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Commit 7ecd6548 authored by Langella Olivier's avatar Langella Olivier
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new controls on decoy and contaminant widgets

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with 179 additions and 282 deletions
src/gui/project_view/project_view.ui
+ 25
− 24
View file @ 7ecd6548
...@@ -199,9 +199,9 @@ ...@@ -199,9 +199,9 @@
</spacer> </spacer>
</item> </item>
<item> <item>
<widget class="QPushButton" name="fdr_button"> <widget class="QPushButton" name="apply_fdr_button">
<property name="text"> <property name="text">
<string>OK</string> <string>apply</string>
</property> </property>
</widget> </widget>
</item> </item>
...@@ -376,22 +376,6 @@ ...@@ -376,22 +376,6 @@
</customwidgets> </customwidgets>
<resources/> <resources/>
<connections> <connections>
<connection>
<sender>fdr_button</sender>
<signal>clicked()</signal>
<receiver>ProjectView</receiver>
<slot>doFdrChanged()</slot>
<hints>
<hint type="sourcelabel">
<x>448</x>
<y>219</y>
</hint>
<hint type="destinationlabel">
<x>484</x>
<y>334</y>
</hint>
</hints>
</connection>
<connection> <connection>
<sender>precision_unit_combobox</sender> <sender>precision_unit_combobox</sender>
<signal>currentIndexChanged(QString)</signal> <signal>currentIndexChanged(QString)</signal>
...@@ -399,8 +383,8 @@ ...@@ -399,8 +383,8 @@
<slot>doMassPrecisionUnitChanged(QString)</slot> <slot>doMassPrecisionUnitChanged(QString)</slot>
<hints> <hints>
<hint type="sourcelabel"> <hint type="sourcelabel">
<x>119</x> <x>253</x>
<y>104</y> <y>113</y>
</hint> </hint>
<hint type="destinationlabel"> <hint type="destinationlabel">
<x>489</x> <x>489</x>
...@@ -431,8 +415,8 @@ ...@@ -431,8 +415,8 @@
<slot>doFilterChanged()</slot> <slot>doFilterChanged()</slot>
<hints> <hints>
<hint type="sourcelabel"> <hint type="sourcelabel">
<x>119</x> <x>131</x>
<y>104</y> <y>101</y>
</hint> </hint>
<hint type="destinationlabel"> <hint type="destinationlabel">
<x>815</x> <x>815</x>
...@@ -447,8 +431,8 @@ ...@@ -447,8 +431,8 @@
<slot>doApplyFilter()</slot> <slot>doApplyFilter()</slot>
<hints> <hints>
<hint type="sourcelabel"> <hint type="sourcelabel">
<x>119</x> <x>448</x>
<y>104</y> <y>136</y>
</hint> </hint>
<hint type="destinationlabel"> <hint type="destinationlabel">
<x>689</x> <x>689</x>
...@@ -472,6 +456,22 @@ ...@@ -472,6 +456,22 @@
</hint> </hint>
</hints> </hints>
</connection> </connection>
<connection>
<sender>apply_fdr_button</sender>
<signal>clicked()</signal>
<receiver>ProjectView</receiver>
<slot>doApplyDecoy()</slot>
<hints>
<hint type="sourcelabel">
<x>424</x>
<y>201</y>
</hint>
<hint type="destinationlabel">
<x>682</x>
<y>284</y>
</hint>
</hints>
</connection>
</connections> </connections>
<slots> <slots>
<slot>doFdrChanged()</slot> <slot>doFdrChanged()</slot>
...@@ -481,5 +481,6 @@ ...@@ -481,5 +481,6 @@
<slot>doSelectContaminantSource()</slot> <slot>doSelectContaminantSource()</slot>
<slot>doFilterChanged()</slot> <slot>doFilterChanged()</slot>
<slot>doApplyFilter()</slot> <slot>doApplyFilter()</slot>
<slot>doApplyDecoy()</slot>
</slots> </slots>
</ui> </ui>
src/gui/project_view/projectwindow.cpp
+ 41
− 136
View file @ 7ecd6548
...@@ -126,22 +126,20 @@ ProjectWindow::ProjectWindow(MainWindow *parent) ...@@ -126,22 +126,20 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
ProjectWindow::~ProjectWindow() ProjectWindow::~ProjectWindow()
{ {
qDebug() << "ProjectWindow::~ProjectWindow"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// if (_p_ms_data_file != nullptr) delete _p_ms_data_file; // if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
_worker_thread.quit(); _worker_thread.quit();
_worker_thread.wait(); _worker_thread.wait();
qDebug() << "ProjectWindow::~ProjectWindow1"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete ui; delete ui;
qDebug() << "ProjectWindow::~ProjectWindow2"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete _p_fasta_str_li;
qDebug() << "ProjectWindow::~ProjectWindow3";
delete _p_edit_modifications; delete _p_edit_modifications;
qDebug() << "ProjectWindow::~ProjectWindow5"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete _p_edit_label_methods; delete _p_edit_label_methods;
