diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index ed01661a447c04af949d9c5295fb0d6920424df7..e58a405aa703172280b0f58592b35ea42896b5df 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -23,9 +23,6 @@
* 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 "exportmasschroqdialog.h"
@@ -39,11 +36,13 @@
#include <pappsomspp/msrun/alignment/msrunretentiontime.h>
#include <pappsomspp/msfile/msfileaccessor.h>
#include <pappsomspp/pappsoexception.h>
+#include "../../mainwindow.h"
-ExportMasschroqDialog::ExportMasschroqDialog(QWidget *parent)
+ExportMasschroqDialog::ExportMasschroqDialog(MainWindow *parent)
: QDialog(parent), ui(new Ui::ExportMasschroqDialog)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ mp_main = parent;
ui->setupUi(this);
this->setModal(true);
@@ -68,9 +67,9 @@ ExportMasschroqDialog::~ExportMasschroqDialog()
}
void
-ExportMasschroqDialog::setProject(const Project *p_project)
+ExportMasschroqDialog::setProjectSPtr(ProjectSp p_project)
{
- mp_project = p_project;
+ msp_project = p_project;
fillMsrunListComboBox();
}
@@ -160,6 +159,13 @@ ExportMasschroqDialog::getMasschroqFileParameters() const
}
+void
+ExportMasschroqDialog::reject()
+{
+ msp_project = nullptr;
+ QDialog::reject();
+}
+
void
ExportMasschroqDialog::accept()
{
@@ -203,6 +209,7 @@ ExportMasschroqDialog::accept()
{
ZivyParams zivy_params = ui->zivyParamWidget->getZivyParams();
zivy_params.saveSettings();
+ msp_project = nullptr;
QDialog::accept();
}
else
@@ -223,7 +230,7 @@ ExportMasschroqDialog::doCheckMsrunFilepath()
ui->msrunFilepathOkLabel->setHidden(true);
bool is_ok = true;
for(IdentificationDataSourceSp p_ident_data_source :
- mp_project->getIdentificationDataSourceStore()
+ msp_project->getIdentificationDataSourceStore()
.getIdentificationDataSourceList())
{
MsRunSp msrun_sp = p_ident_data_source->getMsRunSp();
@@ -279,105 +286,133 @@ ExportMasschroqDialog::doBrowseMsrunDirectory()
void
ExportMasschroqDialog::doFindBestMsrunForAlignment()
{
- bool is_ok = true;
- for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
- {
- if(msrun_sp->findMsRunFile())
- {
- }
- else
- {
- is_ok = false;
- ui->warningDirectoryLabel->setText(
- tr("%1 not found : Please choose the directory to look for this MS "
- "run file.")
- .arg(msrun_sp.get()->getFileName()));
- ui->directorySelectWidget->setHidden(false);
- break;
- }
- }
- try
- {
- mp_project->prepareMsrunRetentionTimesForAlignment();
-
- MsRunSp ms_run_best_reference;
- std::size_t best_number = 0;
- for(auto &msrun_ref_sp : mp_project->getMsRunStore().getMsRunList())
- {
- if(ms_run_best_reference == nullptr)
- {
- ms_run_best_reference = msrun_ref_sp;
- }
+ mp_main->showWaitingMessage(tr("Looking for MSrun reference"));
+ emit operateFindBestMsrunForAlignment(msp_project);
+ /*
+bool is_ok = true;
+for(auto &msrun_sp : msp_project->getMsRunStore().getMsRunList())
+ {
+ if(msrun_sp->findMsRunFile())
+ {
+ }
+ else
+ {
+ is_ok = false;
+ ui->warningDirectoryLabel->setText(
+ tr("%1 not found : Please choose the directory to look for this MS "
+ "run file.")
