdbml.cpp
@@ -336,7 +336,7 @@ ProticdbMl::writeIdentificationDataSource(
_output_stream->writeStartElement("processingMethod");
// mzXml source file name
writeCvParam("PROTICdbO:0000343",
- p_identification_data_source->getMsRunSp().get()->getFilename(),
+ p_identification_data_source->getMsRunSp().get()->getFileName(),
"MS/MS data source file name");
if(p_identification_data_source->getIdentificationEngine() ==
IdentificationEngine::XTandem)
diff --git a/src/output/xpip.cpp b/src/output/xpip.cpp
index 51a542c8af1fdea4e8f46993b030cc2460b59d0b..f740efcd0c163b0e3266dd1ed270e0714fbf7cf7 100644
--- a/src/output/xpip.cpp
+++ b/src/output/xpip.cpp
@@ -325,10 +325,10 @@ Xpip::writeMsrunList(const MsRunStore &msrun_store)
_output_stream->writeAttribute("format",
QString("%1").arg(static_cast<std::int8_t>(
msrun_sp.get()->getMzFormat())));
- QFileInfo mz_info(msrun_sp.get()->getFilename());
+ QFileInfo mz_info(msrun_sp.get()->getFileName());
if(mz_info.exists())
{
- _output_stream->writeAttribute("path", msrun_sp.get()->getFilename());
+ _output_stream->writeAttribute("path", msrun_sp.get()->getFileName());
}
else
{
diff --git a/src/utils/msrunstore.cpp b/src/utils/msrunstore.cpp
index 2a3719c49621132199a3f3ce4c87a8c6a5b9cc5c..e2641ffdd336babc2aeb7e0a3edab55d8fcd9a40 100644
--- a/src/utils/msrunstore.cpp
+++ b/src/utils/msrunstore.cpp
@@ -79,12 +79,12 @@ MsRunStore::getInstance(const QString &location)
_map_msrun.end(),
[location](const MsRunSp &msrun_sp) {
if(msrun_sp.get()->getSampleName() ==
- msrun_sp.get()->getFilename())
+ msrun_sp.get()->getFileName())
{
return msrun_sp.get()->getSampleName() ==
QFileInfo(location).baseName();
}
- return msrun_sp.get()->getFilename() == location;
+ return msrun_sp.get()->getFileName() == location;
});
}
if(it != _map_msrun.end())
diff --git a/src/utils/msrunstore.h b/src/utils/msrunstore.h
index e0853179a944d34dab9ff0e289cfb4976386ad08..4828d825eb73d93d2d31339c17390d2896db85b2 100644
--- a/src/utils/msrunstore.h
+++ b/src/utils/msrunstore.h
@@ -29,8 +29,7 @@
*implementation
******************************************************************************/
-#ifndef MSRUNSTORE_H
-#define MSRUNSTORE_H
+#pragma once
#include <QString>
#include <map>
@@ -52,4 +51,3 @@ class MsRunStore
std::vector<MsRunSp> _map_msrun;
};
-#endif // MSRUNSTORE_H