From 8428480c56ab93cc828bfd6e454075251c0d0c09 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Fri, 16 Oct 2020 15:22:18 +0200
Subject: [PATCH 01/18] Export Xic To csv added
---
src/CMakeLists.txt | 1 +
src/gui/project_view/projectwindow.cpp | 17 +++++++++-
src/gui/project_view/projectwindow.h | 4 +++
src/gui/workerthread.cpp | 25 ++++++++++++++
src/gui/workerthread.h | 4 ++-
src/gui/xic_view/xic_box/xic_box.ui | 17 ++++++----
src/gui/xic_view/xic_box/xicbox.cpp | 8 +++--
src/gui/xic_view/xic_box/xicbox.h | 4 +--
src/gui/xic_view/xic_window.ui | 47 ++++++++++++++++++++++++--
src/gui/xic_view/xicwindow.cpp | 28 +++++++++++++++
src/gui/xic_view/xicwindow.h | 2 ++
src/main.cpp | 1 +
12 files changed, 142 insertions(+), 16 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 31306669..946b28a0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -105,6 +105,7 @@ set(CPP_FILES
output/ods/simplesheet.cpp
output/ods/spectrasheet.cpp
output/ods/spectrasheetall.cpp
+ output/ods/xicareasheet.cpp
output/exportfastafile.cpp
output/masschroqml.cpp
output/masschroqprm.cpp
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index 33b2d0ad..5d46f14f 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -111,6 +111,7 @@ ProjectWindow::ProjectWindow(MainWindow *parent)
&ProjectWindow::operateMassChroqExportDialog,
main_window,
&MainWindow::doActionMassChroQ);
+
//
// grouping
/*
@@ -1140,6 +1141,20 @@ ProjectWindow::doCleanMsRunReaders()
void
ProjectWindow::doOpenMassChroQDialog()
{
- qDebug() << "AAAAAAAA";
emit operateMassChroqExportDialog();
}
+
+void
+ProjectWindow::doExportXicAreaToCsv(QString filename,
+ std::vector<XicBox *> xic_boxs)
+{
+ qDebug() << "Export Xic to csv";
+ showWaitingMessage("Export All XIC area to CSV");
+ emit operateWriteXicAreaInCsv(filename, xic_boxs);
+}
+void
+ProjectWindow::doExportXicAreaToCsvFinished()
+{
+ hideWaitingMessage();
+ qDebug() << "Export Finished";
+}
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index 0fd7272d..b2c2fa27 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -94,6 +94,8 @@ class ProjectWindow : public QMainWindow
void doBestMsRunForAlignmentFinished(MsRunSp msrun_sp);
void doCleanMsRunReaders();
void doOpenMassChroQDialog();
+ void doExportXicAreaToCsv(QString filename, std::vector<XicBox *> xic_boxs);
+ void doExportXicAreaToCsvFinished();
// void setColor(const QColor &color);
// void setShape(Shape shape);
@@ -115,6 +117,8 @@ class ProjectWindow : public QMainWindow
void projectStatusChanged();
void bestMsRunFound(MsRunSp msrun_sp);
void operateMassChroqExportDialog();
+ void operateWriteXicAreaInCsv(QString filename,
+ std::vector<XicBox *> xic_boxs);
protected:
void doViewPeptideList(IdentificationGroup *p_ident_group,
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 3c932485..58eaa0d7 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -46,6 +46,7 @@
#include "project_view/projectwindow.h"
#include "../core/tandem_run/tandembatchprocess.h"
#include "../core/tandem_run/tandemcondorprocess.h"
+#include "../output/ods/xicareasheet.h"
#include <QSettings>
WorkerThread::WorkerThread(MainWindow *p_main_window)
@@ -225,6 +226,15 @@ WorkerThread::connectProjectWindow(ProjectWindow *p_project_window)
&WorkerThread::operationFinished,
p_project_window,
&ProjectWindow::doOperationFinished);
+
+ connect(p_project_window,
+ &ProjectWindow::operateWriteXicAreaInCsv,
+ this,
+ &WorkerThread::doWriteXicAreaInCsv);
+ connect(this,
+ &WorkerThread::exportXicToCsvFinished,
+ p_project_window,
+ &ProjectWindow::doExportXicAreaToCsvFinished);
qDebug();
}
@@ -861,3 +871,18 @@ WorkerThread::doCheckMsrunFilePath(ProjectSp msp_project)
emit checkingMsrunFilePathFinished(msrun_sp);
}
+
+void
+WorkerThread::doWriteXicAreaInCsv(QString filename,
+ std::vector<XicBox *> xic_boxs)
+{
+ CalcWriterInterface *p_writer = nullptr;
+
+ emit loadingMessage(tr("writing TSV files, please wait"));
+ p_writer = new TsvDirectoryWriter(filename);
+ XicAreaSheet(p_writer, xic_boxs);
+ bool all_data = true;
+ XicAreaSheet(p_writer, xic_boxs, all_data);
+ p_writer->close();
+ emit exportXicToCsvFinished();
+}
diff --git a/src/gui/workerthread.h b/src/gui/workerthread.h
index ba3f9322..0b38f33b 100644
--- a/src/gui/workerthread.h
+++ b/src/gui/workerthread.h
@@ -37,6 +37,7 @@
#include "../utils/workmonitor.h"
#include "../core/tandem_run/tandemrunbatch.h"
#include "../gui/export/export_masschroq_dialog/masschroqfileparameters.h"
+#include "../gui/xic_view/xic_box/xicbox.h"
class MainWindow;
class ProjectWindow;
@@ -87,7 +88,7 @@ class WorkerThread : public QObject
void doFindBestMsrunForAlignment(ProjectSp project_sp,
MsRunAlignmentGroupSp alignment_group);
void doCheckMsrunFilePath(ProjectSp project_sp);
-
+ void doWriteXicAreaInCsv(QString filename, std::vector<XicBox *> xic_boxs);
signals:
void loadingMessage(QString message);
@@ -108,6 +109,7 @@ class WorkerThread : public QObject
* that was not found if so
*/
void checkingMsrunFilePathFinished(MsRunSp msrun_sp);
+ void exportXicToCsvFinished();
private:
WorkMonitor *_p_work_monitor;
diff --git a/src/gui/xic_view/xic_box/xic_box.ui b/src/gui/xic_view/xic_box/xic_box.ui
index 4b2afe9b..df7e1572 100644
--- a/src/gui/xic_view/xic_box/xic_box.ui
+++ b/src/gui/xic_view/xic_box/xic_box.ui
@@ -87,6 +87,9 @@
<property name="text">
<string>new XIC</string>
</property>
+ <property name="icon">
+ <iconset theme="tab-new"/>
+ </property>
</widget>
</item>
<item>
@@ -152,15 +155,15 @@
<item>
<widget class="QToolButton" name="close_button">
<property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
+ <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
- <width>24</width>
- <height>24</height>
+ <width>16000</width>
+ <height>1600</height>
</size>
</property>
<property name="acceptDrops">
@@ -173,8 +176,7 @@
<string/>
</property>
<property name="icon">
- <iconset resource="../../../xtpcpp.qrc">
- <normaloff>:/icons/resources/icons/mit/jamicons/icon_close.svg</normaloff>:/icons/resources/icons/mit/jamicons/icon_close.svg</iconset>
+ <iconset theme="window-close"/>
</property>
<property name="iconSize">
<size>
@@ -383,8 +385,8 @@
<slot>onIsotopicDistributionClick()</slot>
<hints>
<hint type="sourcelabel">
- <x>1004</x>
- <y>32</y>
+ <x>980</x>
+ <y>39</y>
</hint>
<hint type="destinationlabel">
<x>1163</x>
@@ -400,5 +402,6 @@
<slot>onXicWidgetClick(double,double)</slot>
<slot>setXicPeakList(pappso::XicXicPeakPairList)</slot>
<slot>onIsotopicDistributionClick()</slot>
+ <slot>onExportToCsvClick()</slot>
</slots>
</ui>
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 7bd6ba88..1ed5dec4 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -563,13 +563,11 @@ XicBox::setIsotopeMassList(
// histogram
if(m_theoreticalRatioBars == nullptr)
{
- qDebug() << "ZZZZZZZZZZZZZ";
m_theoreticalRatioBars =
new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis);
}
else
{
- qDebug() << "EEEEEEEEEEE";
m_theoreticalRatioBars->data()->clear();
}
m_theoreticalRatioBars->setName("th. ratio");
@@ -778,3 +776,9 @@ XicBox::addCommonRt(std::vector<std::size_t> &common_peak_rt_measure_list,
*/
}
}
+
+std::vector<XicBoxNaturalIsotope>
+XicBox::getNaturalIsotopList() const
+{
+ return _natural_isotope_list;
+}
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index c424f9cc..2eff49b8 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -68,6 +68,7 @@ class XicBox : public QWidget
void setPeptideEvidence(const PeptideEvidence *p_peptide_evidence);
void setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
MsRunSp msrun_sp);
+ std::vector<XicBoxNaturalIsotope> getNaturalIsotopList() const;
signals:
void loadXic(MsRunSp p_msrun,
@@ -118,8 +119,7 @@ class XicBox : public QWidget
std::vector<pappso::XicWidget *> _xic_widget_list;
QCPBars *m_observedAreaBars = nullptr;
-
- bool _scaled = false;
+ bool _scaled = false;
// QFrame * _popup_peak_info = nullptr;
};
diff --git a/src/gui/xic_view/xic_window.ui b/src/gui/xic_view/xic_window.ui
index 1047423e..10b6f003 100644
--- a/src/gui/xic_view/xic_window.ui
+++ b/src/gui/xic_view/xic_window.ui
@@ -82,11 +82,35 @@
</property>
</spacer>
</item>
+ <item>
+ <widget class="QToolButton" name="export_toolButton">
+ <property name="text">
+ <string>...</string>
+ </property>
+ <property name="icon">
+ <iconset theme="spreadsheet">
+ <normaloff>.</normaloff>.</iconset>
+ </property>
+ <property name="iconSize">
+ <size>
+ <width>24</width>
+ <height>24</height>
+ </size>
+ </property>
+ <property name="autoRaise">
+ <bool>true</bool>
+ </property>
+ </widget>
+ </item>
<item>
<widget class="QPushButton" name="edit_zivy_params_pushbutton">
<property name="text">
<string>Edit</string>
</property>
+ <property name="icon">
+ <iconset theme="edit">
+ <normaloff>.</normaloff>.</iconset>
+ </property>
</widget>
</item>
</layout>
@@ -103,7 +127,7 @@
<x>0</x>
<y>0</y>
<width>1172</width>
- <height>499</height>
+ <height>495</height>
</rect>
</property>
<layout class="QVBoxLayout" name="verticalLayout"/>
@@ -187,8 +211,8 @@
<slot>doEditZivyParams()</slot>
<hints>
<hint type="sourcelabel">
- <x>710</x>
- <y>59</y>
+ <x>1182</x>
+ <y>61</y>
</hint>
<hint type="destinationlabel">
<x>918</x>
@@ -212,12 +236,29 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>export_toolButton</sender>
+ <signal>clicked()</signal>
+ <receiver>XicWindow</receiver>
+ <slot>doExportXicToCsv()</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>1084</x>
+ <y>42</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>1496</x>
+ <y>107</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>xicPrecisionChanged(pappso::PrecisionPtr)</slot>
<slot>rtUnitChanged(QAbstractButton*)</slot>
<slot>doEditZivyParams()</slot>
<slot>doXicExtractionMethodChanged(pappso::XicExtractMethod)</slot>
+ <slot>doExportXicToCsv()</slot>
</slots>
<buttongroups>
<buttongroup name="rt_unit_buttongroup"/>
diff --git a/src/gui/xic_view/xicwindow.cpp b/src/gui/xic_view/xicwindow.cpp
index 06373f04..f8abdb6c 100644
--- a/src/gui/xic_view/xicwindow.cpp
+++ b/src/gui/xic_view/xicwindow.cpp
@@ -60,6 +60,10 @@ XicWindow::XicWindow(ProjectWindow *parent)
&ZivyDialog::accepted,
this,
&XicWindow::doAcceptedZivyDialog);
+ connect(this,
+ &XicWindow::operateXicAreaToCsv,
+ _project_window,
+ &ProjectWindow::doExportXicAreaToCsv);
#if QT_VERSION >= 0x050000
// Qt5 code
@@ -185,3 +189,27 @@ XicWindow::doXicExtractionMethodChanged(pappso::XicExtractMethod xic_method
{
emit reExtractXicNeeded();
}
+
+void
+XicWindow::doExportXicToCsv()
+{
+ QSettings settings;
+ QString default_location = settings.value("path/export_ods", "").toString();
+
+ QString filename =
+ QFileDialog::getSaveFileName(this,
+ tr("Save CSV directory"),
+ QString("%1/new_dir").arg(default_location));
+
+ settings.setValue("path/export_ods", QFileInfo(filename).absolutePath());
+
+
+ std::vector<XicBox *> xic_boxs;
+
+ for(int i = 0; i < ui->verticalLayout->layout()->count(); i++)
+ {
+ xic_boxs.push_back(
+ dynamic_cast<XicBox *>(ui->verticalLayout->itemAt(i)->widget()));
+ }
+ emit operateXicAreaToCsv(filename, xic_boxs);
+}
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index d20888a3..5435a009 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/src/gui/xic_view/xicwindow.h
@@ -74,10 +74,12 @@ class XicWindow : public QMainWindow
void doEditZivyParams();
