diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 4ccd2196345abad23535c73f7d38f1e962a74b7d..790e6ddb18acfe5d582e3618b1e7046d5ac0e087 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -102,6 +102,7 @@ std::size_t IdentificationGroup::countSubGroup()const {
void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
+ qDebug() << "IdentificationGroup::startGrouping begin ";
if (_p_grp_experiment != nullptr) {
delete _p_grp_experiment;
}
@@ -116,4 +117,5 @@ void IdentificationGroup::startGrouping (const GroupingType & grouping_type) {
p_protein_match->setGroupInstance(_group_store);
}
+ qDebug() << "IdentificationGroup::startGrouping end ";
}
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 0b046a4c658b1cc9bc164998ef2c87c5e989435f..e00020a32482f2fa526f5f43f5abdd7206ee2429 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -228,7 +228,7 @@ pappso::pappso_double ProteinMatch::getEvalue(const pappso::MsRunIdSp & sp_msrun
if (p_peptide_match->getMsRunIdSp().get() == sp_msrun_id.get()) {
auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
if (ret.second == false) {
- if (ret.first->second < evalue) {//get best evalue for sequence
+ if (ret.first->second > evalue) {//get best evalue for sequence
ret.first->second = evalue;
}
}
@@ -238,7 +238,7 @@ pappso::pappso_double ProteinMatch::getEvalue(const pappso::MsRunIdSp & sp_msrun
//overall samples
auto ret = map_sequence_evalue.insert(std::pair<QString, pappso::pappso_double>(sequence, evalue));
if (ret.second == false) {
- if (ret.first->second < evalue) {//get best evalue for sequence
+ if (ret.first->second > evalue) {//get best evalue for sequence
ret.first->second = evalue;
}
}
diff --git a/src/gui/peptide_list_view/peptidelistwindow.cpp b/src/gui/peptide_list_view/peptidelistwindow.cpp
index 02b9295664e487734b1ec6837c2cf18cc8476495..ed693ec9ca72e1312ea15e5b77ef4f8ec42d1705 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.cpp
+++ b/src/gui/peptide_list_view/peptidelistwindow.cpp
@@ -45,8 +45,8 @@ PeptideListWindow::PeptideListWindow(ProjectWindow *parent):
ui->tableView->setSortingEnabled(true);
//connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
-
-
+
+
#if QT_VERSION >= 0x050000
// Qt5 code
/*
@@ -56,7 +56,12 @@ PeptideListWindow::PeptideListWindow(ProjectWindow *parent):
*/
#else
// Qt4 code
-connect (this, SIGNAL(peptideDataChanged()), _peptide_table_model_p, SLOT(onPeptideDataChanged()));
+ connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+
+ connect (this, SIGNAL(peptideDataChanged()), _peptide_table_model_p, SLOT(onPeptideDataChanged()));
+
+ connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
+
/*
connect(&workerThread, SIGNAL(finished()), worker, SLOT(deleteLater()));
connect(this, SIGNAL(operateMsDataFile(QString)), worker,SLOT(doMsDataFileLoad(QString)));
@@ -79,10 +84,11 @@ PeptideListWindow::~PeptideListWindow()
void PeptideListWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
}
-void PeptideListWindow::setProteinMatch(Project * p_project, ProteinMatch * p_protein_match) {
+void PeptideListWindow::setProteinMatch(IdentificationGroup * p_identification_group, ProteinMatch * p_protein_match) {
if (_p_protein_match != p_protein_match) {
+ _p_identification_group = p_identification_group;
_p_protein_match = p_protein_match;
- _peptide_table_model_p->setProteinMatch(p_project, p_protein_match);
+ _peptide_table_model_p->setProteinMatch( p_protein_match);
_p_proxy_model->setSourceModel(_peptide_table_model_p);
ui->proteinLabel->setText(p_protein_match->getProteinXtpSp().get()->getDescription());
}
diff --git a/src/gui/peptide_list_view/peptidelistwindow.h b/src/gui/peptide_list_view/peptidelistwindow.h
index d944854174aa95f1fc319775a70b55c233a7d242..b788acd4a7dc53dfd5ba8cea8f71e779d8f883c4 100644
--- a/src/gui/peptide_list_view/peptidelistwindow.h
+++ b/src/gui/peptide_list_view/peptidelistwindow.h
@@ -46,7 +46,7 @@ public:
explicit PeptideListWindow(ProjectWindow * parent = 0);
~PeptideListWindow();
- void setProteinMatch(Project * p_project, ProteinMatch * p_protein_match);
+ void setProteinMatch(IdentificationGroup * p_identification_group, ProteinMatch * p_protein_match);