qDebug() << "ProjectWindow::~ProjectWindow6"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete _p_waiting_message_dialog; delete _p_waiting_message_dialog;
qDebug() << "ProjectWindow::~ProjectWindow end"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
Project * Project *
...@@ -153,29 +151,29 @@ void ...@@ -153,29 +151,29 @@ void
ProjectWindow::setDefaultProteinListWindow( ProjectWindow::setDefaultProteinListWindow(
ProteinListWindow *p_protein_list_window) ProteinListWindow *p_protein_list_window)
{ {
qDebug() << "ProjectWindow::setDefaultProteinListWindow begin"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_current_protein_list_window = p_protein_list_window; _p_current_protein_list_window = p_protein_list_window;
qDebug() << "ProjectWindow::setDefaultProteinListWindow end"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void void
ProjectWindow::connectNewPtmIslandListWindow() ProjectWindow::connectNewPtmIslandListWindow()
{ {
qDebug() << "ProjectWindow::connectNewPtmIslandListWindow begin"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_current_ptm_island_list_window = new PtmIslandListWindow(this); _p_current_ptm_island_list_window = new PtmIslandListWindow(this);
_ptm_island_list_window_collection.push_back( _ptm_island_list_window_collection.push_back(
_p_current_ptm_island_list_window); _p_current_ptm_island_list_window);
qDebug() << "ProjectWindow::connectNewPtmIslandListWindow end"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void void
ProjectWindow::connectNewProteinListWindow() ProjectWindow::connectNewProteinListWindow()
{ {
qDebug() << "ProjectWindow::connectNewProteinListWindow begin"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_current_protein_list_window = new ProteinListWindow(this); _p_current_protein_list_window = new ProteinListWindow(this);
_protein_list_window_collection.push_back(_p_current_protein_list_window); _protein_list_window_collection.push_back(_p_current_protein_list_window);
qDebug() << "ProjectWindow::connectNewProteinListWindow end"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void void
...@@ -395,69 +393,6 @@ ProjectWindow::computeMassPrecision() ...@@ -395,69 +393,6 @@ ProjectWindow::computeMassPrecision()
} }
qDebug() << "ProjectWindow::computeMassPrecision end"; qDebug() << "ProjectWindow::computeMassPrecision end";
} }
void
ProjectWindow::doFdrChanged()
{
qDebug() << "ProjectWindow::doFdrChanged begin ";
try
{
showWaitingMessage(tr("FDR modifications"));
doDisplayLoadingMessage(tr("tagging decoy proteins"));
if(ui->decoy_regexp_radiobutton->isChecked())
{
_project_sp.get()->getProteinStore().setRegexpDecoyPattern(
ui->decoy_protein_regexp_line_edit->text());
}
else
{
_project_sp.get()->getProteinStore().clearDecoys();
QModelIndexList index_list =
ui->decoy_database_listview->selectionModel()->selectedIndexes();
if(index_list.size() > 0)
{
qDebug() << "ProjectWindow::doFdrChanged index_list.size()="
<< index_list.size();
for(QModelIndex index : index_list)
{
if(index.data(Qt::UserRole).canConvert<FastaFile *>())
{
FastaFile *p_fasta_file =
index.data(Qt::UserRole).value<FastaFile *>();
p_fasta_file->setDecoys(
_project_sp.get()->getProteinStore());
}
else
{
throw pappso::PappsoException(
QObject::tr("can not convert to FastaFile "
"index.data().canConvert<FastaFile *>()"));
}
}
}
}
doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters(
_project_sp.get()->getAutomaticFilterParameters());
// re group
emit operateGrouping(_project_sp);
}
catch(pappso::PappsoException exception_pappso)
{
hideWaitingMessage();
QMessageBox::warning(
this, tr("Unable to compute FDR :"), exception_pappso.qwhat());
}
catch(std::exception exception_std)
{
hideWaitingMessage();
QMessageBox::warning(
this, tr("Unable to compute FDR :"), exception_std.what());
}
qDebug() << "ProjectWindow::doFdrChanged end ";
}
void void
ProjectWindow::refresh() ProjectWindow::refresh()
{ {
...@@ -475,6 +410,14 @@ ProjectWindow::doContaminantSelectionChanged() ...@@ -475,6 +410,14 @@ ProjectWindow::doContaminantSelectionChanged()
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void
ProjectWindow::doDecoySelectionChanged()
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