void doAcceptedZivyDialog();
void doXicExtractionMethodChanged(pappso::XicExtractMethod xic_method);
+ void doExportXicToCsv();
signals:
void reExtractXicNeeded();
void rtUnitChangeNeeded();
+ void operateXicAreaToCsv(QString filename, std::vector<XicBox *> xic_boxs);
protected:
diff --git a/src/main.cpp b/src/main.cpp
index 3ff915de..d98d2172 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -57,6 +57,7 @@ main(int argc, char *argv[])
qRegisterMetaType<IdentificationDataSourceSp>("IdentificationDataSourceSp");
qRegisterMetaType<ContaminantRemovalMode>("ContaminantRemovalMode");
qRegisterMetaType<PtmMode>("PtmMode");
+ qRegisterMetaType<std::vector<XicBox *>>("<std::vector<XicBox *>>");
// qRegisterMetaType<pappso::PeakIonIsotopeMatch>("pappso::PeakIonIsotopeMatch");
--
GitLab
From a674ed2ae29a13c437c92f2e285f3a76db779ee5 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Fri, 16 Oct 2020 15:46:37 +0200
Subject: [PATCH 02/18] Correct no group selected for best reference
---
.../exportmasschroqdialog.cpp | 34 ++++++++++++-------
.../exportmasschroqdialog.h | 13 ++++---
2 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index 8d2f1071..177f8f25 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -256,11 +256,19 @@ ExportMasschroqDialog::doBrowseMsrunDirectory()
void
ExportMasschroqDialog::doFindBestMsrunForAlignment()
{
- mp_main->showWaitingMessage(tr("Looking for MSrun reference"));
- MsRunAlignmentGroupSp group =
- msp_alignmentGroups.at(ui->group_listView->currentIndex().row());
+ if(msp_selected_group != nullptr)
+ {
+ mp_main->showWaitingMessage(tr("Looking for MSrun reference"));
- emit operateFindBestMsrunForAlignment(msp_project, group);
+ emit operateFindBestMsrunForAlignment(msp_project, msp_selected_group);
+ }
+ else
+ {
+ QMessageBox::warning(
+ this,
+ "Select a group",
+ "The reference is linked to a group.\n You have to select one.");
+ }
}
void
@@ -328,22 +336,22 @@ ExportMasschroqDialog::doShowMsRunsInAlignmentGroup(QModelIndex index)
{
ui->listWidget->clear();
ui->msrun_list_combo_box->clear();
- MsRunAlignmentGroupSp selected_group = msp_alignmentGroups.at(index.row());
+ msp_selected_group = msp_alignmentGroups.at(index.row());
ui->groupBox_5->setTitle("Ms runs in " +
- selected_group->getMsRunAlignmentGroupName());
- for(MsRunSp ms_run : selected_group->getMsRunsInAlignmentGroup())
+ msp_selected_group->getMsRunAlignmentGroupName());
+ for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
{
ui->listWidget->addItem(ms_run->getSampleName());
ui->msrun_list_combo_box->addItem(ms_run->getSampleName());
}
- if(selected_group->getMsRunReference() != nullptr)
+ if(msp_selected_group->getMsRunReference() != nullptr)
{
std::list<MsRunSp>::iterator it;
- it = std::find(selected_group->getMsRunsInAlignmentGroup().begin(),
- selected_group->getMsRunsInAlignmentGroup().end(),
- selected_group->getMsRunReference());
- int idx =
- std::distance(selected_group->getMsRunsInAlignmentGroup().begin(), it);
+ it = std::find(msp_selected_group->getMsRunsInAlignmentGroup().begin(),
+ msp_selected_group->getMsRunsInAlignmentGroup().end(),
+ msp_selected_group->getMsRunReference());
+ int idx = std::distance(
+ msp_selected_group->getMsRunsInAlignmentGroup().begin(), it);
ui->msrun_list_combo_box->setCurrentIndex(idx);
}
else
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
index 2d4c1353..94f10f30 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
@@ -71,13 +71,6 @@ class ExportMasschroqDialog : public QDialog
void setBestMsrunForAlignment(MsRunSp msrun_sp);
void setCheckMsrunFilePathOk(MsRunSp msrun_sp);
- private:
- Ui::ExportMasschroqDialog *ui;
- ProjectSp msp_project;
- MainWindow *mp_main;
- std::vector<MsRunAlignmentGroupSp> msp_alignmentGroups;
- QStandardItemModel *mp_poModel;
-
protected slots:
void doCheckMsrunFilepath();
void doBrowseMsrunDirectory();
@@ -85,4 +78,10 @@ class ExportMasschroqDialog : public QDialog
void doShowMsRunsInAlignmentGroup(QModelIndex index);
private:
+ Ui::ExportMasschroqDialog *ui;
+ ProjectSp msp_project;
+ MainWindow *mp_main;
+ std::vector<MsRunAlignmentGroupSp> msp_alignmentGroups;
+ QStandardItemModel *mp_poModel;
+ MsRunAlignmentGroupSp msp_selected_group;
};
--
GitLab
From 5fafd9e3aa9133db67a188bbaba2385413f84e50 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Mon, 26 Oct 2020 16:40:56 +0100
Subject: [PATCH 03/18] Add group name instead of fractiona1
https://forgemia.inra.fr/pappso/xtpcpp/-/issues/35
---
src/CMakeLists.txt | 2 +-
src/gui/workerthread.cpp | 20 ++++++++++----------
src/output/masschroqml.cpp | 6 +++++-
3 files changed, 16 insertions(+), 12 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 946b28a0..f139c7c1 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -105,7 +105,7 @@ set(CPP_FILES
output/ods/simplesheet.cpp
output/ods/spectrasheet.cpp
output/ods/spectrasheetall.cpp
- output/ods/xicareasheet.cpp
+ #output/ods/xicareasheet.cpp
output/exportfastafile.cpp
output/masschroqml.cpp
output/masschroqprm.cpp
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 58eaa0d7..3d65526f 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -46,7 +46,7 @@
#include "project_view/projectwindow.h"
#include "../core/tandem_run/tandembatchprocess.h"
#include "../core/tandem_run/tandemcondorprocess.h"
-#include "../output/ods/xicareasheet.h"
+//#include "../output/ods/xicareasheet.h"
#include <QSettings>
WorkerThread::WorkerThread(MainWindow *p_main_window)
@@ -876,13 +876,13 @@ void
WorkerThread::doWriteXicAreaInCsv(QString filename,
std::vector<XicBox *> xic_boxs)
{
- CalcWriterInterface *p_writer = nullptr;
-
- emit loadingMessage(tr("writing TSV files, please wait"));
- p_writer = new TsvDirectoryWriter(filename);
- XicAreaSheet(p_writer, xic_boxs);
- bool all_data = true;
- XicAreaSheet(p_writer, xic_boxs, all_data);
- p_writer->close();
- emit exportXicToCsvFinished();
+// CalcWriterInterface *p_writer = nullptr;
+//
+// emit loadingMessage(tr("writing TSV files, please wait"));
+// p_writer = new TsvDirectoryWriter(filename);
+// XicAreaSheet(p_writer, xic_boxs);
+// bool all_data = true;
+// XicAreaSheet(p_writer, xic_boxs, all_data);
+// p_writer->close();
+// emit exportXicToCsvFinished();
}
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index b07344f4..3b6fcb9d 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -263,10 +263,13 @@ MassChroQml::writeQuantificationTraces()
void
MassChroQml::writeQuantify()
{
+ for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
+ {
//<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
_output_stream->writeStartElement("quantify");
_output_stream->writeAttribute("id", "q1");
- _output_stream->writeAttribute("withingroup", "fractiona1");
+
+ _output_stream->writeAttribute("withingroup", group_sp->getMsRunAlignmentGroupName());
_output_stream->writeAttribute("quantification_method_id", "quant1");
//<peptides_in_peptide_list mode="real_or_mean" />
//</quantify>
@@ -301,6 +304,7 @@ MassChroQml::writeQuantify()
//</quantify>
_output_stream->writeEndElement();
+ }
}
void
--
GitLab
From 24408577d56f22fb2ccce0d68fa94c861f29394b Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 27 Oct 2020 09:57:28 +0100
Subject: [PATCH 04/18] change deprecated dirOnly option
---
src/gui/tandem_run_dialog/tandemrundialog.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index 11a5e05a..c4c2e32f 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -407,7 +407,7 @@ TandemRunDialog::selectTdfFolder()
QString default_tdf_location =
settings.value("path/tandemrun_tdf_directory", "").toString();
QFileDialog directories_dialog;
- directories_dialog.setFileMode(QFileDialog::DirectoryOnly);
+ directories_dialog.setOption(QFileDialog::ShowDirsOnly, true);
directories_dialog.setOption(QFileDialog::DontUseNativeDialog, true);
directories_dialog.setWindowTitle("Select the timsTOF folders");
QListView *lView = directories_dialog.findChild<QListView *>("listView");
--
GitLab
From a2e0ce65fc7fe01a327d7c8aa14b0b6b4dce678f Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 27 Oct 2020 11:08:11 +0100
Subject: [PATCH 05/18] Add protein detail link to the ptmIsland window
https://forgemia.inra.fr/pappso/xtpcpp/-/issues/29
---
src/gui/project_view/projectwindow.h | 1 +
src/gui/ptm_island_list_view/ptmislandlistwindow.cpp | 9 +++++++++
src/gui/ptm_island_list_view/ptmislandlistwindow.h | 1 +
src/gui/ptm_island_list_view/ptmislandproxymodel.cpp | 8 ++++----
src/gui/ptm_island_list_view/ptmislandtablemodel.cpp | 6 ++++++
src/gui/ptm_island_list_view/ptmislandtablemodel.h | 2 ++
6 files changed, 23 insertions(+), 4 deletions(-)
diff --git a/src/gui/project_view/projectwindow.h b/src/gui/project_view/projectwindow.h
index b2c2fa27..e8f06cab 100644
--- a/src/gui/project_view/projectwindow.h
+++ b/src/gui/project_view/projectwindow.h
@@ -54,6 +54,7 @@ class ProjectWindow : public QMainWindow
friend class ProteinListWindow;
friend class PeptideListWindow;
friend class MsRunIdListWindow;
+ friend class PtmIslandListWindow;
public:
explicit ProjectWindow(MainWindow *parent = 0);
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index b9a80f64..f5fe74ba 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -215,6 +215,15 @@ PtmIslandListWindow::askViewPtmPeptideList(PtmIsland *ptm_island)
_p_current_ptm_peptide_list_window->show();
}
+void PtmIslandListWindow::askProteinDetailView(ProteinMatch* p_protein_match)
+{
+ qDebug() << "begin";
+ _project_window->doViewProteinDetail(p_protein_match);
+ qDebug() << "end";
+ // updateStatusBar();
+}
+
+
const IdentificationGroup *
PtmIslandListWindow::getIdentificationGroup() const
{
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index e5f49d37..68af6eda 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -76,6 +76,7 @@ class PtmIslandListWindow : public QMainWindow
protected:
void askViewPtmPeptideList(PtmIsland *ptm_island);
+ void askProteinDetailView(ProteinMatch *p_protein_match);
private:
void connectNewPtmPeptideListWindow();
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index 2cb3ca31..3b97bd39 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -169,18 +169,18 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
qDebug() << "PtmIslandProxyModel::onTableClicked begin "
<< this->mapToSource(index).row();
- //_protein_table_model_p->onTableClicked(this->mapToSource(index));
+// _protein_table_model_p->onTableClicked(this->mapToSource(index));
QModelIndex source_index(this->mapToSource(index));
int row = source_index.row();
int col = source_index.column();
- // ProteinMatch* p_protein_match =
- // _p_ptm_island_table_model->getIdentificationGroup()->getProteinMatchList().at(row);
+ ProteinMatch* p_protein_match =
+ _p_ptm_island_table_model->getIdentificationGroup()->getProteinMatchList().at(row);
if((col == (std::int8_t)PtmIslandListColumn::accession) ||
(col == (std::int8_t)PtmIslandListColumn::description))
{
- //_p_ptm_island_table_model->askPtmProteinDetailView(p_protein_match);
+ _p_ptm_island_list_window->askProteinDetailView(p_protein_match);
}
else
{
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 660556ec..bf560909 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -150,6 +150,12 @@ PtmIslandTableModel::setIdentificationGroup(
this->_p_ptm_island_list_window->resizeColumnsToContents();
