From 7ecd65489442066139e078c9a6a39921d84c690d Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Mon, 15 Oct 2018 19:21:00 +0200
Subject: [PATCH] new controls on decoy and contaminant widgets
---
src/gui/project_view/project_view.ui | 49 ++---
src/gui/project_view/projectwindow.cpp | 177 ++++--------------
src/gui/project_view/projectwindow.h | 5 +-
.../contaminant_widget/contaminantwidget.cpp | 67 ++++---
src/gui/widgets/decoy_widget/decoy_widget.ui | 80 ++------
src/gui/widgets/decoy_widget/decoywidget.cpp | 79 +++++---
src/utils/fastafilestore.cpp | 4 +-
7 files changed, 179 insertions(+), 282 deletions(-)
diff --git a/src/gui/project_view/project_view.ui b/src/gui/project_view/project_view.ui
index b89a7c5dd..e3bdb7040 100644
--- a/src/gui/project_view/project_view.ui
+++ b/src/gui/project_view/project_view.ui
@@ -199,9 +199,9 @@
</spacer>
</item>
<item>
- <widget class="QPushButton" name="fdr_button">
+ <widget class="QPushButton" name="apply_fdr_button">
<property name="text">
- <string>OK</string>
+ <string>apply</string>
</property>
</widget>
</item>
@@ -376,22 +376,6 @@
</customwidgets>
<resources/>
<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>
<sender>precision_unit_combobox</sender>
<signal>currentIndexChanged(QString)</signal>
@@ -399,8 +383,8 @@
<slot>doMassPrecisionUnitChanged(QString)</slot>
<hints>
<hint type="sourcelabel">
- <x>119</x>
- <y>104</y>
+ <x>253</x>
+ <y>113</y>
</hint>
<hint type="destinationlabel">
<x>489</x>
@@ -431,8 +415,8 @@
<slot>doFilterChanged()</slot>
<hints>
<hint type="sourcelabel">
- <x>119</x>
- <y>104</y>
+ <x>131</x>
+ <y>101</y>
</hint>
<hint type="destinationlabel">
<x>815</x>
@@ -447,8 +431,8 @@
<slot>doApplyFilter()</slot>
<hints>
<hint type="sourcelabel">
- <x>119</x>
- <y>104</y>
+ <x>448</x>
+ <y>136</y>
</hint>
<hint type="destinationlabel">
<x>689</x>
@@ -472,6 +456,22 @@
</hint>
</hints>
</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>
<slots>
<slot>doFdrChanged()</slot>
@@ -481,5 +481,6 @@
<slot>doSelectContaminantSource()</slot>
<slot>doFilterChanged()</slot>
<slot>doApplyFilter()</slot>
+ <slot>doApplyDecoy()</slot>
</slots>
</ui>
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 8ee7b7e54..2d8240d6c 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -126,22 +126,20 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
ProjectWindow::~ProjectWindow()
{
- qDebug() << "ProjectWindow::~ProjectWindow";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
_worker_thread.quit();
_worker_thread.wait();
- qDebug() << "ProjectWindow::~ProjectWindow1";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete ui;
- qDebug() << "ProjectWindow::~ProjectWindow2";
- delete _p_fasta_str_li;
- qDebug() << "ProjectWindow::~ProjectWindow3";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete _p_edit_modifications;
- qDebug() << "ProjectWindow::~ProjectWindow5";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete _p_edit_label_methods;
- qDebug() << "ProjectWindow::~ProjectWindow6";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
delete _p_waiting_message_dialog;
- qDebug() << "ProjectWindow::~ProjectWindow end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
Project *
@@ -153,29 +151,29 @@ void
ProjectWindow::setDefaultProteinListWindow(
ProteinListWindow *p_protein_list_window)
{
- qDebug() << "ProjectWindow::setDefaultProteinListWindow begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_current_protein_list_window = p_protein_list_window;
- qDebug() << "ProjectWindow::setDefaultProteinListWindow end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
ProjectWindow::connectNewPtmIslandListWindow()
{
- qDebug() << "ProjectWindow::connectNewPtmIslandListWindow begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_current_ptm_island_list_window = new PtmIslandListWindow(this);
_ptm_island_list_window_collection.push_back(
_p_current_ptm_island_list_window);
- qDebug() << "ProjectWindow::connectNewPtmIslandListWindow end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
ProjectWindow::connectNewProteinListWindow()
{
- qDebug() << "ProjectWindow::connectNewProteinListWindow begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_current_protein_list_window = new ProteinListWindow(this);
_protein_list_window_collection.push_back(_p_current_protein_list_window);
- qDebug() << "ProjectWindow::connectNewProteinListWindow end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
@@ -395,69 +393,6 @@ ProjectWindow::computeMassPrecision()