ui->apply_fdr_button->setEnabled(true);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void void
ProjectWindow::doAutomaticFilterParametersChanged( ProjectWindow::doAutomaticFilterParametersChanged(
AutomaticFilterParameters parameters) AutomaticFilterParameters parameters)
...@@ -687,39 +630,17 @@ ProjectWindow::doViewProteinList(IdentificationGroup *p_identification_group) ...@@ -687,39 +630,17 @@ ProjectWindow::doViewProteinList(IdentificationGroup *p_identification_group)
void void
ProjectWindow::setProjectSp(ProjectSp project_sp) ProjectWindow::setProjectSp(ProjectSp project_sp)
{ {
qDebug() << "ProjectWindow::setProjectSp begin"; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_project_sp = project_sp; _project_sp = project_sp;
ui->decoy_regexp_radiobutton->setChecked(true);
ui->decoy_regexp_groupbox->setVisible(true);
ui->decoy_database_groupbox->setVisible(false);
if(_project_sp.get()->getProteinStore().getDecoyFastaFileList().size() > 0)
{
ui->decoy_database_files_radiobutton->setChecked(true);
ui->decoy_regexp_groupbox->setVisible(false);
ui->decoy_database_groupbox->setVisible(true);
}
ui->contaminant_widget->getProjectContaminants(_project_sp.get()); ui->contaminant_widget->getProjectContaminants(_project_sp.get());
ui->decoy_widget->getProjectDecoys(_project_sp.get());
qDebug() << "ProjectWindow::setProjectSp begin " qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _project_sp.get()->getFastaFileStore().getFastaFileList().size(); << _project_sp.get()->getFastaFileStore().getFastaFileList().size();
_fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList(); _fastafile_list = _project_sp.get()->getFastaFileStore().getFastaFileList();
_p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
for(FastaFileSp fasta_file : _fastafile_list)
{
QStandardItem *item;
item =
new QStandardItem(QString("%1").arg(fasta_file.get()->getFilename()));
item->setEditable(false);
item->setData(QVariant::fromValue(fasta_file.get()), Qt::UserRole);
_p_fasta_str_li->appendRow(item);
// item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
for(auto &&p_window : _ptm_island_list_window_collection) for(auto &&p_window : _ptm_island_list_window_collection)
{ {
delete p_window; delete p_window;
...@@ -783,7 +704,8 @@ ProjectWindow::setProjectSp(ProjectSp project_sp) ...@@ -783,7 +704,8 @@ ProjectWindow::setProjectSp(ProjectSp project_sp)
_p_xic_window = nullptr; _p_xic_window = nullptr;
} }
qDebug() << " ProjectWindow::setProjectSp size=" qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " ProjectWindow::setProjectSp size="
<< identification_list.size(); << identification_list.size();
if(identification_list.size() == 1) if(identification_list.size() == 1)
{ {
...@@ -836,19 +758,18 @@ ProjectWindow::setProjectSp(ProjectSp project_sp) ...@@ -836,19 +758,18 @@ ProjectWindow::setProjectSp(ProjectSp project_sp)
//_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP()); //_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
//_protein_list_window->show(); //_protein_list_window->show();
ui->decoy_protein_regexp_line_edit->setText(
_project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
refresh(); refresh();
this->setEnabled(true); this->setEnabled(true);
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// doAutomaticFilterParametersChanged(params); // doAutomaticFilterParametersChanged(params);
// doFdrChanged(); // doFdrChanged();
} }
void void
ProjectWindow::doIdentificationsComboboxChanged(int index_in) ProjectWindow::doIdentificationsComboboxChanged(int index_in)
{ {
qDebug() << "ProjectWindow::doIdentificationsComboboxChanged begin ";
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
for(int index = 0; index < ui->identifications_combobox->count(); index++) for(int index = 0; index < ui->identifications_combobox->count(); index++)
{ {
qobject_cast<IdentificationGroupWidget *>( qobject_cast<IdentificationGroupWidget *>(
...@@ -858,7 +779,8 @@ ProjectWindow::doIdentificationsComboboxChanged(int index_in) ...@@ -858,7 +779,8 @@ ProjectWindow::doIdentificationsComboboxChanged(int index_in)
qobject_cast<IdentificationGroupWidget *>( qobject_cast<IdentificationGroupWidget *>(
