From 98f77814dd5358715564d2ec3be37d006c270725 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 6 Jun 2019 17:07:18 +0200
Subject: [PATCH] WIP: using new pappsoms++ library
---
.../identificationdatasource.cpp | 4 ++--
src/core/msrun.cpp | 24 +++++++++----------
src/core/msrun.h | 9 +++----
.../exportmasschroqdialog.cpp | 2 +-
src/gui/peptide_detail_view/peptidewindow.cpp | 2 +-
.../peptide_list_view/peptidelistwindow.cpp | 4 ++--
.../protein_list_view/proteinlistwindow.cpp | 4 ++--
.../proteintableproxymodel.cpp | 2 +-
src/gui/xic_view/xic_box/xicbox.cpp | 8 +++----
src/gui/xic_view/xicworkerthread.cpp | 2 +-
src/output/masschroqml.cpp | 2 +-
src/output/mcqrspectralcount.cpp | 2 +-
src/output/ods/samplesheet.cpp | 2 +-
src/output/proticdbml.cpp | 2 +-
src/output/xpip.cpp | 4 ++--
src/utils/msrunstore.cpp | 4 ++--
src/utils/msrunstore.h | 4 +---
17 files changed, 38 insertions(+), 43 deletions(-)
diff --git a/src/core/identification_sources/identificationdatasource.cpp b/src/core/identification_sources/identificationdatasource.cpp
index d1c701709..cabdf57e8 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 5935f6058..534766121 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 81677f42e..94b300cfa 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 589ae1fe8..3f841cbe8 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 33d21dad5..78da5131f 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 d95537718..a56f7145b 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 c07b7aa67..4a0f1551a 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 7ebb39c35..a0d2ff594 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 f5354fcbc..9cb7b2265 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 8b9e2386e..e038f0588 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 dd2df3379..1baa9b397 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 5f0346f49..60c8e45c0 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 5fe39259f..7f4f15705 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 ada23f214..527fc88b9 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 51a542c8a..f740efcd0 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 2a3719c49..e2641ffdd 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 e0853179a..4828d825e 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
--
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