}
+
+IdentificationGroup * PtmIslandTableModel::getIdentificationGroup()
+{
+ return _p_identification_group;
+}
+
const PtmGroupingExperiment *
PtmIslandTableModel::getPtmGroupingExperiment() const
{
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 38581f36..4a3711a9 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -68,6 +68,8 @@ class PtmIslandTableModel : public QAbstractTableModel
~PtmIslandTableModel();
void setIdentificationGroup(IdentificationGroup *p_identification_group);
+ IdentificationGroup * getIdentificationGroup();
+
virtual int
rowCount(const QModelIndex &parent = QModelIndex()) const override;
virtual int
--
GitLab
From 18b829b6e2a0fa56644a4f0edb2887be4d645b14 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 27 Oct 2020 16:16:27 +0100
Subject: [PATCH 06/18] Add column management to PTM island list window
---
.../ptm_island_list_view.ui | 29 +++++++++-
.../ptmislandlistwindow.cpp | 56 +++++++++++++++++--
.../ptmislandlistwindow.h | 27 ++++++++-
.../ptmislandproxymodel.cpp | 37 ++++++++++++
.../ptmislandproxymodel.h | 10 +++-
.../ptmislandtablemodel.cpp | 5 ++
.../ptmislandtablemodel.h | 4 +-
7 files changed, 158 insertions(+), 10 deletions(-)
diff --git a/src/gui/ptm_island_list_view/ptm_island_list_view.ui b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
index 10d234c1..631e1ade 100644
--- a/src/gui/ptm_island_list_view/ptm_island_list_view.ui
+++ b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
@@ -79,11 +79,38 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>25</height>
+ <height>22</height>
</rect>
</property>
+ <widget class="QMenu" name="menu_Columns">
+ <property name="title">
+ <string>&Columns</string>
+ </property>
+ </widget>
+ <widget class="QMenu" name="menu_Show_Only">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ <property name="title">
+ <string>&Show Only</string>
+ </property>
+ <addaction name="actionChecked_PTM"/>
+ </widget>
+ <addaction name="menu_Columns"/>
+ <addaction name="menu_Show_Only"/>
</widget>
<widget class="QStatusBar" name="statusbar"/>
+ <action name="actionChecked_PTM">
+ <property name="checkable">
+ <bool>true</bool>
+ </property>
+ <property name="enabled">
+ <bool>true</bool>
+ </property>
+ <property name="text">
+ <string>Checked PTM</string>
+ </property>
+ </action>
</widget>
<resources/>
<connections>
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index f5fe74ba..619d0bf1 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -36,6 +36,33 @@
#include <QSettings>
#include "../ptm_peptide_list_view/ptmpeptidelistwindow.h"
+PtmIslandListQActionColumn::PtmIslandListQActionColumn ( PtmIslandListWindow* parent, PtmIslandListColumn column )
+: QAction(parent)
+{
+ this->setText(PtmIslandTableModel::getTitle(column));
+
+ this->setCheckable(true);
+ this->setChecked(parent->getPtmIslandListColumnDisplay(column));
+
+ m_column = column;
+ mp_ptmIslandWindow = parent;
+
+ connect(this,
+ &PtmIslandListQActionColumn::toggled,
+ this,
+ &PtmIslandListQActionColumn::doToggled);
+}
+
+PtmIslandListQActionColumn::~PtmIslandListQActionColumn()
+{
+}
+
+void PtmIslandListQActionColumn::doToggled ( bool toggled )
+{
+ setChecked(toggled);
+ mp_ptmIslandWindow->setPtmIslandListColumnDisplay(m_column, toggled);
+}
+
PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent)
: QMainWindow(parent), ui(new Ui::PtmIslandListWindow)
@@ -60,7 +87,7 @@ PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent)
_statusbar_displayed_label = new QLabel("");
ui->statusbar->addWidget(_statusbar_displayed_label);
-
+
#if QT_VERSION >= 0x050000
// Qt5 code
connect(this,
@@ -140,6 +167,28 @@ PtmIslandListWindow::setIdentificationGroup(
qDebug() << "PtmIslandListWindow::setIdentificationGroup end";
}
+void PtmIslandListWindow::setPtmIslandListColumnDisplay ( PtmIslandListColumn column, bool toggled )
+{
+ _ptm_proxy_model_p->setPtmIslandListColumnDisplay(column, toggled);
+}
+
+bool PtmIslandListWindow::getPtmIslandListColumnDisplay ( PtmIslandListColumn column ) const
+{
+ return _ptm_proxy_model_p->getPtmIslandListColumnDisplay(column);
+}
+
+void PtmIslandListWindow::setColumnMenuList()
+{
+ PtmIslandListQActionColumn *p_action;
+ qInfo() << _ptm_table_model_p->columnCount();
+ for(int i = 0; i < _ptm_table_model_p->columnCount(); i++)
+ {
+ p_action = new PtmIslandListQActionColumn(
+ this, PtmIslandTableModel::getPtmIslandListColumn(i));
+ ui->menu_Columns->addAction(p_action);
+ }
+}
+
void
PtmIslandListWindow::doIdentificationGroupGrouped(
IdentificationGroup *p_identification_group)
@@ -177,7 +226,7 @@ PtmIslandListWindow::doIdentificationPtmGroupGrouped(
.arg(p_ptm_grouping_experiment->getPtmIslandList().size()));
// ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
}
-
+ setColumnMenuList();
qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped end";
}
@@ -223,14 +272,12 @@ void PtmIslandListWindow::askProteinDetailView(ProteinMatch* p_protein_match)
// updateStatusBar();
}
-
const IdentificationGroup *
PtmIslandListWindow::getIdentificationGroup() const
{
return _p_identification_group;
}
-
void
PtmIslandListWindow::updateStatusBar()
{
@@ -244,7 +291,6 @@ PtmIslandListWindow::updateStatusBar()
}
}
-
void
PtmIslandListWindow::doPtmSearchEdit(QString ptm_search_string)
{
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index 68af6eda..1787da1d 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -32,6 +32,7 @@
#define PTMISLANDLISTWINDOW_H
#include <QMainWindow>
#include <QLabel>
+#include <QAction>
#include "ptmislandtablemodel.h"
#include "ptmislandproxymodel.h"
#include "../../core/identificationgroup.h"
@@ -45,6 +46,24 @@ namespace Ui
class PtmIslandListWindow;
}
+class PtmIslandListWindow;
+class PtmIslandListQActionColumn : public QAction
+{
+ Q_OBJECT
+ public:
+ explicit PtmIslandListQActionColumn(PtmIslandListWindow *parent,
+ PtmIslandListColumn column);
+ ~PtmIslandListQActionColumn();
+
+
+ public slots:
+ void doToggled(bool toggled);
+
+ private:
+ PtmIslandListWindow *mp_ptmIslandWindow;
+ PtmIslandListColumn m_column;
+};
+
class PtmIslandListWindow : public QMainWindow
{
Q_OBJECT
@@ -57,8 +76,12 @@ class PtmIslandListWindow : public QMainWindow
void resizeColumnsToContents();
const IdentificationGroup *getIdentificationGroup() const;
ProjectWindow *getProjectWindowP();
-
-
+ void setPtmIslandListColumnDisplay(PtmIslandListColumn column,
+ bool toggled);
+ bool
+ getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
+ void setColumnMenuList();
+
public slots:
void
doIdentificationPtmGroupGrouped(IdentificationGroup *p_identification_group);
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index 3b97bd39..77c49a1f 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -28,6 +28,7 @@
*implementation
******************************************************************************/
+#include <QSettings>
#include "ptmislandproxymodel.h"
#include "ptmislandtablemodel.h"
#include "ptmislandlistwindow.h"
@@ -43,12 +44,30 @@ PtmIslandProxyModel::PtmIslandProxyModel(
_p_ptm_island_table_model = ptm_table_model_p;
_ptm_search_string = "";
_search_on = "accession";
+ m_column_display.resize(30);
+ qDebug() << "Test creation data";
+ QSettings settings;
+ for(std::size_t i = 0; i < m_column_display.size(); i++)
+ {
+ m_column_display[i] =
+ settings
+ .value(QString("ptm_island_columns/%1")
+ .arg(_p_ptm_island_table_model->getTitle(
+ (PtmIslandListColumn)i)),
+ "true")
+ .toBool();
+ }
}
PtmIslandProxyModel::~PtmIslandProxyModel()
{
}
+bool PtmIslandProxyModel::filterAcceptsColumn ( int source_column, const QModelIndex& source_parent ) const
+{
+ return m_column_display[source_column];
+}
+
bool
PtmIslandProxyModel::filterAcceptsRow(int source_row,
const QModelIndex &source_parent
@@ -194,6 +213,24 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
qDebug() << "PtmIslandProxyModel::onTableClicked end " << index.row();
}
+bool PtmIslandProxyModel::getPtmIslandListColumnDisplay (PtmIslandListColumn column ) const
+{
+ return m_column_display[(std::int8_t)column];
+}
+
+void PtmIslandProxyModel::setPtmIslandListColumnDisplay (PtmIslandListColumn column, bool toggled )
+{
+ qDebug() << "begin " << toggled;
+ beginResetModel();
+ QSettings settings;
+ settings.setValue(QString("ptm_island_columns/%1")
+ .arg(_p_ptm_island_table_model->getTitle(column)),
+ toggled);
+
+ m_column_display[(std::int8_t)column] = toggled;
+ endResetModel();
+}
+
void
PtmIslandProxyModel::setSearchOn(QString search_on)
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.h b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
index b65464b8..b0f6a996 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
@@ -33,6 +33,7 @@
#include <QAbstractTableModel>
#include <QSortFilterProxyModel>
+#include "ptmislandtablemodel.h"
class PtmIslandListWindow;
@@ -45,19 +46,26 @@ class PtmIslandProxyModel : public QSortFilterProxyModel
PtmIslandProxyModel(PtmIslandListWindow *p_ptm_island_list_window,
PtmIslandTableModel *ptm_table_model_p);
~PtmIslandProxyModel();
+ bool filterAcceptsColumn(int source_column,
+ const QModelIndex &source_parent) const override;
bool filterAcceptsRow(int source_row,
const QModelIndex &source_parent) const override;
void setSearchOn(QString search_on);
void setPtmSearchString(QString ptm_search_string);
-
+ void setPtmIslandListColumnDisplay(PtmIslandListColumn column,
+ bool toggled);
+ bool
+ getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
+
public slots:
void onTableClicked(const QModelIndex &index);
private:
PtmIslandListWindow *_p_ptm_island_list_window;
PtmIslandTableModel *_p_ptm_island_table_model;
+ std::vector<bool> m_column_display;
QString _search_on;
QString _ptm_search_string;
};
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index bf560909..bb26f5bb 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -57,6 +57,11 @@ PtmIslandTableModel::getDescription(PtmIslandListColumn column)
// qDebug() << "ProteinTableModel::columnCount end ";
}
+PtmIslandListColumn PtmIslandTableModel::getPtmIslandListColumn ( std::int8_t column )
+{
+ return static_cast<PtmIslandListColumn>(column);
+}
+
const QString
PtmIslandTableModel::getTitle(std::int8_t column)
{
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 4a3711a9..96274847 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -81,7 +81,9 @@ class PtmIslandTableModel : public QAbstractTableModel
static const QString getTitle(PtmIslandListColumn column);
static const QString getDescription(PtmIslandListColumn column);
-
+ static PtmIslandListColumn
+ getPtmIslandListColumn(std::int8_t column);
+
const PtmGroupingExperiment *getPtmGroupingExperiment() const;
public slots:
--
GitLab
From 7444e2a7176677223617f23aa379b11ea44855d1 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 27 Oct 2020 17:04:57 +0100
Subject: [PATCH 07/18] Add checked column to manage ptm island
---
.../ptm_island_list_view.ui | 18 +++++++++-
.../ptmislandlistwindow.cpp | 8 ++++-
.../ptmislandlistwindow.h | 7 ++--
.../ptmislandproxymodel.cpp | 33 +++++++++++++++++--
.../ptmislandproxymodel.h | 3 +-
.../ptmislandtablemodel.cpp | 29 ++++++++++++++--
.../ptmislandtablemodel.h | 28 ++++++++--------
7 files changed, 98 insertions(+), 28 deletions(-)