}
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
ProjectWindow::refresh()
{
@@ -475,6 +410,14 @@ ProjectWindow::doContaminantSelectionChanged()
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
+void
+ProjectWindow::doDecoySelectionChanged()
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ ui->apply_fdr_button->setEnabled(true);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}
+
void
ProjectWindow::doAutomaticFilterParametersChanged(
AutomaticFilterParameters parameters)
@@ -687,39 +630,17 @@ ProjectWindow::doViewProteinList(IdentificationGroup *p_identification_group)
void
ProjectWindow::setProjectSp(ProjectSp project_sp)
{
- qDebug() << "ProjectWindow::setProjectSp begin";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_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->decoy_widget->getProjectDecoys(_project_sp.get());
- qDebug() << "ProjectWindow::setProjectSp begin "
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _project_sp.get()->getFastaFileStore().getFastaFileList().size();
_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)
{
delete p_window;
@@ -783,7 +704,8 @@ ProjectWindow::setProjectSp(ProjectSp project_sp)
_p_xic_window = nullptr;
}
- qDebug() << " ProjectWindow::setProjectSp size="
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << " ProjectWindow::setProjectSp size="
<< identification_list.size();
if(identification_list.size() == 1)
{
@@ -836,19 +758,18 @@ ProjectWindow::setProjectSp(ProjectSp project_sp)
//_protein_list_window->setIdentificationGroup(_project_sp.get()->getCurrentIdentificationGroupP());
//_protein_list_window->show();
- ui->decoy_protein_regexp_line_edit->setText(
- _project_sp.get()->getProteinStore().getRegexpDecoy().pattern());
-
refresh();
this->setEnabled(true);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
// doAutomaticFilterParametersChanged(params);
// doFdrChanged();
}
void
ProjectWindow::doIdentificationsComboboxChanged(int index_in)
{
- qDebug() << "ProjectWindow::doIdentificationsComboboxChanged begin ";
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
for(int index = 0; index < ui->identifications_combobox->count(); index++)
{
qobject_cast<IdentificationGroupWidget *>(
@@ -858,7 +779,8 @@ ProjectWindow::doIdentificationsComboboxChanged(int index_in)
qobject_cast<IdentificationGroupWidget *>(
qvariant_cast<QObject *>(ui->identifications_combobox->itemData(index_in)))
->setVisible(true);
- qDebug() << "ProjectWindow::doIdentificationsComboboxChanged end ";
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
@@ -901,8 +823,7 @@ ProjectWindow::doIdentificationGroupEdited(
{
showWaitingMessage(tr("Updating identification group"));
- qDebug() << "ProjectWindow::doIdentificationGroupEdited emit "
- "operateGroupingOnIdentification(_project_sp) ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit operateGroupingOnIdentification(p_identification_group,
_project_sp.get()->getGroupingType());
}
@@ -918,7 +839,8 @@ ProjectWindow::viewError(QString error)
void
ProjectWindow::doAcceptedLabelingMethod()
{
- qDebug() << "ProjectWindow::doAcceptedLabelingMethod";
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
showWaitingMessage(tr("Apply labeling method"));
LabelingMethodSp labeling_method_sp =
@@ -928,8 +850,7 @@ ProjectWindow::doAcceptedLabelingMethod()
doDisplayLoadingMessage(tr("labeling peptides"));
- qDebug() << "ProjectWindow::doAcceptedLabelingMethod emit "
- "operateGrouping(_project_sp) ";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit operateGrouping(_project_sp);
}
@@ -937,7 +858,8 @@ ProjectWindow::doAcceptedLabelingMethod()
void
ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence)
{
- qDebug() << "ProjectWindow::openInXicViewer begin";
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
if(_p_xic_window == nullptr)
{
_p_xic_window = new XicWindow(this);
@@ -946,38 +868,22 @@ ProjectWindow::openInXicViewer(const PeptideEvidence *p_peptide_evidence)
_p_xic_window->show();
_p_xic_window->addXic(p_peptide_evidence);
- qDebug() << "ProjectWindow::openInXicViewer end";
-}
-
-void
-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";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
+
void
ProjectWindow::doFilterChanged()
{
ui->apply_filter_button->setEnabled(true);
- ui->fdr_button->setEnabled(true);
+ ui->apply_fdr_button->setEnabled(true);
}
void
ProjectWindow::doApplyDecoy()
{
- ui->fdr_button->setEnabled(false);
+ ui->apply_fdr_button->setEnabled(false);