qvariant_cast<QObject *>(ui->identifications_combobox->itemData(index_in))) qvariant_cast<QObject *>(ui->identifications_combobox->itemData(index_in)))
->setVisible(true); ->setVisible(true);
qDebug() << "ProjectWindow::doIdentificationsComboboxChanged end ";
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void void
...@@ -901,8 +823,7 @@ ProjectWindow::doIdentificationGroupEdited( ...@@ -901,8 +823,7 @@ ProjectWindow::doIdentificationGroupEdited(
{ {
showWaitingMessage(tr("Updating identification group")); showWaitingMessage(tr("Updating identification group"));
qDebug() << "ProjectWindow::doIdentificationGroupEdited emit " qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
"operateGroupingOnIdentification(_project_sp) ";
emit operateGroupingOnIdentification(p_identification_group, emit operateGroupingOnIdentification(p_identification_group,
_project_sp.get()->getGroupingType()); _project_sp.get()->getGroupingType());
} }
...@@ -918,7 +839,8 @@ ProjectWindow::viewError(QString error) ...@@ -918,7 +839,8 @@ ProjectWindow::viewError(QString error)
void void
ProjectWindow::doAcceptedLabelingMethod() ProjectWindow::doAcceptedLabelingMethod()
{ {
qDebug() << "ProjectWindow::doAcceptedLabelingMethod";
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
showWaitingMessage(tr("Apply labeling method")); showWaitingMessage(tr("Apply labeling method"));
LabelingMethodSp labeling_method_sp = LabelingMethodSp labeling_method_sp =
...@@ -928,8 +850,7 @@ ProjectWindow::doAcceptedLabelingMethod() ...@@ -928,8 +850,7 @@ ProjectWindow::doAcceptedLabelingMethod()
doDisplayLoadingMessage(tr("labeling peptides")); doDisplayLoadingMessage(tr("labeling peptides"));
qDebug() << "ProjectWindow::doAcceptedLabelingMethod emit " qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
"operateGrouping(_project_sp) ";
emit operateGrouping(_project_sp); emit operateGrouping(_project_sp);
} }
...@@ -937,7 +858,8 @@ ProjectWindow::doAcceptedLabelingMethod() ...@@ -937,7 +858,8 @@ ProjectWindow::doAcceptedLabelingMethod()
void void
ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence) ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence)
{ {
qDebug() << "ProjectWindow::openInXicViewer begin";
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_p_xic_window == nullptr) if(_p_xic_window == nullptr)
{ {
_p_xic_window = new XicWindow(this); _p_xic_window = new XicWindow(this);
...@@ -946,38 +868,22 @@ ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence) ...@@ -946,38 +868,22 @@ ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence)
_p_xic_window->show(); _p_xic_window->show();
_p_xic_window->addXic(p_peptide_evidence); _p_xic_window->addXic(p_peptide_evidence);
qDebug() << "ProjectWindow::openInXicViewer end";
}
void qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
ProjectWindow::doSelectDecoySource()
{
qDebug() << "ProjectWindow::doSelectDecoySource begin";
ui->decoy_database_groupbox->setVisible(false);
ui->decoy_regexp_groupbox->setVisible(false);
if(ui->decoy_database_files_radiobutton->isChecked())
{
ui->decoy_database_groupbox->setVisible(true);
}
else
{
ui->decoy_regexp_groupbox->setVisible(true);
}
qDebug() << "ProjectWindow::doSelectDecoySource end";
} }
void void
ProjectWindow::doFilterChanged() ProjectWindow::doFilterChanged()
{ {
ui->apply_filter_button->setEnabled(true); ui->apply_filter_button->setEnabled(true);
ui->fdr_button->setEnabled(true); ui->apply_fdr_button->setEnabled(true);
} }
void void
ProjectWindow::doApplyDecoy() ProjectWindow::doApplyDecoy()
{ {
ui->fdr_button->setEnabled(false); ui->apply_fdr_button->setEnabled(false);
// doAutomaticFilterParametersChanged(automatic_filter); // doAutomaticFilterParametersChanged(automatic_filter);
try try
{ {
...@@ -991,8 +897,7 @@ ProjectWindow::doApplyDecoy() ...@@ -991,8 +897,7 @@ ProjectWindow::doApplyDecoy()
doDisplayLoadingMessage(tr("updating filters")); doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters( _project_sp.get()->updateAutomaticFilters(
_project_sp.get()->getAutomaticFilterParameters()); _project_sp.get()->getAutomaticFilterParameters());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit operateGrouping(_project_sp); emit operateGrouping(_project_sp);
......