void edited();
public slots:
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index c29eaf643a72b25357695d8908dbb76c0c37f11d..27d9e3d4aa5742ac25a02a76a655ba8f75e372d2 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -39,9 +39,8 @@ PeptideTableModel::PeptideTableModel(QObject *parent)
}
-void PeptideTableModel::setProteinMatch(Project * p_project, ProteinMatch * p_protein_match) {
+void PeptideTableModel::setProteinMatch(ProteinMatch * p_protein_match) {
qDebug() << "PeptideTableModel::setProteinMatch begin " ;
- _p_project = p_project;
_p_protein_match = p_protein_match;
QModelIndex topLeft = createIndex(0,0);
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index 78514420a4930a848a764574f493d4cb1b290a40..8cd2455286e2c86bf14ed847491db8444910033d 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -39,7 +39,7 @@ public:
QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
- void setProteinMatch(Project * p_project, ProteinMatch * p_protein_match);
+ void setProteinMatch(ProteinMatch * p_protein_match);
ProteinMatch * getProteinMatch();
signals:
void peptideMatchClicked(PeptideMatch * p_peptide_match);
@@ -50,7 +50,6 @@ public slots:
void onTableClicked(const QModelIndex &index);
private :
- Project * _p_project;
ProteinMatch * _p_protein_match= nullptr;
};
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index b754827d11f7c1070c6ea01a0567e9c81d3b3856..45d9fa46923a124dabd537f5aa68d016e449bb0a 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -28,6 +28,8 @@
#include "gui/protein_list_view/proteinlistwindow.h"
#include <QDebug>
#include <QApplication>
+#include <QMessageBox>
+#include <pappsomspp/pappsoexception.h>
ProjectWindow::ProjectWindow(MainWindow *parent):
@@ -74,20 +76,6 @@ void ProjectWindow::connectNewProteinListWindow() {
_p_current_protein_list_window = new ProteinListWindow(this);
_protein_list_window_collection.push_back(_p_current_protein_list_window);
-#if QT_VERSION >= 0x050000
- // Qt5 code
- /*
- connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
- connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
- connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
- */
-#else
-// Qt4 code
-//connect (_p_current_protein_list_window, SIGNAL(proteinMatchDoubleClicked(ProteinMatch *)), this,SLOT(doViewProteinDetail(ProteinMatch *)));
- connect (this, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), _p_current_protein_list_window,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-
-#endif
-
qDebug() << "ProjectWindow::connectNewProteinListWindow end";
}
@@ -97,19 +85,6 @@ void ProjectWindow::connectNewProteinDetailWindow() {
_p_current_protein_detail_window = new ProteinWindow(this);
_protein_detail_window_collection.push_back(_p_current_protein_detail_window);
-#if QT_VERSION >= 0x050000
- // Qt5 code
- /*
- connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
- connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
- connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
- */
-#else
-// Qt4 code
- //connect (_p_current_peptide_list_window, SIGNAL(proteinMatchClicked(ProteinMatch *)), this,SLOT(doViewPeptideList(ProteinMatch *)));
-
-#endif
-
qDebug() << "ProjectWindow::connectNewProteinDetailWindow end";
}
@@ -119,47 +94,62 @@ void ProjectWindow::connectNewPeptideListWindow() {
_p_current_peptide_list_window = new PeptideListWindow(this);
_peptide_list_window_collection.push_back(_p_current_peptide_list_window);
-#if QT_VERSION >= 0x050000
- // Qt5 code
- /*
- connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
- connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
- connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
- */
-#else
-// Qt4 code
- //connect (_p_current_peptide_list_window, SIGNAL(proteinMatchClicked(ProteinMatch *)), this,SLOT(doViewPeptideList(ProteinMatch *)));
- //connect (_p_current_peptide_list_window, SIGNAL(identificationGroupEdited(IdentificationGroup *)), this,SLOT(doIdentificationGroupEdited(IdentificationGroup *)));
- // connect (this, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), _p_current_peptide_list_window,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
-