diff --git a/src/gui/ptm_island_list_view/ptm_island_list_view.ui b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
index 631e1ade..84599b85 100644
--- a/src/gui/ptm_island_list_view/ptm_island_list_view.ui
+++ b/src/gui/ptm_island_list_view/ptm_island_list_view.ui
@@ -89,7 +89,7 @@
</widget>
<widget class="QMenu" name="menu_Show_Only">
<property name="enabled">
- <bool>false</bool>
+ <bool>true</bool>
</property>
<property name="title">
<string>&Show Only</string>
@@ -146,6 +146,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>actionChecked_PTM</sender>
+ <signal>toggled(bool)</signal>
+ <receiver>PtmIslandListWindow</receiver>
+ <slot>doNotCheckedHide(bool)</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>-1</x>
+ <y>-1</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>412</x>
+ <y>201</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>doNotValidHide(bool)</slot>
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 619d0bf1..010c2173 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -180,7 +180,6 @@ bool PtmIslandListWindow::getPtmIslandListColumnDisplay ( PtmIslandListColumn co
void PtmIslandListWindow::setColumnMenuList()
{
PtmIslandListQActionColumn *p_action;
- qInfo() << _ptm_table_model_p->columnCount();
for(int i = 0; i < _ptm_table_model_p->columnCount(); i++)
{
p_action = new PtmIslandListQActionColumn(
@@ -189,6 +188,13 @@ void PtmIslandListWindow::setColumnMenuList()
}
}
+void PtmIslandListWindow::doNotCheckedHide ( bool hide )
+{
+ _ptm_proxy_model_p->hideNotChecked(hide);
+ emit ptmIslandDataChanged();
+}
+
+
void
PtmIslandListWindow::doIdentificationGroupGrouped(
IdentificationGroup *p_identification_group)
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index 1787da1d..1fa23da7 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -28,8 +28,8 @@
*implementation
******************************************************************************/
-#ifndef PTMISLANDLISTWINDOW_H
-#define PTMISLANDLISTWINDOW_H
+#pragma once
+
#include <QMainWindow>
#include <QLabel>
#include <QAction>
@@ -92,6 +92,7 @@ class PtmIslandListWindow : public QMainWindow
void updateStatusBar();
void doPtmSearchEdit(QString ptm_search_string);
void doSearchOn(QString search_on);
+ void doNotCheckedHide(bool hide);
signals:
@@ -117,5 +118,3 @@ class PtmIslandListWindow : public QMainWindow
QLabel *_statusbar_displayed_label;
QLabel *_statusbar_ptm_islands_label;
};
-
-#endif // PTMISLANDLISTWINDOW_H
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index 77c49a1f..7a4501d8 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -81,9 +81,20 @@ PtmIslandProxyModel::filterAcceptsRow(int source_row,
_p_ptm_island_table_model->getPtmGroupingExperiment()
->getPtmIslandList()
.at(source_row);
+ ProteinMatch *protein_match =
+ _p_ptm_island_table_model->getIdentificationGroup()
+ ->getProteinMatchList()
+ .at(source_row);
+ // qDebug() << "Prote
// qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match "
// << source_row;
-
+ if(m_hideNotChecked)
+ {
+ if(!protein_match->isChecked())
+ {
+ return false;
+ }
+ }
if(!_ptm_search_string.isEmpty())
{
if(_search_on == "accession")
@@ -195,8 +206,19 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
ProteinMatch* p_protein_match =
_p_ptm_island_table_model->getIdentificationGroup()->getProteinMatchList().at(row);
-
- if((col == (std::int8_t)PtmIslandListColumn::accession) ||
+
+ if(col == (std::int8_t)PtmIslandListColumn::checked)
+ {
+ if(p_protein_match->isChecked())
+ {
+ p_protein_match->setChecked(false);
+ }
+ else
+ {
+ p_protein_match->setChecked(true);
+ }
+ }
+ else if((col == (std::int8_t)PtmIslandListColumn::accession) ||
(col == (std::int8_t)PtmIslandListColumn::description))
{
_p_ptm_island_list_window->askProteinDetailView(p_protein_match);
@@ -231,6 +253,11 @@ void PtmIslandProxyModel::setPtmIslandListColumnDisplay (PtmIslandListColumn col
endResetModel();
}
+void PtmIslandProxyModel::hideNotChecked ( bool hide )
+{
+ m_hideNotChecked = hide;
+}
+
void
PtmIslandProxyModel::setSearchOn(QString search_on)
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.h b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
index b0f6a996..2bcccaf5 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
@@ -52,7 +52,7 @@ class PtmIslandProxyModel : public QSortFilterProxyModel
const QModelIndex &source_parent) const override;
void setSearchOn(QString search_on);
-
+ void hideNotChecked(bool hide);
void setPtmSearchString(QString ptm_search_string);
void setPtmIslandListColumnDisplay(PtmIslandListColumn column,
bool toggled);
@@ -66,6 +66,7 @@ class PtmIslandProxyModel : public QSortFilterProxyModel
PtmIslandListWindow *_p_ptm_island_list_window;
PtmIslandTableModel *_p_ptm_island_table_model;
std::vector<bool> m_column_display;
+ bool m_hideNotChecked = true;
QString _search_on;
QString _ptm_search_string;
};
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index bb26f5bb..498d11d9 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -67,7 +67,9 @@ PtmIslandTableModel::getTitle(std::int8_t column)
{
switch(column)
{
-
+ case(std::int8_t)PtmIslandListColumn::checked:
+ return "Checked";
+ break;
case(std::int8_t)PtmIslandListColumn::spectrum:
return "spectrum";
break;
@@ -106,7 +108,9 @@ PtmIslandTableModel::getDescription(std::int8_t column)
{
switch(column)
{
-
+ case(std::int8_t)PtmIslandListColumn::checked:
+ return "Checked PTM";
+ break;
case(std::int8_t)PtmIslandListColumn::spectrum:
return "number of distinct spectrum assigned to this PTM island";
break;
@@ -224,6 +228,21 @@ PtmIslandTableModel::data(const QModelIndex &index, int role) const
int col = index.column();
switch(role)
{
+ case Qt::CheckStateRole:
+ if(col == (std::int8_t)PtmIslandListColumn::checked) // add a checkbox to cell(1,0)
+ {
+ if(_p_identification_group->getProteinMatchList()
+ .at(row)
+ ->isChecked())
+ {
+ return Qt::Checked;
+ }
+ else
+ {
+ return Qt::Unchecked;
+ }
+ }
+ break;
case Qt::SizeHintRole:
// qDebug() << "ProteinTableModel::headerData " <<
// ProteinTableModel::getColumnWidth(section);
@@ -236,7 +255,9 @@ PtmIslandTableModel::data(const QModelIndex &index, int role) const
}
switch(col)
{
-
+ case(std::int8_t)PtmIslandListColumn::checked:
+ return QVariant();
+ break;
case(std::int8_t)PtmIslandListColumn::spectrum:
return QVariant((quint64)getPtmGroupingExperiment()
->getPtmIslandList()
@@ -342,6 +363,8 @@ PtmIslandTableModel::getColumnWidth(int column)
qDebug() << "PtmIslandTableModel::getColumnWidth " << column;
switch(column)
{
+ case(int)PtmIslandListColumn::checked:
+ break;
case(int)PtmIslandListColumn::accession:
qDebug() << "PtmIslandTableModel::getColumnWidth accession " << column;
return 250;
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index 96274847..dd38a98a 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
-#ifndef PTMISLANDTABLEMODEL_H
-#define PTMISLANDTABLEMODEL_H
+#pragma once
#include <QAbstractTableModel>
#include "../../core/identificationgroup.h"
@@ -43,17 +42,18 @@
enum class PtmIslandListColumn : std::int8_t
{
- ptm_island_id = 0, ///< ptm_island_id
- accession = 1, ///< protein accession
- description = 2, ///< protein description
- ptm_position_list = 3, ///< ptm position list
- spectrum = 4, ///< count sample scans
- ptm_spectrum = 5, ///< count scan with ptm
- sequence = 6, ///< unique sequence count
- multiptm = 7, ///< count multi ptm peptide match
- ptm_island_start = 8, ///< start position of the ptm island on the protein
- ptm_island_length = 9, ///< length of the ptm island
- last = 10,
+ checked = 0, ///< checked ptm
+ ptm_island_id = 1, ///< ptm_island_id
+ accession = 2, ///< protein accession
+ description = 3, ///< protein description
+ ptm_position_list = 4, ///< ptm position list
+ spectrum = 5, ///< count sample scans
+ ptm_spectrum = 6, ///< count scan with ptm
+ sequence = 7, ///< unique sequence count
+ multiptm = 8, ///< count multi ptm peptide match
+ ptm_island_start = 9, ///< start position of the ptm island on the protein
+ ptm_island_length = 10, ///< length of the ptm island
+ last = 11,
};
@@ -98,5 +98,3 @@ class PtmIslandTableModel : public QAbstractTableModel
IdentificationGroup *_p_identification_group = nullptr;
PtmIslandListWindow *_p_ptm_island_list_window = nullptr;
};
-
-#endif // PTMISLANDTABLEMODEL_H
--
GitLab
From 145079c1011d01d91343169af15b907e71226a6a Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 09:21:33 +0100
Subject: [PATCH 08/18] add xicareasheet
---
src/output/ods/xicareasheet.cpp | 132 ++++++++++++++++++++++++++++++++
src/output/ods/xicareasheet.h | 52 +++++++++++++
2 files changed, 184 insertions(+)
create mode 100644 src/output/ods/xicareasheet.cpp
create mode 100644 src/output/ods/xicareasheet.h
diff --git a/src/output/ods/xicareasheet.cpp b/src/output/ods/xicareasheet.cpp
new file mode 100644
index 00000000..1e790aad
--- /dev/null
+++ b/src/output/ods/xicareasheet.cpp
@@ -0,0 +1,132 @@
+/**
+ * \file /output/xicareasheet.cpp
+ * \date 16/10/2020
+ * \author Olivier Langella
+ * \brief ODS grouping sheet
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2020 Thomas Renne <thomas.renne@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Thomas Renne <thomas.renne@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+
+#include "xicareasheet.h"
+
+XicAreaSheet::XicAreaSheet(CalcWriterInterface *p_writer,
+ const std::vector<XicBox *> xic_boxs,
+ bool all_data)
+{
+ mp_writer = p_writer;
+
+ mp_xicBoxList = xic_boxs;
+
+ OdsTableSettings table_settings;
+ table_settings.setVerticalSplit(1);
+ mp_writer->setCurrentOdsTableSettings(table_settings);
+ if(all_data)
+ {
+ mp_writer->writeSheet("xic_all_data");
+ writeHeadersAllData();
+ for(XicBox *xic : mp_xicBoxList)
+ {
+ writeXicAllData(xic);
+ }
+ }
+ else
+ {
+ mp_writer->writeSheet("xic_area");
+ writeHeaders();
+ for(XicBox *xic : mp_xicBoxList)
+ {
+ writeAreaPeackdata(xic);
+ }
+ }
+}
+
+void
+XicAreaSheet::writeHeaders()
+{
+ mp_writer->writeLine();
+ mp_writer->setCellAnnotation("ms run name");
+ mp_writer->writeCell("msrun");
+ mp_writer->setCellAnnotation("area of the peak");
+ mp_writer->writeCell("area");
+ mp_writer->setCellAnnotation("left boundary of the peak");
+ mp_writer->writeCell("rt_begin");
+ mp_writer->setCellAnnotation(
+ "retention time of the max intensity in the peak");
+ mp_writer->writeCell("rt_max");
+ mp_writer->setCellAnnotation("right boundary of the peak");
+ mp_writer->writeCell("rt_end");
+ mp_writer->setCellAnnotation("Isotope");
+ mp_writer->writeCell("isotope");
+}
+
+void
+XicAreaSheet::writeHeadersAllData()
+{
+ mp_writer->writeLine();
+ mp_writer->setCellAnnotation("ms run name");
+ mp_writer->writeCell("msrun");
+ mp_writer->setCellAnnotation("Isotope");
+ mp_writer->writeCell("isotope");
+ mp_writer->setCellAnnotation("retention time of point");
+ mp_writer->writeCell("rt");
+ mp_writer->setCellAnnotation("intensity of point");
+ mp_writer->writeCell("intensity");
+}
+
+
+void
+XicAreaSheet::writeAreaPeackdata(XicBox *xic_box)
+{
+ for(XicBoxNaturalIsotope isotope : xic_box->getNaturalIsotopList())
+ {
+ for(pappso::TracePeakCstSPtr trace : isotope.detected_peak_list)
+ {
+ mp_writer->writeLine();
+ mp_writer->writeCell("");
+ mp_writer->writeCell(trace->getArea());
+ mp_writer->writeCell(trace->getLeftBoundary().x);