src/gui/project_view/projectwindow.h
+ 1
− 4
View file @ 7ecd6548
...@@ -67,8 +67,6 @@ class ProjectWindow : public QMainWindow ...@@ -67,8 +67,6 @@ class ProjectWindow : public QMainWindow
void doViewProteinList(IdentificationGroup *p_identification_group = nullptr); void doViewProteinList(IdentificationGroup *p_identification_group = nullptr);
void setDefaultProteinListWindow(ProteinListWindow *p_protein_list_window); void setDefaultProteinListWindow(ProteinListWindow *p_protein_list_window);
void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters); void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
void doFdrChanged();
void doSelectDecoySource();
void doMassPrecisionUnitChanged(QString combo_value); void doMassPrecisionUnitChanged(QString combo_value);
void doOperationFailed(QString); void doOperationFailed(QString);
void doOperationFinished(); void doOperationFinished();
...@@ -82,6 +80,7 @@ class ProjectWindow : public QMainWindow ...@@ -82,6 +80,7 @@ class ProjectWindow : public QMainWindow
void doViewPeptideDetail(PeptideEvidence *peptide_evidence); void doViewPeptideDetail(PeptideEvidence *peptide_evidence);
void doFilterChanged(); void doFilterChanged();
void doApplyFilter(); void doApplyFilter();
void doApplyDecoy();
// void setColor(const QColor &color); // void setColor(const QColor &color);
// void setShape(Shape shape); // void setShape(Shape shape);
signals: signals:
...@@ -141,9 +140,7 @@ class ProjectWindow : public QMainWindow ...@@ -141,9 +140,7 @@ class ProjectWindow : public QMainWindow
ProjectSp _project_sp; ProjectSp _project_sp;
QStandardItemModel *_p_fasta_str_li;
std::vector<FastaFileSp> _fastafile_list; std::vector<FastaFileSp> _fastafile_list;
WaitingMessageDialog *_p_waiting_message_dialog; WaitingMessageDialog *_p_waiting_message_dialog;
// QCPBars *_p_bars; // QCPBars *_p_bars;
}; };
src/gui/widgets/contaminant_widget/contaminantwidget.cpp
+ 42
− 25
View file @ 7ecd6548
...@@ -120,41 +120,56 @@ ContaminantWidget::setProjectContaminants(Project *p_project) ...@@ -120,41 +120,56 @@ ContaminantWidget::setProjectContaminants(Project *p_project)
{ {
qDebug() << "ContaminantWidget::setProjectContaminants begin"; qDebug() << "ContaminantWidget::setProjectContaminants begin";
_emit_changed = false; _emit_changed = false;
if(ui->contaminant_file_radiobutton->isChecked()) try
{ {
QModelIndexList index_list = if(ui->contaminant_file_radiobutton->isChecked())
ui->contaminant_database_listview->selectionModel()->selectedIndexes();
p_project->getProteinStore().clearContaminants();
if(index_list.size() > 0)
{ {
for(QModelIndex index : index_list) QModelIndexList index_list =
ui->contaminant_database_listview->selectionModel()
->selectedIndexes();
p_project->getProteinStore().clearContaminants();
if(index_list.size() > 0)
{ {
if(index.data(Qt::UserRole).canConvert<FastaFileSp>()) for(QModelIndex index : index_list)
{
FastaFileSp p_fasta_file =
index.data(Qt::UserRole).value<FastaFileSp>();
p_fasta_file.get()->setContaminants(
p_project->getProteinStore());
}
else
{ {
throw pappso::PappsoException( if(index.data(Qt::UserRole).canConvert<FastaFileSp>())
QObject::tr("can not convert to FastaFile " {
"index.data().canConvert<FastaFile *>()")); FastaFileSp p_fasta_file =
index.data(Qt::UserRole).value<FastaFileSp>();
p_fasta_file.get()->setContaminants(
p_project->getProteinStore());
}
else
{
throw pappso::PappsoException(
QObject::tr("can not convert to FastaFile "
"index.data().canConvert<FastaFile *>()"));
}
} }
} }
}
if(_no_project) if(_no_project)
{