+ .arg(msrun_sp.get()->getFileName()));
+ ui->directorySelectWidget->setHidden(false);
+ break;
+ }
+ }
+try
+ {
+ msp_project->prepareMsrunRetentionTimesForAlignment();
+
+ MsRunSp ms_run_best_reference;
+ std::size_t best_number = 0;
+ for(auto &msrun_ref_sp : msp_project->getMsRunStore().getMsRunList())
+ {
+ if(ms_run_best_reference == nullptr)
+ {
+ ms_run_best_reference = msrun_ref_sp;
+ }
+
+ std::size_t min_number = std::numeric_limits<std::size_t>::max();
+ for(auto &msrun_sp : msp_project->getMsRunStore().getMsRunList())
+ {
+ if(msrun_sp.get() != msrun_ref_sp.get())
+ {
+ pappso::Trace trace;
+ trace = msrun_sp.get()
+ ->getMsRunRetentionTimePtr()
+ ->getCommonDeltaRt(msrun_ref_sp.get()
+ ->getMsRunRetentionTimePtr()
+ ->getSeamarks());
+ if(trace.size() < min_number)
+ {
+ min_number = trace.size();
+ }
+ }
+ }
+
+ if(min_number > best_number)
+ {
+ best_number = min_number;
+
+ ms_run_best_reference = msrun_ref_sp;
+ }
+ }
+ if(ms_run_best_reference != nullptr)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << ms_run_best_reference.get()->getXmlId()
+ << " best_number=" << best_number;
+
+ for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
+ {
+ MsRunSp msrun_sp = qvariant_cast<MsRunSp>(
+ ui->msrun_list_combo_box->itemData(index));
+ if(msrun_sp.get() == ms_run_best_reference.get())
+ {
+ ui->msrun_list_combo_box->setCurrentIndex(index);
+ }
+ }
+ }
+ }
+catch(pappso::PappsoException &error)
+ {
+ QMessageBox msgBox;
+ msgBox.setWindowTitle("Error");
+ msgBox.setText(
+ tr("Error preparing MS run retention times: %1").arg(error.qwhat()));
+ msgBox.setIcon(QMessageBox::Critical);
+ msgBox.exec();
+ }
+ */
+}
- std::size_t min_number = std::numeric_limits<std::size_t>::max();
- for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
- {
- if(msrun_sp.get() != msrun_ref_sp.get())
- {
- pappso::Trace trace;
- trace = msrun_sp.get()
- ->getMsRunRetentionTimePtr()
- ->getCommonDeltaRt(msrun_ref_sp.get()
- ->getMsRunRetentionTimePtr()
- ->getSeamarks());
- if(trace.size() < min_number)
- {
- min_number = trace.size();
- }
- }
- }
+void
+ExportMasschroqDialog::setBestMsrunForAlignment(MsRunSp best_msrun_sp)
+{
- if(min_number > best_number)
- {
- best_number = min_number;
+ mp_main->hideWaitingMessage();
+ if(best_msrun_sp != nullptr)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << best_msrun_sp.get()->getXmlId();
- ms_run_best_reference = msrun_ref_sp;
- }
- }
- if(ms_run_best_reference != nullptr)
+ for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
- << ms_run_best_reference.get()->getXmlId()
- << " best_number=" << best_number;
-
- for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
+ MsRunSp msrun_sp =
+ qvariant_cast<MsRunSp>(ui->msrun_list_combo_box->itemData(index));
+ if(msrun_sp.get() == best_msrun_sp.get())
{
- MsRunSp msrun_sp = qvariant_cast<MsRunSp>(
- ui->msrun_list_combo_box->itemData(index));
- if(msrun_sp.get() == ms_run_best_reference.get())
- {
- ui->msrun_list_combo_box->setCurrentIndex(index);
- }
+ ui->msrun_list_combo_box->setCurrentIndex(index);
}
}
}
- catch(pappso::PappsoException &error)
- {
- QMessageBox msgBox;
- msgBox.setWindowTitle("Error");
- msgBox.setText(
- tr("Error preparing MS run retention times: %1").arg(error.qwhat()));
- msgBox.setIcon(QMessageBox::Critical);
- msgBox.exec();
- }
}
-
void
ExportMasschroqDialog::fillMsrunListComboBox()
{
ui->msrun_list_combo_box->clear();
-
- int index = -1;
- for(auto &msrun_sp : mp_project->getMsRunStore().getMsRunList())
+ if(msp_project != nullptr)
{
- index = 0;
- ui->msrun_list_combo_box->addItem(
- QString("%1").arg(msrun_sp.get()->getSampleName()),
- QVariant::fromValue(msrun_sp));
- }
- if(index != -1)
- { // -1 for not found
- ui->msrun_list_combo_box->setCurrentIndex(index);
+
+ int index = -1;
+ for(auto &msrun_sp : msp_project->getMsRunStore().getMsRunList())
+ {
+ index = 0;
+ ui->msrun_list_combo_box->addItem(
+ QString("%1").arg(msrun_sp.get()->getSampleName()),