+ mp_writer->writeCell(trace->getMaxXicElement().x);
+ mp_writer->writeCell(trace->getRightBoundary().x);
+ mp_writer->writeCell(
+ int(isotope.peptide_natural_isotope_sp->getIsotopeNumber()));
+ }
+ }
+}
+
+void
+XicAreaSheet::writeXicAllData(XicBox *xic_box)
+{
+ for(XicBoxNaturalIsotope isotope : xic_box->getNaturalIsotopList())
+ {
+ for(std::size_t i = 0; i < isotope.xic_sp->xValues().size(); i++)
+ {
+ mp_writer->writeLine();
+ mp_writer->writeCell("");
+ mp_writer->writeCell(
+ int(isotope.peptide_natural_isotope_sp->getIsotopeNumber()));
+ mp_writer->writeCell(isotope.xic_sp->xValues().at(i));
+ mp_writer->writeCell(isotope.xic_sp->yValues().at(i));
+ }
+ }
+}
diff --git a/src/output/ods/xicareasheet.h b/src/output/ods/xicareasheet.h
new file mode 100644
index 00000000..c6a9a143
--- /dev/null
+++ b/src/output/ods/xicareasheet.h
@@ -0,0 +1,52 @@
+/**
+ * \file /output/xicareasheet.h
+ * \date 16/10/2020
+ * \author Thomas Renne
+ * \brief ODS grouping sheet
+ */
+
+/*******************************************************************************
+ * Copyright (c) 2020 Thomas Renne <thomas.renne@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Thomas Renne <thomas.renne@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+#pragma once
+
+#include <odsstream/calcwriterinterface.h>
+#include "../../core/project.h"
+#include "../../gui/xic_view/xic_box/xicbox.h"
+
+class XicAreaSheet
+{
+ public:
+ XicAreaSheet(CalcWriterInterface *p_writer,
+ const std::vector<XicBox *> xic_boxs,
+ bool all_data = false);
+
+ private:
+ void writeAreaPeackdata(XicBox *xic_box);
+ void writeXicAllData(XicBox *xic_box);
+ void writeHeaders();
+ void writeHeadersAllData();
+
+ private:
+ std::vector<XicBox *> mp_xicBoxList;
+ CalcWriterInterface *mp_writer;
+};
--
GitLab
From e9b60531ecf6ffbd8eceaa63fb8e3d7b284af3c4 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 09:23:25 +0100
Subject: [PATCH 09/18] Add xicarea in other objects
---
src/CMakeLists.txt | 2 +-
src/gui/workerthread.cpp | 20 ++++++++++----------
2 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f139c7c1..946b28a0 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -105,7 +105,7 @@ set(CPP_FILES
output/ods/simplesheet.cpp
output/ods/spectrasheet.cpp
output/ods/spectrasheetall.cpp
- #output/ods/xicareasheet.cpp
+ output/ods/xicareasheet.cpp
output/exportfastafile.cpp
output/masschroqml.cpp
output/masschroqprm.cpp
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 3d65526f..58eaa0d7 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -46,7 +46,7 @@
#include "project_view/projectwindow.h"
#include "../core/tandem_run/tandembatchprocess.h"
#include "../core/tandem_run/tandemcondorprocess.h"
-//#include "../output/ods/xicareasheet.h"
+#include "../output/ods/xicareasheet.h"
#include <QSettings>
WorkerThread::WorkerThread(MainWindow *p_main_window)
@@ -876,13 +876,13 @@ void
WorkerThread::doWriteXicAreaInCsv(QString filename,
std::vector<XicBox *> xic_boxs)
{
-// CalcWriterInterface *p_writer = nullptr;
-//
-// emit loadingMessage(tr("writing TSV files, please wait"));
-// p_writer = new TsvDirectoryWriter(filename);
-// XicAreaSheet(p_writer, xic_boxs);
-// bool all_data = true;
-// XicAreaSheet(p_writer, xic_boxs, all_data);
-// p_writer->close();
-// emit exportXicToCsvFinished();
+ CalcWriterInterface *p_writer = nullptr;
+
+ emit loadingMessage(tr("writing TSV files, please wait"));
+ p_writer = new TsvDirectoryWriter(filename);
+ XicAreaSheet(p_writer, xic_boxs);
+ bool all_data = true;
+ XicAreaSheet(p_writer, xic_boxs, all_data);
+ p_writer->close();
+ emit exportXicToCsvFinished();
}
--
GitLab
From d354844472b5717a90ab38eb7895439e4c1c107e Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 09:24:53 +0100
Subject: [PATCH 10/18] Correct format indentation
---
.../ptmislandlistwindow.cpp | 39 +++++++++------
.../ptmislandlistwindow.h | 10 ++--
.../ptmislandproxymodel.cpp | 47 +++++++++++--------
.../ptmislandproxymodel.h | 13 ++---
.../ptmislandtablemodel.cpp | 11 +++--
.../ptmislandtablemodel.h | 29 ++++++------
6 files changed, 81 insertions(+), 68 deletions(-)
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 010c2173..8d1b86fa 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -36,8 +36,9 @@
#include <QSettings>
#include "../ptm_peptide_list_view/ptmpeptidelistwindow.h"
-PtmIslandListQActionColumn::PtmIslandListQActionColumn ( PtmIslandListWindow* parent, PtmIslandListColumn column )
-: QAction(parent)
+PtmIslandListQActionColumn::PtmIslandListQActionColumn(
+ PtmIslandListWindow *parent, PtmIslandListColumn column)
+ : QAction(parent)
{
this->setText(PtmIslandTableModel::getTitle(column));
@@ -57,7 +58,8 @@ PtmIslandListQActionColumn::~PtmIslandListQActionColumn()
{
}
-void PtmIslandListQActionColumn::doToggled ( bool toggled )
+void
+PtmIslandListQActionColumn::doToggled(bool toggled)
{
setChecked(toggled);
mp_ptmIslandWindow->setPtmIslandListColumnDisplay(m_column, toggled);
@@ -87,7 +89,7 @@ PtmIslandListWindow::PtmIslandListWindow(ProjectWindow *parent)
_statusbar_displayed_label = new QLabel("");
ui->statusbar->addWidget(_statusbar_displayed_label);
-
+
#if QT_VERSION >= 0x050000
// Qt5 code
connect(this,
@@ -167,19 +169,24 @@ PtmIslandListWindow::setIdentificationGroup(
qDebug() << "PtmIslandListWindow::setIdentificationGroup end";
}
-void PtmIslandListWindow::setPtmIslandListColumnDisplay ( PtmIslandListColumn column, bool toggled )
+void
+PtmIslandListWindow::setPtmIslandListColumnDisplay(PtmIslandListColumn column,
+ bool toggled)
{
- _ptm_proxy_model_p->setPtmIslandListColumnDisplay(column, toggled);
+ _ptm_proxy_model_p->setPtmIslandListColumnDisplay(column, toggled);
}
-bool PtmIslandListWindow::getPtmIslandListColumnDisplay ( PtmIslandListColumn column ) const
+bool
+PtmIslandListWindow::getPtmIslandListColumnDisplay(
+ PtmIslandListColumn column) const
{
- return _ptm_proxy_model_p->getPtmIslandListColumnDisplay(column);
+ return _ptm_proxy_model_p->getPtmIslandListColumnDisplay(column);
}
-void PtmIslandListWindow::setColumnMenuList()
+void
+PtmIslandListWindow::setColumnMenuList()
{
- PtmIslandListQActionColumn *p_action;
+ PtmIslandListQActionColumn *p_action;
for(int i = 0; i < _ptm_table_model_p->columnCount(); i++)
{
p_action = new PtmIslandListQActionColumn(
@@ -188,10 +195,11 @@ void PtmIslandListWindow::setColumnMenuList()
}
}
-void PtmIslandListWindow::doNotCheckedHide ( bool hide )
+void
+PtmIslandListWindow::doNotCheckedHide(bool hide)
{
- _ptm_proxy_model_p->hideNotChecked(hide);
- emit ptmIslandDataChanged();
+ _ptm_proxy_model_p->hideNotChecked(hide);
+ emit ptmIslandDataChanged();
}
@@ -232,7 +240,7 @@ PtmIslandListWindow::doIdentificationPtmGroupGrouped(
.arg(p_ptm_grouping_experiment->getPtmIslandList().size()));
// ui->ptm_island_tableview->resizeRowToContents(_ptm_table_model_p->rowCount());
}
- setColumnMenuList();
+ setColumnMenuList();
qDebug() << "PtmIslandListWindow::doIdentificationPtmGroupGrouped end";
}
@@ -270,7 +278,8 @@ PtmIslandListWindow::askViewPtmPeptideList(PtmIsland *ptm_island)
_p_current_ptm_peptide_list_window->show();
}
-void PtmIslandListWindow::askProteinDetailView(ProteinMatch* p_protein_match)
+void
+PtmIslandListWindow::askProteinDetailView(ProteinMatch *p_protein_match)
{
qDebug() << "begin";
_project_window->doViewProteinDetail(p_protein_match);
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index 1fa23da7..a4cfea46 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -52,7 +52,7 @@ class PtmIslandListQActionColumn : public QAction
Q_OBJECT
public:
explicit PtmIslandListQActionColumn(PtmIslandListWindow *parent,
- PtmIslandListColumn column);
+ PtmIslandListColumn column);
~PtmIslandListQActionColumn();
@@ -76,12 +76,10 @@ class PtmIslandListWindow : public QMainWindow
void resizeColumnsToContents();
const IdentificationGroup *getIdentificationGroup() const;
ProjectWindow *getProjectWindowP();
- void setPtmIslandListColumnDisplay(PtmIslandListColumn column,
- bool toggled);
- bool
- getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
+ void setPtmIslandListColumnDisplay(PtmIslandListColumn column, bool toggled);
+ bool getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
void setColumnMenuList();
-
+
public slots:
void
doIdentificationPtmGroupGrouped(IdentificationGroup *p_identification_group);
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index 7a4501d8..024cb563 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -51,10 +51,10 @@ PtmIslandProxyModel::PtmIslandProxyModel(
{
m_column_display[i] =
settings
- .value(QString("ptm_island_columns/%1")
- .arg(_p_ptm_island_table_model->getTitle(
- (PtmIslandListColumn)i)),
- "true")
+ .value(
+ QString("ptm_island_columns/%1")
+ .arg(_p_ptm_island_table_model->getTitle((PtmIslandListColumn)i)),
+ "true")
.toBool();
}
}
@@ -63,9 +63,11 @@ PtmIslandProxyModel::~PtmIslandProxyModel()
{
}
-bool PtmIslandProxyModel::filterAcceptsColumn ( int source_column, const QModelIndex& source_parent ) const
+bool
+PtmIslandProxyModel::filterAcceptsColumn(int source_column,
+ const QModelIndex &source_parent) const
{
- return m_column_display[source_column];
+ return m_column_display[source_column];
}
bool
@@ -81,7 +83,7 @@ PtmIslandProxyModel::filterAcceptsRow(int source_row,
_p_ptm_island_table_model->getPtmGroupingExperiment()
->getPtmIslandList()
.at(source_row);
- ProteinMatch *protein_match =
+ ProteinMatch *protein_match =
_p_ptm_island_table_model->getIdentificationGroup()
->getProteinMatchList()
.at(source_row);
@@ -199,17 +201,19 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
qDebug() << "PtmIslandProxyModel::onTableClicked begin "
<< this->mapToSource(index).row();
-// _protein_table_model_p->onTableClicked(this->mapToSource(index));
+ // _protein_table_model_p->onTableClicked(this->mapToSource(index));
QModelIndex source_index(this->mapToSource(index));
int row = source_index.row();
int col = source_index.column();
- ProteinMatch* p_protein_match =
- _p_ptm_island_table_model->getIdentificationGroup()->getProteinMatchList().at(row);
-
+ ProteinMatch *p_protein_match =
+ _p_ptm_island_table_model->getIdentificationGroup()
+ ->getProteinMatchList()
+ .at(row);
+
if(col == (std::int8_t)PtmIslandListColumn::checked)
- {
- if(p_protein_match->isChecked())
+ {
+ if(p_protein_match->isChecked())
{
p_protein_match->setChecked(false);
}
@@ -217,9 +221,9 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
{
p_protein_match->setChecked(true);
}
- }
+ }
else if((col == (std::int8_t)PtmIslandListColumn::accession) ||
- (col == (std::int8_t)PtmIslandListColumn::description))
+ (col == (std::int8_t)PtmIslandListColumn::description))
{
_p_ptm_island_list_window->askProteinDetailView(p_protein_match);
}
@@ -235,12 +239,16 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
qDebug() << "PtmIslandProxyModel::onTableClicked end " << index.row();
}
-bool PtmIslandProxyModel::getPtmIslandListColumnDisplay (PtmIslandListColumn column ) const
+bool
+PtmIslandProxyModel::getPtmIslandListColumnDisplay(
+ PtmIslandListColumn column) const
{
return m_column_display[(std::int8_t)column];
}
-void PtmIslandProxyModel::setPtmIslandListColumnDisplay (PtmIslandListColumn column, bool toggled )
+void
+PtmIslandProxyModel::setPtmIslandListColumnDisplay(PtmIslandListColumn column,