// doAutomaticFilterParametersChanged(automatic_filter);
try
{
@@ -991,8 +897,7 @@ ProjectWindow::doApplyDecoy()
doDisplayLoadingMessage(tr("updating filters"));
_project_sp.get()->updateAutomaticFilters(
_project_sp.get()->getAutomaticFilterParameters());
-
-
+
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
emit operateGrouping(_project_sp);
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 6ff7aa6cb..836e4d3da 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -67,8 +67,6 @@ class ProjectWindow : public QMainWindow
void doViewProteinList(IdentificationGroup *p_identification_group = nullptr);
void setDefaultProteinListWindow(ProteinListWindow *p_protein_list_window);
void doAutomaticFilterParametersChanged(AutomaticFilterParameters parameters);
- void doFdrChanged();
- void doSelectDecoySource();
void doMassPrecisionUnitChanged(QString combo_value);
void doOperationFailed(QString);
void doOperationFinished();
@@ -82,6 +80,7 @@ class ProjectWindow : public QMainWindow
void doViewPeptideDetail(PeptideEvidence *peptide_evidence);
void doFilterChanged();
void doApplyFilter();
+ void doApplyDecoy();
// void setColor(const QColor &color);
// void setShape(Shape shape);
signals:
@@ -141,9 +140,7 @@ class ProjectWindow : public QMainWindow
ProjectSp _project_sp;
- QStandardItemModel *_p_fasta_str_li;
std::vector<FastaFileSp> _fastafile_list;
WaitingMessageDialog *_p_waiting_message_dialog;
// QCPBars *_p_bars;
};
-
diff --git a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
index 2ab9d7847..5e167b1d4 100644
--- a/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
+++ b/src/gui/widgets/contaminant_widget/contaminantwidget.cpp
@@ -120,41 +120,56 @@ ContaminantWidget::setProjectContaminants(Project *p_project)
{
qDebug() << "ContaminantWidget::setProjectContaminants begin";
_emit_changed = false;
- if(ui->contaminant_file_radiobutton->isChecked())
+ try
{
- QModelIndexList index_list =
- ui->contaminant_database_listview->selectionModel()->selectedIndexes();
- p_project->getProteinStore().clearContaminants();
- if(index_list.size() > 0)
+ if(ui->contaminant_file_radiobutton->isChecked())
{
- 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>())
- {
- FastaFileSp p_fasta_file =
- index.data(Qt::UserRole).value<FastaFileSp>();
- p_fasta_file.get()->setContaminants(
- p_project->getProteinStore());
- }
- else
+ for(QModelIndex index : index_list)
{
- throw pappso::PappsoException(
- QObject::tr("can not convert to FastaFile "
- "index.data().canConvert<FastaFile *>()"));
+ if(index.data(Qt::UserRole).canConvert<FastaFileSp>())
+ {
+ 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(
- ui->contaminant_protein_regexp_line_edit->text());
- ui->control_list_widget->setVisible(false);
+ _emit_changed = true;
+ throw exception_std;
}
_emit_changed = true;
qDebug() << "ContaminantWidget::setProjectContaminants end";
@@ -200,7 +215,9 @@ ContaminantWidget::doSelectFastaFile()
settings.value("path/fastafiles_directory", "").toString();
QStringList filenames = QFileDialog::getOpenFileNames(
- this, tr("FASTA files"), default_fasta_location,
+ this,
+ tr("FASTA files"),
+ default_fasta_location,
tr("FASTA files (*.fasta);;all files (*)"));
if(filenames.size() > 0)
diff --git a/src/gui/widgets/decoy_widget/decoy_widget.ui b/src/gui/widgets/decoy_widget/decoy_widget.ui
index 2530fec86..1f6656a07 100644
--- a/src/gui/widgets/decoy_widget/decoy_widget.ui
+++ b/src/gui/widgets/decoy_widget/decoy_widget.ui
@@ -17,7 +17,7 @@
<item>
<widget class="QGroupBox" name="decoy_groupbox">
<property name="title">
- <string>Contaminants</string>
+ <string>Decoys</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_6">
<item>
@@ -28,7 +28,7 @@
<string>select decoys from fasta files</string>
</property>
<property name="text">
- <string>decoy file</string>
+ <string>deco&y file</string>
</property>
<property name="checked">
<bool>true</bool>
@@ -136,82 +136,34 @@
</hints>
</connection>
<connection>
- <sender>contaminant_regexp_radiobutton</sender>
- <signal>clicked()</signal>
- <receiver>ContaminantWidget</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>
+ <sender>decoy_protein_regexp_line_edit</sender>
+ <signal>textChanged(QString)</signal>
+ <receiver>DecoyWidget</receiver>
<slot>doChanged()</slot>
<hints>
<hint type="sourcelabel">
- <x>317</x>
- <y>102</y>
+ <x>167</x>
+ <y>267</y>
</hint>
<hint type="destinationlabel">
- <x>714</x>
- <y>107</y>
+ <x>657</x>
+ <y>303</y>
</hint>
</hints>
</connection>
<connection>