+ QVariant::fromValue(msrun_sp));
+ }
+ if(index != -1)
+ { // -1 for not found
+ ui->msrun_list_combo_box->setCurrentIndex(index);
+ }
}
}
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
index 005ed7b0c51a9f7a1dddf64967df0d5827cf4700..18d2c14dd73f03a18268694f2bef8eb74b6919c6 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
@@ -39,25 +39,36 @@ namespace Ui
class ExportMasschroqDialog;
}
+class MainWindow;
+
class ExportMasschroqDialog : public QDialog
{
Q_OBJECT
public:
- explicit ExportMasschroqDialog(QWidget *parent);
+ explicit ExportMasschroqDialog(MainWindow *parent);
~ExportMasschroqDialog();
void accept() override;
+ void reject() override;
void setMasschroqFileParameters(const MasschroqFileParameters ¶ms);
MasschroqFileParameters getMasschroqFileParameters() const;
- void setProject(const Project *p_project);
+ void setProjectSPtr(ProjectSp p_project);
+
+ signals:
+ // void peptideChanged(pappso::PeptideSp peptide);
+ void operateFindBestMsrunForAlignment(ProjectSp project_sp);
+
+ public slots:
+ void setBestMsrunForAlignment(MsRunSp msrun_sp);
private:
Ui::ExportMasschroqDialog *ui;
- const Project *mp_project;
+ ProjectSp msp_project;
+ MainWindow *mp_main;
protected slots:
void doCheckMsrunFilepath();
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index bce4fb0def3d1e3d375613fcc3999fb77b5f2ebc..4dfdb40e28fd43d8d6de609d893adee0ce24d7b5 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -33,7 +33,6 @@
#include "ui_main.h"
#include <pappsomspp/pappsoexception.h>
#include "../utils/utils.h"
-#include "workerthread.h"
#include "output/xpip.h"
#include "export/export_masschroq_dialog/masschroqfileparameters.h"
@@ -45,8 +44,8 @@ MainWindow::MainWindow(QWidget *parent) : QMainWindow(parent), ui(new Ui::Main)
setWindowTitle(QString("%1 %2").arg(SOFTWARE_NAME).arg(XTPCPP_VERSION));
setWindowIcon(QIcon(":/xtpcpp_icon/resources/xtandempipeline_icon.svg"));
- WorkerThread *worker = new WorkerThread(this);
- worker->moveToThread(&_worker_thread);
+ mp_worker = new WorkerThread(this);
+ mp_worker->moveToThread(&_worker_thread);
_worker_thread.start();
_p_load_results_dialog = new LoadResultsDialog(this);
@@ -577,6 +576,16 @@ MainWindow::doActionMassChroQ()
&ExportMasschroqDialog::accepted,
this,
&MainWindow::doAcceptedExportMasschroqDialog);
+
+ connect(_p_export_masschroq_dialog,
+ &ExportMasschroqDialog::operateFindBestMsrunForAlignment,
+ mp_worker,
+ &WorkerThread::doFindBestMsrunForAlignment);
+
+ connect(mp_worker,
+ &WorkerThread::findingBestMsrunForAlignmentFinished,
+ _p_export_masschroq_dialog,
+ &ExportMasschroqDialog::setBestMsrunForAlignment);
}
MasschroqFileParameters params;
@@ -584,7 +593,7 @@ MainWindow::doActionMassChroQ()
if(_project_sp.get() != nullptr)
{
_p_export_masschroq_dialog->setMasschroqFileParameters(params);
- _p_export_masschroq_dialog->setProject(this->_project_sp.get());
+ _p_export_masschroq_dialog->setProjectSPtr(this->_project_sp);
}
_p_export_masschroq_dialog->show();
_p_export_masschroq_dialog->raise();
diff --git a/src/gui/mainwindow.h b/src/gui/mainwindow.h
index ff285e4a766b676c2a74d5d687284963f4d8162a..4ec575c57ec69718d2ba48f19cff8c88d244f943 100644
--- a/src/gui/mainwindow.h
+++ b/src/gui/mainwindow.h
@@ -42,6 +42,7 @@
#include "utils/httpversion.h"
#include "gui/edit/edit_settings/editsettings.h"
#include "gui/export/export_masschroq_dialog/exportmasschroqdialog.h"
+#include "workerthread.h"
namespace Ui
@@ -127,7 +128,7 @@ class MainWindow : public QMainWindow
void setProjectSp(ProjectSp project_sp);
- private:
+ public:
void showWaitingMessage(const QString title);
void hideWaitingMessage();
void viewError(QString error);
@@ -136,6 +137,8 @@ class MainWindow : public QMainWindow
QCoreApplication *_p_app;
Ui::Main *ui;
QThread _worker_thread;
+ WorkerThread *mp_worker;
+
ProjectSp _project_sp = nullptr;
ProjectWindow *_project_window = nullptr;