+ bool toggled)
{
qDebug() << "begin " << toggled;
beginResetModel();
@@ -253,9 +261,10 @@ void PtmIslandProxyModel::setPtmIslandListColumnDisplay (PtmIslandListColumn col
endResetModel();
}
-void PtmIslandProxyModel::hideNotChecked ( bool hide )
+void
+PtmIslandProxyModel::hideNotChecked(bool hide)
{
- m_hideNotChecked = hide;
+ m_hideNotChecked = hide;
}
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.h b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
index 2bcccaf5..1d8acdce 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
-#ifndef PTMISLANDPROXYMODEL_H
-#define PTMISLANDPROXYMODEL_H
+#pragma once
#include <QAbstractTableModel>
#include <QSortFilterProxyModel>
@@ -54,11 +53,9 @@ class PtmIslandProxyModel : public QSortFilterProxyModel
void setSearchOn(QString search_on);
void hideNotChecked(bool hide);
void setPtmSearchString(QString ptm_search_string);
- void setPtmIslandListColumnDisplay(PtmIslandListColumn column,
- bool toggled);
- bool
- getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
-
+ void setPtmIslandListColumnDisplay(PtmIslandListColumn column, bool toggled);
+ bool getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
+
public slots:
void onTableClicked(const QModelIndex &index);
@@ -70,5 +67,3 @@ class PtmIslandProxyModel : public QSortFilterProxyModel
QString _search_on;
QString _ptm_search_string;
};
-
-#endif // PTMISLANDPROXYMODEL_H
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 498d11d9..ef47c324 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -57,9 +57,10 @@ PtmIslandTableModel::getDescription(PtmIslandListColumn column)
// qDebug() << "ProteinTableModel::columnCount end ";
}
-PtmIslandListColumn PtmIslandTableModel::getPtmIslandListColumn ( std::int8_t column )
+PtmIslandListColumn
+PtmIslandTableModel::getPtmIslandListColumn(std::int8_t column)
{
- return static_cast<PtmIslandListColumn>(column);
+ return static_cast<PtmIslandListColumn>(column);
}
const QString
@@ -160,7 +161,8 @@ PtmIslandTableModel::setIdentificationGroup(
this->_p_ptm_island_list_window->resizeColumnsToContents();
}
-IdentificationGroup * PtmIslandTableModel::getIdentificationGroup()
+IdentificationGroup *
+PtmIslandTableModel::getIdentificationGroup()
{
return _p_identification_group;
}
@@ -229,7 +231,8 @@ PtmIslandTableModel::data(const QModelIndex &index, int role) const
switch(role)
{
case Qt::CheckStateRole:
- if(col == (std::int8_t)PtmIslandListColumn::checked) // add a checkbox to cell(1,0)
+ if(col == (std::int8_t)
+ PtmIslandListColumn::checked) // add a checkbox to cell(1,0)
{
if(_p_identification_group->getProteinMatchList()
.at(row)
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.h b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
index dd38a98a..fe9648fc 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.h
@@ -42,16 +42,16 @@
enum class PtmIslandListColumn : std::int8_t
{
- checked = 0, ///< checked ptm
- ptm_island_id = 1, ///< ptm_island_id
- accession = 2, ///< protein accession
- description = 3, ///< protein description
- ptm_position_list = 4, ///< ptm position list
- spectrum = 5, ///< count sample scans
- ptm_spectrum = 6, ///< count scan with ptm
- sequence = 7, ///< unique sequence count
- multiptm = 8, ///< count multi ptm peptide match
- ptm_island_start = 9, ///< start position of the ptm island on the protein
+ checked = 0, ///< checked ptm
+ ptm_island_id = 1, ///< ptm_island_id
+ accession = 2, ///< protein accession
+ description = 3, ///< protein description
+ ptm_position_list = 4, ///< ptm position list
+ spectrum = 5, ///< count sample scans
+ ptm_spectrum = 6, ///< count scan with ptm
+ sequence = 7, ///< unique sequence count
+ multiptm = 8, ///< count multi ptm peptide match
+ ptm_island_start = 9, ///< start position of the ptm island on the protein
ptm_island_length = 10, ///< length of the ptm island
last = 11,
@@ -68,8 +68,8 @@ class PtmIslandTableModel : public QAbstractTableModel
~PtmIslandTableModel();
void setIdentificationGroup(IdentificationGroup *p_identification_group);
- IdentificationGroup * getIdentificationGroup();
-
+ IdentificationGroup *getIdentificationGroup();
+
virtual int
rowCount(const QModelIndex &parent = QModelIndex()) const override;
virtual int
@@ -81,9 +81,8 @@ class PtmIslandTableModel : public QAbstractTableModel
static const QString getTitle(PtmIslandListColumn column);
static const QString getDescription(PtmIslandListColumn column);
- static PtmIslandListColumn
- getPtmIslandListColumn(std::int8_t column);
-
+ static PtmIslandListColumn getPtmIslandListColumn(std::int8_t column);
+
const PtmGroupingExperiment *getPtmGroupingExperiment() const;
public slots:
--
GitLab
From dec86f8acdbedf3a5d8e5aa9ad19f37acdf2f1d7 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 10:39:57 +0100
Subject: [PATCH 11/18] add msrun to xic export
---
src/gui/xic_view/xic_box/xicbox.cpp | 6 ++++++
src/gui/xic_view/xic_box/xicbox.h | 1 +
src/output/ods/xicareasheet.cpp | 4 ++--
src/resources/icons/apache/firefox/check_icon.svg | 9 +++++++--
4 files changed, 16 insertions(+), 4 deletions(-)
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index 1ed5dec4..5533d0e0 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/src/gui/xic_view/xic_box/xicbox.cpp
@@ -337,6 +337,12 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
ui->isotopic_distribution_spinbox->value());
}
+MsRunSp
+XicBox::getMsRunSp()
+{
+ return _msrun_sp;
+}
+
void
XicBox::setXic(std::vector<pappso::XicCstSPtr> xic_sp_list)
{
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 2eff49b8..56fe9318 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/src/gui/xic_view/xic_box/xicbox.h
@@ -69,6 +69,7 @@ class XicBox : public QWidget
void setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
MsRunSp msrun_sp);
std::vector<XicBoxNaturalIsotope> getNaturalIsotopList() const;
+ MsRunSp getMsRunSp();
signals:
void loadXic(MsRunSp p_msrun,
diff --git a/src/output/ods/xicareasheet.cpp b/src/output/ods/xicareasheet.cpp
index 1e790aad..fdf87642 100644
--- a/src/output/ods/xicareasheet.cpp
+++ b/src/output/ods/xicareasheet.cpp
@@ -103,7 +103,7 @@ XicAreaSheet::writeAreaPeackdata(XicBox *xic_box)
for(pappso::TracePeakCstSPtr trace : isotope.detected_peak_list)
{
mp_writer->writeLine();
- mp_writer->writeCell("");
+ mp_writer->writeCell(xic_box->getMsRunSp()->getFileName());
mp_writer->writeCell(trace->getArea());
mp_writer->writeCell(trace->getLeftBoundary().x);
mp_writer->writeCell(trace->getMaxXicElement().x);
@@ -122,7 +122,7 @@ XicAreaSheet::writeXicAllData(XicBox *xic_box)
for(std::size_t i = 0; i < isotope.xic_sp->xValues().size(); i++)
{
mp_writer->writeLine();
- mp_writer->writeCell("");
+ mp_writer->writeCell(xic_box->getMsRunSp()->getFileName());
mp_writer->writeCell(
int(isotope.peptide_natural_isotope_sp->getIsotopeNumber()));
mp_writer->writeCell(isotope.xic_sp->xValues().at(i));
diff --git a/src/resources/icons/apache/firefox/check_icon.svg b/src/resources/icons/apache/firefox/check_icon.svg
index 29832431..4ab81080 100644
--- a/src/resources/icons/apache/firefox/check_icon.svg
+++ b/src/resources/icons/apache/firefox/check_icon.svg
@@ -1,2 +1,7 @@
-
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" focusable="false" width="1em" height="1em" style="-ms-transform: rotate(360deg); -webkit-transform: rotate(360deg); transform: rotate(360deg);" preserveAspectRatio="xMidYMid meet" viewBox="0 0 512 512"><path fill="#60bc03" d="M484.065 66.324l-71.534-41.759c-8.811-5.143-20.123-2.17-25.266 6.641L211.883 331.642L96.414 264.236c-7.143-4.17-16.314-1.76-20.484 5.384l-45.284 77.573c-4.17 7.143-1.76 16.314 5.384 20.484l205.968 120.235c7.143 4.17 16.314 1.76 20.484-5.384l1.669-2.86c.034-.056.074-.106.107-.163L490.706 91.59c5.143-8.811 2.17-20.123-6.641-25.266z"/><rect x="0" y="0" width="512" height="512" fill="rgba(0, 0, 0, 0)" /></svg>
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!-- Generator: Adobe Illustrator 19.2.0, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" focusable="false" width="1em" height="1em" style="-ms-transform: rotate(360deg); -webkit-transform: rotate(360deg); transform: rotate(360deg);" preserveAspectRatio="xMidYMid meet" viewBox="0 0 512 512">
+ <path fill="#60bc03" d="M484.065 66.324l-71.534-41.759c-8.811-5.143-20.123-2.17-25.266 6.641L211.883 331.642L96.414 264.236c-7.143-4.17-16.314-1.76-20.484 5.384l-45.284 77.573c-4.17 7.143-1.76 16.314 5.384 20.484l205.968 120.235c7.143 4.17 16.314 1.76 20.484-5.384l1.669-2.86c.034-.056.074-.106.107-.163L490.706 91.59c5.143-8.811 2.17-20.123-6.641-25.266z"/>
+ <rect x="0" y="0" width="512" height="512" fill="rgba(0, 0, 0, 0)" />
+</svg>
--
GitLab
From f8582d20222acbde5762325f29172332cf8effc5 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 11:58:18 +0100
Subject: [PATCH 12/18] Correct wrong index protein details from PTM island
---
src/grouping/ptm/ptmgroupingexperiment.cpp | 2 +-
src/grouping/ptm/ptmgroupingexperiment.h | 2 +-
src/grouping/ptm/ptmisland.cpp | 6 +++---
src/grouping/ptm/ptmisland.h | 6 +++---
.../ptm_island_list_view/ptmislandlistwindow.cpp | 14 +++++++++-----
.../ptm_island_list_view/ptmislandproxymodel.cpp | 7 ++++---
6 files changed, 21 insertions(+), 16 deletions(-)
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index 827a8d57..2e25dcf0 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -152,7 +152,7 @@ PtmGroupingExperiment::setValidationState(ValidationState validation_state)
_peptide_validation_state = validation_state;
}
void
-PtmGroupingExperiment::addProteinMatch(const ProteinMatch *p_protein_match)
+PtmGroupingExperiment::addProteinMatch(ProteinMatch *p_protein_match)
{
if(p_protein_match->getValidationState() >= _peptide_validation_state)
{
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index bf1cdfae..7ceaeb83 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -50,7 +50,7 @@ class PtmGroupingExperiment
* experiment
*/
void setValidationState(ValidationState validation_state);
- void addProteinMatch(const ProteinMatch *p_protein_match);
+ void addProteinMatch(ProteinMatch *p_protein_match);
void startGrouping();
/** @brief get the ptm island subgroup list
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 25568a90..6f7bfc41 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -36,7 +36,7 @@
#include <pappsomspp/utils.h>
#include <set>
-PtmIsland::PtmIsland(const ProteinMatch *p_protein_match, unsigned int position)
+PtmIsland::PtmIsland(ProteinMatch *p_protein_match, unsigned int position)
: _protein_match_p(p_protein_match)
{
_position_list.push_back(position);
@@ -142,8 +142,8 @@ PtmIsland::setProteinNumber(unsigned int prot_number)
{
_prot_number = prot_number;
}
-const ProteinMatch *
-PtmIsland::getProteinMatch() const
+ProteinMatch *
+PtmIsland::getProteinMatch()
{
return _protein_match_p;
}
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index e02d24fa..02700617 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -48,7 +48,7 @@ typedef std::shared_ptr<PtmIsland> PtmIslandSp;
class PtmIsland
{
public:
- PtmIsland(const ProteinMatch *p_protein_match, unsigned int position);
+ PtmIsland(ProteinMatch *p_protein_match, unsigned int position);
PtmIsland(const PtmIsland &other);
~PtmIsland();