-#endif
-
qDebug() << "ProjectWindow::connectNewPeptideListWindow end";
}
void ProjectWindow::refreshGroup(IdentificationGroup * p_ident_group) {
qDebug() << "ProjectWindow::refreshGroup begin";
- vector< MsRunIdSp > ms_run_list = p_ident_group->getMsRunIdSpList();
- ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
-
- ui->group_number_display->setText(QString("%1").arg(p_ident_group->countGroup()));
- ui->subgroup_number_display->setText(QString("%1").arg(p_ident_group->countSubGroup()));
- ui->protein_number_display->setText(QString("%1").arg(p_ident_group->countGrouped()));
- emit identificationGroupGrouped(p_ident_group);
+ if (p_ident_group == nullptr) {
+ qDebug() << "ProjectWindow::refreshGroup p_ident_group == nullptr";
+ }
+ else {
+ try {
+ vector< MsRunIdSp > ms_run_list = p_ident_group->getMsRunIdSpList();
+ ui->sample_number_display->setText(QString("%1").arg(ms_run_list.size()));
+
+ ui->group_number_display->setText(QString("%1").arg(p_ident_group->countGroup()));
+ ui->subgroup_number_display->setText(QString("%1").arg(p_ident_group->countSubGroup()));
+ ui->protein_number_display->setText(QString("%1").arg(p_ident_group->countGrouped()));
+ emit identificationGroupGrouped(p_ident_group);
+ }
+ catch (pappso::PappsoException exception_pappso) {
+ QMessageBox::warning(this,
+ tr("Unable to display project :"), exception_pappso.qwhat());
+ }
+ catch (std::exception exception_std) {
+ QMessageBox::warning(this,
+ tr("Unable to display project :"), exception_std.what());
+ }
+ }
qDebug() << "ProjectWindow::refreshGroup end";
}
void ProjectWindow::doIdentificationGroupEdited(IdentificationGroup * p_ident_group) {
- qDebug() << "ProjectWindow::doIdentificationGroupEdited begin";
- p_ident_group->startGrouping(_project_sp.get()->getGroupingType());
-
-
- refreshGroup(p_ident_group);
+ qDebug() << "ProjectWindow::doIdentificationGroupEdited begin " << p_ident_group;
+ if (p_ident_group == nullptr) {
+ qDebug() << "ProjectWindow::doIdentificationGroupEdited p_ident_group == nullptr";
+ }
+ else {
+ try {
+ p_ident_group->startGrouping(_project_sp.get()->getGroupingType());
+
+ }
+ catch (pappso::PappsoException exception_pappso) {
+ QMessageBox::warning(this,
+ tr("Error grouping project :"), exception_pappso.qwhat());
+ }
+ catch (std::exception exception_std) {
+ QMessageBox::warning(this,
+ tr("Error grouping project :"), exception_std.what());
+ }
+
+ refreshGroup(p_ident_group);
+ }
qDebug() << "ProjectWindow::doIdentificationGroupEdited end";
}
-void ProjectWindow::doViewPeptideList(ProteinMatch * protein_match) {
+void ProjectWindow::doViewPeptideList(IdentificationGroup * p_ident_group, ProteinMatch * protein_match) {
qDebug() << "ProjectWindow::doViewPeptideList begin";
@@ -172,7 +162,7 @@ void ProjectWindow::doViewPeptideList(ProteinMatch * protein_match) {
}
- _p_current_peptide_list_window->setProteinMatch(_project_sp.get(), protein_match);
+ _p_current_peptide_list_window->setProteinMatch(p_ident_group, protein_match);
_p_current_peptide_list_window->show();
qDebug() << "ProjectWindow::doViewPeptideList end";
}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index bcf8ee97f5f1ba6a03e962fcbe65326eec930c33..c82caf7bc90824a5ea15a3ac2a85e410ca6d61f3 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -58,7 +58,7 @@ signals:
//void peptideChanged(pappso::PeptideSp peptide);
protected :
- void doViewPeptideList(ProteinMatch * protein_match);
+ void doViewPeptideList(IdentificationGroup * p_ident_group, ProteinMatch * protein_match);
void doViewProteinDetail(ProteinMatch * protein_match);
void doViewPeptideDetail(PeptideMatch * peptide_match);
void doIdentificationGroupEdited(IdentificationGroup * p_identification_group);
diff --git a/src/gui/protein_list_view/proteinlistwindow.cpp b/src/gui/protein_list_view/proteinlistwindow.cpp
index 1b313d2cae58caf1d521fa519cea51917d331089..d58d8dfc21017809493b8ec3835ac428727e26f4 100644
--- a/src/gui/protein_list_view/proteinlistwindow.cpp
+++ b/src/gui/protein_list_view/proteinlistwindow.cpp
@@ -72,6 +72,8 @@ ProteinListWindow::ProteinListWindow(ProjectWindow *parent):
*/
#else
// Qt4 code
+ connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+
connect (this, SIGNAL(proteinDataChanged()), _protein_table_model_p, SLOT(onProteinDataChanged()));
connect(ui->tableView, SIGNAL(clicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableClicked(const QModelIndex &)));
//connect(ui->tableView, SIGNAL(doubleClicked(const QModelIndex &)), _p_proxy_model, SLOT(onTableDoubleClicked(const QModelIndex &)));
@@ -106,7 +108,7 @@ void ProteinListWindow::showAccessionColumn(bool show) {
void ProteinListWindow::askPeptideListView(ProteinMatch * p_protein_match) {
qDebug() << "ProteinListWindow::askPeptideListView begin";
- _project_window->doViewPeptideList(p_protein_match);
+ _project_window->doViewPeptideList(_p_identification_group, p_protein_match);
qDebug() << "ProteinListWindow::askPeptideListView end";
//updateStatusBar();
}
diff --git a/src/gui/protein_view/proteinwindow.cpp b/src/gui/protein_view/proteinwindow.cpp
index 9fea5f2e0fe5f2afaf1fe97cb8a131a04f883b32..5dc6e5de5e81cbf596957983a5ae8b3721ade665 100644
--- a/src/gui/protein_view/proteinwindow.cpp
+++ b/src/gui/protein_view/proteinwindow.cpp
@@ -32,6 +32,7 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent):
QMainWindow(parent),
ui(new Ui::ProteinDetailView)
{
+ _p_project_window = parent;
ui->setupUi(this);
/*
*/
@@ -46,6 +47,8 @@ ProteinWindow::ProteinWindow(ProjectWindow *parent):
*/
#else
// Qt4 code
+ connect (_p_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+
//connect(_protein_table_model_p, SIGNAL(layoutChanged()), this, SLOT(updateStatusBar()));
#endif
}
@@ -54,16 +57,19 @@ ProteinWindow::~ProteinWindow()
{
delete ui;
}
+void ProteinWindow::doIdentificationGroupGrouped(IdentificationGroup * p_identification_group) {
+ updateDisplay();
+}
-void ProteinWindow::setProteinMatch(ProteinMatch * p_protein_match) {
+void ProteinWindow::updateDisplay() {
try {
- ui->descriptionLabel->setText(p_protein_match->getProteinXtpSp().get()->getAccession());
- //ui->sequenceLabel->setText(p_protein_match->getProteinXtpSp().get()->getSequence());
- ui->sequenceTextEdit->setText(p_protein_match->getHtmlSequence());
- ui->coverage_label->setText(QString("%1 %").arg(p_protein_match->getCoverage()*100));
- pappso::Peptide peptide(p_protein_match->getProteinXtpSp().get()->getSequence());
+ ui->descriptionLabel->setText(_p_protein_match->getProteinXtpSp().get()->getAccession());
+ //ui->sequenceLabel->setText(_p_protein_match->getProteinXtpSp().get()->getSequence());
+ ui->sequenceTextEdit->setText(_p_protein_match->getHtmlSequence());
+ ui->coverage_label->setText(QString("%1 %").arg(_p_protein_match->getCoverage()*100));
+ pappso::Peptide peptide(_p_protein_match->getProteinXtpSp().get()->getSequence());
ui->mw_label->setText(QString("%1 kDa").arg(peptide.getMass()/1000));
- ui->evalue_label->setText(QString("%1 (log10: %2)").arg(p_protein_match->getEvalue()).arg(std::log10(p_protein_match->getEvalue())));
+ ui->evalue_label->setText(QString("%1 (log10: %2)").arg(_p_protein_match->getEvalue()).arg(std::log10(_p_protein_match->getEvalue())));
}
catch (pappso::PappsoException exception_pappso) {
QMessageBox::warning(this,
@@ -73,4 +79,10 @@ void ProteinWindow::setProteinMatch(ProteinMatch * p_protein_match) {
QMessageBox::warning(this,
tr("Unable to display protein details :"), exception_std.what());
}
+
+}
+
+void ProteinWindow::setProteinMatch(ProteinMatch * p_protein_match) {
+ _p_protein_match = p_protein_match;
+ updateDisplay();
}
diff --git a/src/gui/protein_view/proteinwindow.h b/src/gui/protein_view/proteinwindow.h
index f3c024c93f900c2b3010be02e182ccd0ede6089a..3dfeeda52ab5bdd0cd2edca889986687e70b2d2d 100644
--- a/src/gui/protein_view/proteinwindow.h
+++ b/src/gui/protein_view/proteinwindow.h
@@ -42,9 +42,18 @@ public:
explicit ProteinWindow(ProjectWindow * parent = 0);
~ProteinWindow();
void setProteinMatch(ProteinMatch * p_protein_match);
+
+public slots:
+ void doIdentificationGroupGrouped(IdentificationGroup * p_identification_group);
+
+protected :
+ void updateDisplay();
+
private:
Ui::ProteinDetailView *ui;
QTextDocument sequence_text;
+ ProjectWindow * _p_project_window;
+ ProteinMatch * _p_protein_match = nullptr;
};