- <sender>decoy_protein_regexp_line_edit</sender>
- <signal>textChanged(QString)</signal>
+ <sender>decoy_regexp_radiobutton</sender>
+ <signal>clicked()</signal>
<receiver>DecoyWidget</receiver>
- <slot>doChanged()</slot>
+ <slot>doSelectDecoySource()</slot>
<hints>
<hint type="sourcelabel">
- <x>167</x>
- <y>267</y>
+ <x>358</x>
+ <y>57</y>
</hint>
<hint type="destinationlabel">
- <x>657</x>
- <y>303</y>
+ <x>602</x>
+ <y>99</y>
</hint>
</hints>
</connection>
diff --git a/src/gui/widgets/decoy_widget/decoywidget.cpp b/src/gui/widgets/decoy_widget/decoywidget.cpp
index 9c8101f81..b2289982a 100644
--- a/src/gui/widgets/decoy_widget/decoywidget.cpp
+++ b/src/gui/widgets/decoy_widget/decoywidget.cpp
@@ -65,9 +65,11 @@ DecoyWidget::~DecoyWidget()
void
DecoyWidget::setRegexpDecoyPattern(const QString &pattern)
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false;
ui->decoy_protein_regexp_line_edit->setText(pattern);
_emit_changed = true;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
@@ -75,6 +77,7 @@ void
DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list)
{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_p_fasta_str_li->removeRows(0, _p_fasta_str_li->rowCount());
for(FastaFileSp fasta_file : fasta_file_list)
{
@@ -87,16 +90,20 @@ DecoyWidget::setFastaFileList(std::vector<FastaFileSp> fasta_file_list)
_p_fasta_str_li->appendRow(item);
// item->setData(QVariant(QString("%1").arg(fasta_file.get()->getAbsoluteFilePath())),Qt::UserRole);
}
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
DecoyWidget::getProjectDecoys(const Project *p_project)
{
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false;
ui->decoy_regexp_radiobutton->setChecked(true);
ui->decoy_protein_regexp_line_edit->setVisible(true);
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_protein_regexp_line_edit->setVisible(false);
@@ -104,13 +111,15 @@ DecoyWidget::getProjectDecoys(const Project *p_project)
}
ui->decoy_protein_regexp_line_edit->setText(
- p_project->getProteinStore().getRegexpContaminant().pattern());
+ p_project->getProteinStore().getRegexpDecoy().pattern());
this->setFastaFileList(p_project->getFastaFileStore().getFastaFileList());
ui->control_list_widget->setVisible(false);
_no_project = false;
_emit_changed = true;
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
@@ -119,41 +128,56 @@ DecoyWidget::setProjectDecoys(Project *p_project)
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
_emit_changed = false;
- if(ui->decoy_file_radiobutton->isChecked())
+ try
{
- QModelIndexList index_list =
- ui->decoy_database_listview->selectionModel()->selectedIndexes();
- p_project->getProteinStore().clearContaminants();
- if(index_list.size() > 0)
+ if(ui->decoy_file_radiobutton->isChecked())
{
- 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 =
- 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(index.data(Qt::UserRole).canConvert<FastaFileSp>())
+ {
+ FastaFileSp p_fasta_file =
+ index.data(Qt::UserRole).value<FastaFileSp>();
+
+ p_fasta_file.get()->setDecoys(
+ 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().setRegexpDecoyPattern(
+ ui->decoy_protein_regexp_line_edit->text());
+ ui->control_list_widget->setVisible(false);
}
}
- else
+ catch(pappso::PappsoException &exception_pappso)
{
- p_project->getProteinStore().setRegexpContaminantPattern(
- ui->decoy_protein_regexp_line_edit->text());
- ui->control_list_widget->setVisible(false);
+ _emit_changed = true;
+ throw exception_pappso;
+ }
+ catch(std::exception &exception_std)
+ {
+ _emit_changed = true;
+ throw exception_std;
}
_emit_changed = true;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -163,7 +187,8 @@ DecoyWidget::setProjectDecoys(Project *p_project)
void
DecoyWidget::doChanged()
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << _emit_changed;
if(_emit_changed)
emit changed();
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
diff --git a/src/utils/fastafilestore.cpp b/src/utils/fastafilestore.cpp
index 040024de0..224086760 100644
--- a/src/utils/fastafilestore.cpp
+++ b/src/utils/fastafilestore.cpp
@@ -73,8 +73,8 @@ FastaFileStore::getInstance(const FastaFile &location)
const std::vector<FastaFileSp> &
FastaFileStore::getFastaFileList() const
{
- qDebug() << "FastaFileStore::getFastaFileList() begin";
- qDebug() << "FastaFileStore::getFastaFileList() begin"
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< _map_fastafile.size();
return _map_fastafile;
}
--
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