void addPeptideMatch(const PeptideMatch &peptide_match);
@@ -60,7 +60,7 @@ class PtmIsland
bool containsPeptideMatch(const PeptideMatch &element) const;
std::vector<std::size_t> getSampleScanSet() const;
- const ProteinMatch *getProteinMatch() const;
+ ProteinMatch *getProteinMatch();
unsigned int getProteinStartPosition() const;
void setPtmIslandSubgroup(PtmIslandSubgroup *p_ptm_island_subgroup);
void setProteinNumber(unsigned int prot_number);
@@ -82,7 +82,7 @@ class PtmIsland
const std::vector<PeptideMatch> &getPeptideMatchList() const;
private:
- const ProteinMatch *_protein_match_p;
+ ProteinMatch *_protein_match_p;
std::vector<PeptideMatch> _peptide_match_list;
// std::vector<std::size_t> _sample_scan_set;
std::vector<unsigned int> _position_list;
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 8d1b86fa..2514d5cf 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -186,15 +186,19 @@ PtmIslandListWindow::getPtmIslandListColumnDisplay(
void
PtmIslandListWindow::setColumnMenuList()
{
- PtmIslandListQActionColumn *p_action;
- for(int i = 0; i < _ptm_table_model_p->columnCount(); i++)
+ if(ui->menu_Columns->isEmpty())
{
- p_action = new PtmIslandListQActionColumn(
- this, PtmIslandTableModel::getPtmIslandListColumn(i));
- ui->menu_Columns->addAction(p_action);
+ PtmIslandListQActionColumn *p_action;
+ for(int i = 0; i < _ptm_table_model_p->columnCount(); i++)
+ {
+ p_action = new PtmIslandListQActionColumn(
+ this, PtmIslandTableModel::getPtmIslandListColumn(i));
+ ui->menu_Columns->addAction(p_action);
+ }
}
}
+
void
PtmIslandListWindow::doNotCheckedHide(bool hide)
{
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index 024cb563..bd90592f 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -207,9 +207,10 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
int col = source_index.column();
ProteinMatch *p_protein_match =
- _p_ptm_island_table_model->getIdentificationGroup()
- ->getProteinMatchList()
- .at(row);
+ _p_ptm_island_table_model->getPtmGroupingExperiment()
+ ->getPtmIslandList()
+ .at(row)
+ ->getProteinMatch();
if(col == (std::int8_t)PtmIslandListColumn::checked)
{
--
GitLab
From 99c148fd1302cee451bc86128e6d45a21bb57ac2 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 14:16:35 +0100
Subject: [PATCH 13/18] Use same object for Protein checked in PTM and Protein
windows
---
.../ptmislandlistwindow.cpp | 4 ++
.../ptmislandlistwindow.h | 3 +-
.../ptmislandproxymodel.cpp | 6 +-
.../ptmislandtablemodel.cpp | 4 +-
src/output/masschroqml.cpp | 72 ++++++++++---------
5 files changed, 46 insertions(+), 43 deletions(-)
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 2514d5cf..63f1c128 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -198,6 +198,10 @@ PtmIslandListWindow::setColumnMenuList()
}
}
+void PtmIslandListWindow::edited()
+{
+ _project_window->doIdentificationGroupEdited(_p_identification_group);
+}
void
PtmIslandListWindow::doNotCheckedHide(bool hide)
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.h b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
index a4cfea46..6130ba50 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.h
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.h
@@ -79,7 +79,8 @@ class PtmIslandListWindow : public QMainWindow
void setPtmIslandListColumnDisplay(PtmIslandListColumn column, bool toggled);
bool getPtmIslandListColumnDisplay(PtmIslandListColumn column) const;
void setColumnMenuList();
-
+ void edited();
+
public slots:
void
doIdentificationPtmGroupGrouped(IdentificationGroup *p_identification_group);
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index bd90592f..a67a3d0c 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -83,10 +83,7 @@ PtmIslandProxyModel::filterAcceptsRow(int source_row,
_p_ptm_island_table_model->getPtmGroupingExperiment()
->getPtmIslandList()
.at(source_row);
- ProteinMatch *protein_match =
- _p_ptm_island_table_model->getIdentificationGroup()
- ->getProteinMatchList()
- .at(source_row);
+ ProteinMatch *protein_match = sp_ptm_island->getProteinMatch();
// qDebug() << "Prote
// qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match "
// << source_row;
@@ -222,6 +219,7 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
{
p_protein_match->setChecked(true);
}
+ _p_ptm_island_list_window->edited();
}
else if((col == (std::int8_t)PtmIslandListColumn::accession) ||
(col == (std::int8_t)PtmIslandListColumn::description))
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index ef47c324..1af9875f 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -234,9 +234,7 @@ PtmIslandTableModel::data(const QModelIndex &index, int role) const
if(col == (std::int8_t)
PtmIslandListColumn::checked) // add a checkbox to cell(1,0)
{
- if(_p_identification_group->getProteinMatchList()
- .at(row)
- ->isChecked())
+ if(getPtmGroupingExperiment()->getPtmIslandList().at(row)->getProteinMatch()->isChecked())
{
return Qt::Checked;
}
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 3b6fcb9d..10dd89fe 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -263,47 +263,49 @@ MassChroQml::writeQuantificationTraces()
void
MassChroQml::writeQuantify()
{
- for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
+ for(MsRunAlignmentGroupSp group_sp : m_params.alignment_groups)
{
- //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
- _output_stream->writeStartElement("quantify");
- _output_stream->writeAttribute("id", "q1");
-
- _output_stream->writeAttribute("withingroup", group_sp->getMsRunAlignmentGroupName());
- _output_stream->writeAttribute("quantification_method_id", "quant1");
- //<peptides_in_peptide_list mode="real_or_mean" />
- //</quantify>
- //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
- //<peptides_in_peptide_list mode="post_matching"
- // isotope_label_refs="iso1 iso2" />
-
- _output_stream->writeStartElement("peptides_in_peptide_list");
- _output_stream->writeAttribute("mode", "post_matching");
- _output_stream->writeAttribute("ni_min_abundance", "0.8");
+ //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
+ _output_stream->writeStartElement("quantify");
+ _output_stream->writeAttribute("id", "q1");
- LabelingMethod *p_labeling_method =
- _sp_project.get()->getLabelingMethodSp().get();
- if(p_labeling_method != nullptr)
- {
- QStringList isotope_label_ref;
- for(const Label *p_label : p_labeling_method->getLabelList())
+ _output_stream->writeAttribute("withingroup",
+ group_sp->getMsRunAlignmentGroupName());
+ _output_stream->writeAttribute("quantification_method_id", "quant1");
+ //<peptides_in_peptide_list mode="real_or_mean" />
+ //</quantify>
+ //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
+ //<peptides_in_peptide_list mode="post_matching"
+ // isotope_label_refs="iso1 iso2" />
+
+ _output_stream->writeStartElement("peptides_in_peptide_list");
+ _output_stream->writeAttribute("mode", "post_matching");
+ _output_stream->writeAttribute("ni_min_abundance", "0.8");
+
+ LabelingMethod *p_labeling_method =
+ _sp_project.get()->getLabelingMethodSp().get();
+ if(p_labeling_method != nullptr)
{
- isotope_label_ref << p_label->getXmlId();
+ QStringList isotope_label_ref;
+ for(const Label *p_label : p_labeling_method->getLabelList())
+ {
+ isotope_label_ref << p_label->getXmlId();
+ }
+ _output_stream->writeAttribute("isotope_label_refs",
+ isotope_label_ref.join(" "));
}
- _output_stream->writeAttribute("isotope_label_refs",
- isotope_label_ref.join(" "));
- }
- _output_stream->writeEndElement();
+ _output_stream->writeEndElement();
- _output_stream->writeComment(
- "<mz_list>732.317 449.754 552.234 464.251 "
- "381.577 569.771 575.256</mz_list>");
- _output_stream->writeComment(
- "<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt "
- "mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
+ _output_stream->writeComment(
+ "<mz_list>732.317 449.754 552.234 464.251 "
+ "381.577 569.771 575.256</mz_list>");
+ _output_stream->writeComment(
+ "<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n "
+ "<mzrt "
+ "mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
- //</quantify>
- _output_stream->writeEndElement();
+ //</quantify>
+ _output_stream->writeEndElement();
}
}
--
GitLab
From d043d22b72d6dbb3aa48d966a01ffc8e51b46bd4 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 14:39:00 +0100
Subject: [PATCH 14/18] Add Xic export settings
---
src/gui/edit/edit_settings/edit_settings.ui | 34 +++++++++++++++++++--
src/gui/edit/edit_settings/editsettings.cpp | 22 +++++++++++++
src/gui/workerthread.cpp | 21 +++++++++++--
src/output/ods/xicareasheet.cpp | 6 ++--
4 files changed, 76 insertions(+), 7 deletions(-)
diff --git a/src/gui/edit/edit_settings/edit_settings.ui b/src/gui/edit/edit_settings/edit_settings.ui
index d28c7a50..397e318a 100644
--- a/src/gui/edit/edit_settings/edit_settings.ui
+++ b/src/gui/edit/edit_settings/edit_settings.ui
@@ -9,8 +9,8 @@
<rect>
<x>0</x>
<y>0</y>
- <width>366</width>
- <height>348</height>
+ <width>422</width>
+ <height>395</height>
</rect>
</property>
<property name="windowTitle">
@@ -61,6 +61,36 @@
</item>
</layout>
</item>
+ <item>
+ <widget class="QGroupBox" name="groupBox">
+ <property name="title">
+ <string>XIC export</string>
+ </property>
+ <layout class="QHBoxLayout" name="horizontalLayout_4">
+ <item>
+ <widget class="QRadioButton" name="radioButton_3">
+ <property name="text">
+ <string>Area onl&y</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="all_point_radioButton">
+ <property name="text">
+ <string>All points only</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="area_radioButton">
+ <property name="text">
+ <string>Area + All points</string>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ </item>
<item>
<widget class="QGroupBox" name="timstof_setting_group">
<property name="title">
diff --git a/src/gui/edit/edit_settings/editsettings.cpp b/src/gui/edit/edit_settings/editsettings.cpp
index b1e42c80..7b013f9f 100644
--- a/src/gui/edit/edit_settings/editsettings.cpp
+++ b/src/gui/edit/edit_settings/editsettings.cpp
@@ -53,6 +53,17 @@ EditSettings::EditSettings(MainWindow *parent)
{
ui->xic_reader_buffered_button->setChecked(false);
}
+ QString xic_export_type =
+ settings.value("export/xic_files", "area").toString();
+ ui->area_radioButton->setChecked(true);
+ if(xic_export_type == "all")
+ {
+ ui->all_point_radioButton->setChecked(true);
+ }
+ else if(xic_export_type == "both")
+ {
+ ui->radioButton_3->setChecked(true);
+ }
QString tandemwrapper_path =
settings.value("timstof/tandemwrapper_path", "").toString();
@@ -96,6 +107,17 @@ EditSettings::done(int r)
}
settings.setValue("global/xic_extractor", xic_extraction_method);
+ QString xic_export_type = "area";
+ if(ui->all_point_radioButton->isChecked())
+ {
+ xic_export_type = "all";
+ }
+ else if(ui->radioButton_3->isChecked())
+ {
+ xic_export_type = "both";
+ }
+ settings.setValue("export/xic_files", xic_export_type);
+
QString tandemwrapper_path = ui->tandemwrapper_path_line->text();
QFileInfo tandemwrapper_file = QFileInfo(tandemwrapper_path);
if(tandemwrapper_file.exists() && tandemwrapper_file.isExecutable())
diff --git a/src/gui/workerthread.cpp b/src/gui/workerthread.cpp
index 58eaa0d7..2892484a 100644
--- a/src/gui/workerthread.cpp
+++ b/src/gui/workerthread.cpp