ui->control_list_widget->setVisible(true);
}
}
else
{ {
ui->control_list_widget->setVisible(true); p_project->getProteinStore().setRegexpContaminantPattern(
ui->contaminant_protein_regexp_line_edit->text());
ui->control_list_widget->setVisible(false);
} }
} }
else
catch(pappso::PappsoException &exception_pappso)
{
_emit_changed = true;
throw exception_pappso;
}
catch(std::exception &exception_std)
{ {
p_project->getProteinStore().setRegexpContaminantPattern( _emit_changed = true;
ui->contaminant_protein_regexp_line_edit->text()); throw exception_std;
ui->control_list_widget->setVisible(false);
} }
_emit_changed = true; _emit_changed = true;
qDebug() << "ContaminantWidget::setProjectContaminants end"; qDebug() << "ContaminantWidget::setProjectContaminants end";
...@@ -200,7 +215,9 @@ ContaminantWidget::doSelectFastaFile() ...@@ -200,7 +215,9 @@ ContaminantWidget::doSelectFastaFile()
settings.value("path/fastafiles_directory", "").toString(); settings.value("path/fastafiles_directory", "").toString();
QStringList filenames = QFileDialog::getOpenFileNames( QStringList filenames = QFileDialog::getOpenFileNames(
this, tr("FASTA files"), default_fasta_location, this,
tr("FASTA files"),
default_fasta_location,
tr("FASTA files (*.fasta);;all files (*)")); tr("FASTA files (*.fasta);;all files (*)"));
if(filenames.size() > 0) if(filenames.size() > 0)
......
src/gui/widgets/decoy_widget/decoy_widget.ui
+ 16
− 64
View file @ 7ecd6548
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
<item> <item>
<widget class="QGroupBox" name="decoy_groupbox"> <widget class="QGroupBox" name="decoy_groupbox">
<property name="title"> <property name="title">
<string>Contaminants</string> <string>Decoys</string>
</property> </property>
<layout class="QVBoxLayout" name="verticalLayout_6"> <layout class="QVBoxLayout" name="verticalLayout_6">
<item> <item>
...@@ -28,7 +28,7 @@ ...@@ -28,7 +28,7 @@
<string>select decoys from fasta files</string> <string>select decoys from fasta files</string>
</property> </property>
<property name="text"> <property name="text">
<string>decoy file</string> <string>deco&amp;y file</string>
</property> </property>
<property name="checked"> <property name="checked">
<bool>true</bool> <bool>true</bool>
...@@ -136,82 +136,34 @@ ...@@ -136,82 +136,34 @@
</hints> </hints>
</connection> </connection>
<connection> <connection>
<sender>contaminant_regexp_radiobutton</sender> <sender>decoy_protein_regexp_line_edit</sender>
<signal>clicked()</signal> <signal>textChanged(QString)</signal>
<receiver>ContaminantWidget</receiver> <receiver>DecoyWidget</receiver>
<slot>doSelectContaminantSource()</slot>
<hints>
<hint type="sourcelabel">
<x>226</x>
<y>52</y>
</hint>
<hint type="destinationlabel">
<x>670</x>
<y>79</y>
</hint>
</hints>
</connection>
<connection>
<sender>pushButton_2</sender>
<signal>clicked()</signal>
<receiver>ContaminantWidget</receiver>
<slot>doSelectFastaFile()</slot>
<hints>
<hint type="sourcelabel">
<x>333</x>
<y>229</y>
</hint>
<hint type="destinationlabel">
<x>690</x>
<y>146</y>
</hint>
</hints>
</connection>
<connection>
<sender>pushButton</sender>
<signal>clicked()</signal>
<receiver>ContaminantWidget</receiver>
<slot>doClearList()</slot>
<hints>
<hint type="sourcelabel">
<x>269</x>
<y>220</y>
</hint>
<hint type="destinationlabel">
<x>508</x>
<y>201</y>
</hint>
</hints>
</connection>
<connection>
<sender>contaminant_database_listview</sender>
<signal>clicked(QModelIndex)</signal>
<receiver>ContaminantWidget</receiver>
<slot>doChanged()</slot> <slot>doChanged()</slot>
<hints> <hints>