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index e4fb6277f21c5f781141294df6ab571149bb23b9..f8a272924fb254619a467be2fd9ead3bbe881583 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -776,3 +776,79 @@ WorkerThread::doWritingFastaFile(QString filename,
tr("Error while writing FASTA file :\n%1").arg(error.qwhat()));
}
}
+
+
+void
+WorkerThread::doFindBestMsrunForAlignment(ProjectSp project_sp)
+{
+
+ try
+ {
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ emit loadingMessage(tr("looking for the best MSrun reference for alignment, please wait"));
+
+
+ bool is_ok = true;
+ for(auto &msrun_sp : project_sp->getMsRunStore().getMsRunList())
+ {
+ if(msrun_sp->findMsRunFile())
+ {
+ }
+ else
+ {
+ }
+ }
+ project_sp->prepareMsrunRetentionTimesForAlignment();
+
+ MsRunSp ms_run_best_reference;
+ std::size_t best_number = 0;
+ for(auto &msrun_ref_sp : project_sp->getMsRunStore().getMsRunList())
+ {
+ if(ms_run_best_reference == nullptr)
+ {
+ ms_run_best_reference = msrun_ref_sp;
+ }
+
+ std::size_t min_number = std::numeric_limits<std::size_t>::max();
+ for(auto &msrun_sp : project_sp->getMsRunStore().getMsRunList())
+ {
+ if(msrun_sp.get() != msrun_ref_sp.get())
+ {
+ pappso::Trace trace;
+ trace = msrun_sp.get()
+ ->getMsRunRetentionTimePtr()
+ ->getCommonDeltaRt(msrun_ref_sp.get()
+ ->getMsRunRetentionTimePtr()
+ ->getSeamarks());
+ if(trace.size() < min_number)
+ {
+ min_number = trace.size();
+ }
+ }
+ }
+
+ if(min_number > best_number)
+ {
+ best_number = min_number;
+
+ ms_run_best_reference = msrun_ref_sp;
+ }
+ }
+ if(ms_run_best_reference != nullptr)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
+ << ms_run_best_reference.get()->getXmlId()
+ << " best_number=" << best_number;
+ }
+
+ // emit operateXpipFile(filename);
+ emit findingBestMsrunForAlignmentFinished(ms_run_best_reference);
+ }
+ catch(pappso::PappsoException &error)
+ {
+ emit operationFailed(
+ tr("Error looking for the best MSrun reference for alignment :\n%1")
+ .arg(error.qwhat()));
+ }
+}
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index 3929b9d2f0015a4842d1d810e14895211d6c1255..f2e959a8f5300d4fce660eb201ffd2c4c54fe6e8 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
-#ifndef WORKERTHREAD_H
-#define WORKERTHREAD_H
+#pragma once
#include <QThread>
#include <QCloseEvent>
@@ -57,16 +56,19 @@ class WorkerThread : public QObject
public slots:
void doXpipFileLoad(QString filename);
- void doLoadingResults(bool is_individual, AutomaticFilterParameters param,
+ void doLoadingResults(bool is_individual,
+ AutomaticFilterParameters param,
QStringList file_list);
void doWritingXpipFile(QString filename, ProjectSp project_sp);
void doWritingOdsFile(QString filename, QString format, ProjectSp project_sp);
- void doWritingMassChroqFile(QString filename, ProjectSp project_sp,
+ void doWritingMassChroqFile(QString filename,
+ ProjectSp project_sp,
MasschroqFileParameters params);
void doWritingMassChroqPrmFile(QString filename, ProjectSp project_sp);
void doWritingProticFile(QString filename, ProjectSp project_sp);
void doWritingMcqrSpectralCountFile(QString filename, ProjectSp project_sp);
- void doWritingFastaFile(QString filename, ProjectSp project_sp,
+ void doWritingFastaFile(QString filename,
+ ProjectSp project_sp,
ExportFastaType type);
void doGrouping(ProjectSp project_sp);
void doGroupingOnIdentification(IdentificationGroup *p_identification_group,
@@ -74,6 +76,7 @@ class WorkerThread : public QObject
void
doPtmGroupingOnIdentification(IdentificationGroup *p_identification_group);
void doRunningXtandem(TandemRunBatch tandem_run_batch);
+ void doFindBestMsrunForAlignment(ProjectSp project_sp);
signals:
@@ -88,10 +91,9 @@ class WorkerThread : public QObject
IdentificationGroup *p_identification_group);
void operationFinished();
void operationFailed(QString error);
+ void findingBestMsrunForAlignmentFinished(MsRunSp msrun_sp);
private:
WorkMonitor *_p_work_monitor;
MainWindow *_p_main_window;
};
-
-#endif // WORKERTHREAD_H