From 2c853d69d146994688b1bb856bd5c66a1c8fc329 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 7 Dec 2018 10:42:41 +0100
Subject: [PATCH] wait for spectrum loader thread
---
src/gui/peptide_detail_view/peptidewindow.cpp | 3 ++
src/gui/workerthread.h | 2 +-
src/gui/xic_view/xic_box/xicbox.cpp | 46 +++++++++++++------
src/gui/xic_view/xicworkerthread.cpp | 12 ++++-
src/gui/xic_view/xicworkerthread.h | 4 +-
src/input/mascot/mascotdatparser.h | 2 +-
6 files changed, 50 insertions(+), 19 deletions(-)
diff --git a/src/gui/peptide_detail_view/peptidewindow.cpp b/src/gui/peptide_detail_view/peptidewindow.cpp
index 0329c2b5..3ad38966 100644
--- a/src/gui/peptide_detail_view/peptidewindow.cpp
+++ b/src/gui/peptide_detail_view/peptidewindow.cpp
@@ -165,6 +165,9 @@ PeptideWindow::PeptideWindow(ProjectWindow *parent)
PeptideWindow::~PeptideWindow()
{
+
+ _spectrum_loader_thread.quit();
+ _spectrum_loader_thread.wait();
delete ui;
}
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 60168b56..309a35dc 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -48,7 +48,7 @@ class WorkerThread : public QObject
public:
WorkerThread(MainWindow *parent);
WorkerThread(ProjectWindow *parent);
- ~WorkerThread();
+ virtual ~WorkerThread();
protected:
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 3fba0015..c29b9823 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -114,7 +114,7 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
_p_xic_window = parent;
ui->setupUi(this);
- XicWorkerThread *p_worker = new XicWorkerThread();
+ XicWorkerThread *p_worker = new XicWorkerThread(this);
p_worker->moveToThread(&_xic_thread);
_xic_thread.start();
@@ -139,19 +139,29 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
- connect(this, &XicBox::computeIsotopeMassList, p_worker,
+ connect(this,
+ &XicBox::computeIsotopeMassList,
+ p_worker,
&XicWorkerThread::doComputeIsotopeMassList);
- connect(p_worker, &XicWorkerThread::isotopeMassListComputed, this,
+ connect(p_worker,
+ &XicWorkerThread::isotopeMassListComputed,
+ this,
&XicBox::setIsotopeMassList);
- connect(_p_xic_window, &XicWindow::reExtractXicNeeded, this,
- &XicBox::reExtractXic);
- connect(ui->xic_widget, &pappso::XicWidget::xicPeakListChanged, this,
+ connect(
+ _p_xic_window, &XicWindow::reExtractXicNeeded, this, &XicBox::reExtractXic);
+ connect(ui->xic_widget,
+ &pappso::XicWidget::xicPeakListChanged,
+ this,
&XicBox::setXicPeakList);
- connect(ui->xic_widget, &pappso::XicWidget::clicked, this,
+ connect(ui->xic_widget,
+ &pappso::XicWidget::clicked,
+ this,
&XicBox::onXicWidgetClick);
- connect(_p_xic_window, &XicWindow::rtUnitChangeNeeded, this,
+ connect(_p_xic_window,
+ &XicWindow::rtUnitChangeNeeded,
+ this,
&XicBox::onRtUnitChanged);
#else
// Qt4 code
@@ -259,13 +269,15 @@ XicBox::setPeptideEvidence(const PeptideEvidence *p_peptide_evidence)
_p_xic_window->getProjectWindow()
->getProjectP()
->getSameXicPeptideEvidenceList(
- _peptide_evidence_list, _msrun_sp.get(),
+ _peptide_evidence_list,
+ _msrun_sp.get(),
_p_peptide_evidence->getPeptideXtpSp().get(),
_p_peptide_evidence->getCharge());
emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
_p_peptide_evidence->getCharge(),
- _p_xic_window->getXicExtractPrecision(), 0.8);
+ _p_xic_window->getXicExtractPrecision(),