<hint type="sourcelabel"> <hint type="sourcelabel">
<x>317</x> <x>167</x>
<y>102</y> <y>267</y>
</hint> </hint>
<hint type="destinationlabel"> <hint type="destinationlabel">
<x>714</x> <x>657</x>
<y>107</y> <y>303</y>
</hint> </hint>
</hints> </hints>
</connection> </connection>
<connection> <connection>
<sender>decoy_protein_regexp_line_edit</sender> <sender>decoy_regexp_radiobutton</sender>
<signal>textChanged(QString)</signal> <signal>clicked()</signal>
<receiver>DecoyWidget</receiver> <receiver>DecoyWidget</receiver>
<slot>doChanged()</slot> <slot>doSelectDecoySource()</slot>
<hints> <hints>
<hint type="sourcelabel"> <hint type="sourcelabel">
<x>167</x> <x>358</x>
<y>267</y> <y>57</y>
</hint> </hint>
<hint type="destinationlabel"> <hint type="destinationlabel">
<x>657</x> <x>602</x>
<y>303</y> <y>99</y>
</hint> </hint>
</hints> </hints>
</connection> </connection>
......
src/gui/widgets/decoy_widget/decoywidget.cpp
+ 52
− 27
View file @ 7ecd6548
...@@ -65,9 +65,11 @@ DecoyWidget::~DecoyWidget() ...@@ -65,9 +65,11 @@ DecoyWidget::~DecoyWidget()
void void
DecoyWidget::setRegexpDecoyPattern(const QString &pattern) DecoyWidget::setRegexpDecoyPattern(const QString &pattern)
{ {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false; _emit_changed = false;
ui->decoy_protein_regexp_line_edit->setText(pattern); ui->decoy_protein_regexp_line_edit->setText(pattern);
_emit_changed = true; _emit_changed = true;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
...@@ -75,6 +77,7 @@ void ...@@ -75,6 +77,7 @@ void
DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list) DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list)
{ {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount()); _p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
for(FastaFileSp fasta_file : fasta_file_list) for(FastaFileSp fasta_file : fasta_file_list)
{ {
...@@ -87,16 +90,20 @@ DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list) ...@@ -87,16 +90,20 @@ DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list)
_p_fasta_str_li->appendRow(item); _p_fasta_str_li->appendRow(item);
// item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole); // item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
} }
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void void
DecoyWidget::getProjectDecoys(const Project *p_project) DecoyWidget::getProjectDecoys(const Project *p_project)
{ {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false; _emit_changed = false;
ui->decoy_regexp_radiobutton->setChecked(true); ui->decoy_regexp_radiobutton->setChecked(true);
ui->decoy_protein_regexp_line_edit->setVisible(true); ui->decoy_protein_regexp_line_edit->setVisible(true);
ui->decoy_database_listview->setVisible(false); ui->decoy_database_listview->setVisible(false);
if(p_project->getProteinStore().getContaminantFastaFileList().size() > 0) if(p_project->getProteinStore().getDecoyFastaFileList().size() > 0)
{ {
ui->decoy_file_radiobutton->setChecked(true); ui->decoy_file_radiobutton->setChecked(true);
ui->decoy_protein_regexp_line_edit->setVisible(false); ui->decoy_protein_regexp_line_edit->setVisible(false);
...@@ -104,13 +111,15 @@ DecoyWidget::getProjectDecoys(const Project *p_project) ...@@ -104,13 +111,15 @@ DecoyWidget::getProjectDecoys(const Project *p_project)
} }
ui->decoy_protein_regexp_line_edit->setText( ui->decoy_protein_regexp_line_edit->setText(
p_project->getProteinStore().getRegexpContaminant().pattern()); p_project->getProteinStore().getRegexpDecoy().pattern());
this->setFastaFileList(p_project->getFastaFileStore().getFastaFileList()); this->setFastaFileList(p_project->getFastaFileStore().getFastaFileList());
ui->control_list_widget->setVisible(false); ui->control_list_widget->setVisible(false);
_no_project = false; _no_project = false;
_emit_changed = true; _emit_changed = true;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} }
void void
...@@ -119,41 +128,56 @@ DecoyWidget::setProjectDecoys(Project *p_project) ...@@ -119,41 +128,56 @@ DecoyWidget::setProjectDecoys(Project *p_project)
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false; _emit_changed = false;
if(ui->decoy_file_radiobutton->isChecked()) try
{ {
QModelIndexList index_list = if(ui->decoy_file_radiobutton->isChecked())
ui->decoy_database_listview->selectionModel()->selectedIndexes();
p_project->getProteinStore().clearContaminants();
if(index_list.size() > 0)
{ {
for(QModelIndex index : index_list) QModelIndexList index_list =
ui->decoy_database_listview->selectionModel()->selectedIndexes();
p_project->getProteinStore().clearDecoys();
if(index_list.size() > 0)
{ {
if(index.data(Qt::UserRole).canConvert<FastaFileSp>()) for(QModelIndex index : index_list)
{ {
FastaFileSp p_fasta_file = if(index.data(Qt::UserRole).canConvert<FastaFileSp>())
index.data(Qt::UserRole).value<FastaFileSp>(); {
p_fasta_file.get()->setContaminants( FastaFileSp p_fasta_file =
p_project->getProteinStore()); index.data(Qt::UserRole).value<FastaFileSp>();
}
else p_fasta_file.get()->setDecoys(
{ p_project->getProteinStore());
throw pappso::PappsoException( }
QObject::tr("can not convert to FastaFile " else
"index.data().canConvert<FastaFile *>()")); {
throw pappso::PappsoException(
QObject::tr("can not convert to FastaFile "
"index.data().canConvert<FastaFile *>()"));
}
} }
} }
}
if(_no_project)
if(_no_project)
{
ui->control_list_widget->setVisible(true);
}
}
else
{ {
ui->control_list_widget->setVisible(true); p_project->getProteinStore().setRegexpDecoyPattern(
ui->decoy_protein_regexp_line_edit->text());
ui->control_list_widget->setVisible(false);
} }
} }
else catch(pappso::PappsoException &exception_pappso)
{ {
p_project->getProteinStore().setRegexpContaminantPattern( _emit_changed = true;
ui->decoy_protein_regexp_line_edit->text()); throw exception_pappso;
ui->control_list_widget->setVisible(false); }
catch(std::exception &exception_std)
{
_emit_changed = true;
throw exception_std;
} }
_emit_changed = true; _emit_changed = true;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
...@@ -163,7 +187,8 @@ DecoyWidget::setProjectDecoys(Project *p_project) ...@@ -163,7 +187,8 @@ DecoyWidget::setProjectDecoys(Project *p_project)
void void
DecoyWidget::doChanged() DecoyWidget::doChanged()
{ {
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< _emit_changed;
if(_emit_changed) if(_emit_changed)
emit changed(); emit changed();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
......
src/utils/fastafilestore.cpp
+ 2
− 2
View file @ 7ecd6548
...@@ -73,8 +73,8 @@ FastaFileStore::getInstance(const FastaFile &location) ...@@ -73,8 +73,8 @@ FastaFileStore::getInstance(const FastaFile &location)
const std::vector<FastaFileSp> & const std::vector<FastaFileSp> &
FastaFileStore::getFastaFileList() const FastaFileStore::getFastaFileList() const
{ {
qDebug() << "FastaFileStore::getFastaFileList() begin";
qDebug() << "FastaFileStore::getFastaFileList() begin" qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _map_fastafile.size(); << _map_fastafile.size();
return _map_fastafile; return _map_fastafile;
} }
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