+ 0.8);
}
void
@@ -290,7 +302,8 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
_p_xic_window->getProjectWindow()
->getProjectP()
->getSameXicPeptideEvidenceList(
- _peptide_evidence_list, _msrun_sp.get(),
+ _peptide_evidence_list,
+ _msrun_sp.get(),
_p_peptide_evidence->getPeptideXtpSp().get(),
_p_peptide_evidence->getCharge());
//_p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence,
@@ -298,7 +311,8 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
_p_peptide_evidence->getCharge(),
- _p_xic_window->getXicExtractPrecision(), 0.8);
+ _p_xic_window->getXicExtractPrecision(),
+ 0.8);
}
void
@@ -491,7 +505,9 @@ XicBox::setIsotopeMassList(
{nullptr, natural_isotope_average, nullptr, nullptr});
}
- emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
+ emit loadXic(_msrun_sp,
+ mass_list,
+ _p_xic_window->getXicExtractPrecision(),
pappso::XicExtractMethod::max);
// histogram
@@ -565,7 +581,9 @@ XicBox::reExtractXic()
mass_list.push_back(
xic_isotope.peptide_natural_isotope_sp.get()->getMz());
}
- emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
+ emit loadXic(_msrun_sp,
+ mass_list,
+ _p_xic_window->getXicExtractPrecision(),
pappso::XicExtractMethod::max);
qDebug() << "XicBox::reExtractXic end";
}
diff --git a/src/gui/xic_view/xicworkerthread.cpp b/src/gui/xic_view/xicworkerthread.cpp
index 98bc2111..9039b5eb 100644
--- a/src/gui/xic_view/xicworkerthread.cpp
+++ b/src/gui/xic_view/xicworkerthread.cpp
@@ -34,8 +34,15 @@
#include <pappsomspp/exception/exceptionnotfound.h>
#include <QDebug>
+XicWorkerThread::XicWorkerThread(XicBox *parent)
+{
+}
+XicWorkerThread::~XicWorkerThread()
+{
+}
void
-XicWorkerThread::doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list,
+XicWorkerThread::doXicLoad(MsRunSp p_msrun,
+ std::vector<pappso::mz> mz_list,
pappso::PrecisionP precision,
pappso::XicExtractMethod method)
{
@@ -91,7 +98,8 @@ XicWorkerThread::doComputeIsotopeMassList(pappso::PeptideSp peptide_sp,
isotope_mass_list = isotope_list.getByIntensityRatio(
charge, precision, minimum_isotope_pattern_ratio);
- std::sort(isotope_mass_list.begin(), isotope_mass_list.end(),
+ 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()),
diff --git a/src/gui/xic_view/xicworkerthread.h b/src/gui/xic_view/xicworkerthread.h
index ec0428b4..66081f2a 100644
--- a/src/gui/xic_view/xicworkerthread.h
+++ b/src/gui/xic_view/xicworkerthread.h
@@ -35,11 +35,13 @@
#include "../../core/msrun.h"
#include <pappsomspp/xic/xic.h>
#include <pappsomspp/xicextractor/msrunxicextractor.h>
-
+#include "xic_box/xicbox.h"
class XicWorkerThread : public QObject
{
Q_OBJECT
public:
+ XicWorkerThread(XicBox *parent);
+ virtual ~XicWorkerThread();
public slots:
void doXicLoad(MsRunSp p_msrun, std::vector<pappso::mz> mz_list,
pappso::PrecisionP precision, pappso::XicExtractMethod method);
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index e9cc45fa..d3436873 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -113,7 +113,7 @@ class MascotDatParser
unsigned int _number_of_residues = 0;
QString _error_str;
bool _is_decoy_section = false;
- bool _take_only_first_peptide_rank = true;
+ bool _take_only_first_peptide_rank = false;
PeptideLine _current_peptide;
QueryLine _current_query;
--
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