@@ -879,10 +879,25 @@ WorkerThread::doWriteXicAreaInCsv(QString filename,
CalcWriterInterface *p_writer = nullptr;
emit loadingMessage(tr("writing TSV files, please wait"));
+ QSettings settings;
+ QString xic_export_file =
+ settings.value("export/xic_files", "area").toString();
p_writer = new TsvDirectoryWriter(filename);
- XicAreaSheet(p_writer, xic_boxs);
- bool all_data = true;
- XicAreaSheet(p_writer, xic_boxs, all_data);
+ if(xic_export_file == "both")
+ {
+ XicAreaSheet(p_writer, xic_boxs);
+ bool all_data = true;
+ XicAreaSheet(p_writer, xic_boxs, all_data);
+ }
+ else if(xic_export_file == "all")
+ {
+ bool all_data = true;
+ XicAreaSheet(p_writer, xic_boxs, all_data);
+ }
+ else // xic_export_file == "area"
+ {
+ XicAreaSheet(p_writer, xic_boxs);
+ }
p_writer->close();
emit exportXicToCsvFinished();
}
diff --git a/src/output/ods/xicareasheet.cpp b/src/output/ods/xicareasheet.cpp
index fdf87642..c61699b7 100644
--- a/src/output/ods/xicareasheet.cpp
+++ b/src/output/ods/xicareasheet.cpp
@@ -103,7 +103,8 @@ XicAreaSheet::writeAreaPeackdata(XicBox *xic_box)
for(pappso::TracePeakCstSPtr trace : isotope.detected_peak_list)
{
mp_writer->writeLine();
- mp_writer->writeCell(xic_box->getMsRunSp()->getFileName());
+ mp_writer->writeCell(
+ QFileInfo(xic_box->getMsRunSp()->getFileName()).fileName());
mp_writer->writeCell(trace->getArea());
mp_writer->writeCell(trace->getLeftBoundary().x);
mp_writer->writeCell(trace->getMaxXicElement().x);
@@ -122,7 +123,8 @@ XicAreaSheet::writeXicAllData(XicBox *xic_box)
for(std::size_t i = 0; i < isotope.xic_sp->xValues().size(); i++)
{
mp_writer->writeLine();
- mp_writer->writeCell(xic_box->getMsRunSp()->getFileName());
+ mp_writer->writeCell(
+ QFileInfo(xic_box->getMsRunSp()->getFileName()).fileName());
mp_writer->writeCell(
int(isotope.peptide_natural_isotope_sp->getIsotopeNumber()));
mp_writer->writeCell(isotope.xic_sp->xValues().at(i));
--
GitLab
From eed8eb06bcab91d8e6f69ce200c19291b6cb1308 Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 16:35:11 +0100
Subject: [PATCH 15/18] Export only cheched ptm island
---
src/grouping/ptm/ptmisland.cpp | 10 ++++++++++
src/grouping/ptm/ptmisland.h | 3 +++
.../ptm_island_list_view/ptmislandlistwindow.cpp | 2 +-
.../ptm_island_list_view/ptmislandproxymodel.cpp | 16 +++++++---------
.../ptm_island_list_view/ptmislandproxymodel.h | 2 +-
.../ptm_island_list_view/ptmislandtablemodel.cpp | 2 +-
src/output/ods/ptm/ptmislandsheet.cpp | 5 ++++-
7 files changed, 27 insertions(+), 13 deletions(-)
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index 6f7bfc41..cfd53b1b 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -62,6 +62,16 @@ PtmIsland::size() const
return _protein_stop - _protein_start;
}
+bool PtmIsland::isChecked()
+{
+ return m_checked;
+}
+
+void PtmIsland::setChecked(bool check_status)
+{
+ m_checked = check_status;
+}
+
unsigned int
PtmIsland::countSampleScanMultiPtm(
const PtmGroupingExperiment *p_ptm_grouping_experiment) const
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index 02700617..a865d840 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -76,6 +76,8 @@ class PtmIsland
const PtmGroupingExperiment *p_ptm_grouping_experiment) const;
unsigned int getStart() const;
unsigned int size() const;
+ void setChecked(bool check_status);
+ bool isChecked();
std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
@@ -91,6 +93,7 @@ class PtmIsland
/** @brief protein rank number in the PTM subgroup
* */
unsigned int _prot_number = 0;
+ bool m_checked = true;
PtmIslandSubgroup *_ptm_island_subgroup_p = nullptr;
};
diff --git a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
index 63f1c128..caf4eb99 100644
--- a/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandlistwindow.cpp
@@ -200,7 +200,7 @@ PtmIslandListWindow::setColumnMenuList()
void PtmIslandListWindow::edited()
{
- _project_window->doIdentificationGroupEdited(_p_identification_group);
+ _project_window->doPtmIslandGrouping(_p_identification_group);
}
void
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
index a67a3d0c..252fad46 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.cpp
@@ -83,13 +83,12 @@ PtmIslandProxyModel::filterAcceptsRow(int source_row,
_p_ptm_island_table_model->getPtmGroupingExperiment()
->getPtmIslandList()
.at(source_row);
- ProteinMatch *protein_match = sp_ptm_island->getProteinMatch();
// qDebug() << "Prote
// qDebug() << "ProteinTableProxyModel::filterAcceptsRow protein_match "
// << source_row;
if(m_hideNotChecked)
{
- if(!protein_match->isChecked())
+ if(!sp_ptm_island->isChecked())
{
return false;
}
@@ -203,27 +202,26 @@ PtmIslandProxyModel::onTableClicked(const QModelIndex &index)
int row = source_index.row();
int col = source_index.column();
- ProteinMatch *p_protein_match =
- _p_ptm_island_table_model->getPtmGroupingExperiment()
+ PtmIslandSp ptm_island_sp = _p_ptm_island_table_model->getPtmGroupingExperiment()
->getPtmIslandList()
- .at(row)
- ->getProteinMatch();
+ .at(row);
if(col == (std::int8_t)PtmIslandListColumn::checked)
{
- if(p_protein_match->isChecked())
+ if(ptm_island_sp->isChecked())
{
- p_protein_match->setChecked(false);
+ ptm_island_sp->setChecked(false);
}
else
{
- p_protein_match->setChecked(true);
+ ptm_island_sp->setChecked(true);
}
_p_ptm_island_list_window->edited();
}
else if((col == (std::int8_t)PtmIslandListColumn::accession) ||
(col == (std::int8_t)PtmIslandListColumn::description))
{
+ ProteinMatch *p_protein_match = ptm_island_sp->getProteinMatch();
_p_ptm_island_list_window->askProteinDetailView(p_protein_match);
}
else
diff --git a/src/gui/ptm_island_list_view/ptmislandproxymodel.h b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
index 1d8acdce..0f6b02d1 100644
--- a/src/gui/ptm_island_list_view/ptmislandproxymodel.h
+++ b/src/gui/ptm_island_list_view/ptmislandproxymodel.h
@@ -63,7 +63,7 @@ class PtmIslandProxyModel : public QSortFilterProxyModel
PtmIslandListWindow *_p_ptm_island_list_window;
PtmIslandTableModel *_p_ptm_island_table_model;
std::vector<bool> m_column_display;
- bool m_hideNotChecked = true;
+ bool m_hideNotChecked = false;
QString _search_on;
QString _ptm_search_string;
};
diff --git a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
index 1af9875f..45dc6ce3 100644
--- a/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
+++ b/src/gui/ptm_island_list_view/ptmislandtablemodel.cpp
@@ -234,7 +234,7 @@ PtmIslandTableModel::data(const QModelIndex &index, int role) const
if(col == (std::int8_t)
PtmIslandListColumn::checked) // add a checkbox to cell(1,0)
{
- if(getPtmGroupingExperiment()->getPtmIslandList().at(row)->getProteinMatch()->isChecked())
+ if(getPtmGroupingExperiment()->getPtmIslandList().at(row)->isChecked())
{
return Qt::Checked;
}
diff --git a/src/output/ods/ptm/ptmislandsheet.cpp b/src/output/ods/ptm/ptmislandsheet.cpp
index 15c6f86b..97d18c85 100644
--- a/src/output/ods/ptm/ptmislandsheet.cpp
+++ b/src/output/ods/ptm/ptmislandsheet.cpp
@@ -142,7 +142,10 @@ PtmIslandSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
for(auto ptm_island_sp : _p_ptm_grouping_experiment->getPtmIslandList())
{
qDebug();
- ptm_island_list.push_back(ptm_island_sp);
+ if(ptm_island_sp->isChecked())
+ {
+ ptm_island_list.push_back(ptm_island_sp);
+ }
}
qDebug();
std::sort(ptm_island_list.begin(),
--
GitLab
From 05e670eea19dac2cb72100767942d3e43c1dc40a Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Wed, 28 Oct 2020 16:39:10 +0100
Subject: [PATCH 16/18] Export PTm spectra of checked ptm island
---
src/grouping/ptm/ptmisland.cpp | 2 +-
src/grouping/ptm/ptmisland.h | 2 +-
src/output/ods/ptm/ptmspectrasheet.cpp | 72 +++++++++++++++-----------
3 files changed, 43 insertions(+), 33 deletions(-)
diff --git a/src/grouping/ptm/ptmisland.cpp b/src/grouping/ptm/ptmisland.cpp
index cfd53b1b..10b5c86a 100644
--- a/src/grouping/ptm/ptmisland.cpp
+++ b/src/grouping/ptm/ptmisland.cpp
@@ -62,7 +62,7 @@ PtmIsland::size() const
return _protein_stop - _protein_start;
}
-bool PtmIsland::isChecked()
+bool PtmIsland::isChecked() const
{
return m_checked;
}
diff --git a/src/grouping/ptm/ptmisland.h b/src/grouping/ptm/ptmisland.h
index a865d840..9dc609af 100644
--- a/src/grouping/ptm/ptmisland.h
+++ b/src/grouping/ptm/ptmisland.h
@@ -77,7 +77,7 @@ class PtmIsland
unsigned int getStart() const;
unsigned int size() const;
void setChecked(bool check_status);
- bool isChecked();
+ bool isChecked() const;
std::vector<PtmSampleScanSp> getPtmSampleScanSpList() const;
diff --git a/src/output/ods/ptm/ptmspectrasheet.cpp b/src/output/ods/ptm/ptmspectrasheet.cpp
index 21e2523a..b79114dd 100644
--- a/src/output/ods/ptm/ptmspectrasheet.cpp
+++ b/src/output/ods/ptm/ptmspectrasheet.cpp
@@ -237,7 +237,10 @@ PtmSpectraSheet::writeBestPeptideEvidence(
// return _ptm_sample_scan_list.at(row).get()->getObservedPtmPositionList();
for(const PtmIsland *ptm_island : ptmisland_occurence_list)
{
- position_list << ptm_island->getGroupingId();
+ if(ptm_island->isChecked())
+ {
+ position_list << ptm_island->getGroupingId();
+ }
}
_p_writer->writeCell(position_list.join(" "));
@@ -286,41 +289,48 @@ PtmSpectraSheet::writePtmIslandSubgroupSp(
for(PtmIslandSp ptm_island_sp :
ptm_island_subgroup_sp.get()->getPtmIslandList())
{
-
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- for(PeptideMatch peptide_match :
- ptm_island_sp.get()->getPeptideMatchList())
+ if(ptm_island_sp->isChecked())
{
-
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- std::vector<PtmSampleScanOccurence>::iterator it_ptm =
- ptm_sample_scan_occurence_list.begin();
- std::vector<PtmSampleScanOccurence>::iterator it_ptm_end =
- ptm_sample_scan_occurence_list.end();
- while((it_ptm != it_ptm_end) &&
- (it_ptm->ptm_sample_scan.add(peptide_match) == false))
- {
- // peptide added
- it_ptm++;
- }
- if(it_ptm == it_ptm_end)
+ for(PeptideMatch peptide_match :
+ ptm_island_sp.get()->getPeptideMatchList())
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- // peptide NOT added
- PtmSampleScanOccurence new_occurence = {
- PtmSampleScan(peptide_match), std::set<const PtmIsland *>()};
- new_occurence.ptmisland_occurence_list.insert(
- ptm_island_sp.get());
- ptm_sample_scan_occurence_list.push_back(new_occurence);
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- }
- else
- {
- // peptide added
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
- it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ std::vector<PtmSampleScanOccurence>::iterator it_ptm =
+ ptm_sample_scan_occurence_list.begin();
+ std::vector<PtmSampleScanOccurence>::iterator it_ptm_end =
+ ptm_sample_scan_occurence_list.end();
+ while((it_ptm != it_ptm_end) &&
+ (it_ptm->ptm_sample_scan.add(peptide_match) == false))
+ {
+ // peptide added
+ it_ptm++;
+ }
+ if(it_ptm == it_ptm_end)
+ {
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+ << __LINE__;
+ // peptide NOT added
+ PtmSampleScanOccurence new_occurence = {
+ PtmSampleScan(peptide_match),
+ std::set<const PtmIsland *>()};
+ new_occurence.ptmisland_occurence_list.insert(
+ ptm_island_sp.get());
+ ptm_sample_scan_occurence_list.push_back(new_occurence);
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+ << __LINE__;
+ }
+ else
+ {
+ // peptide added
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+ << __LINE__;
+ it_ptm->ptmisland_occurence_list.insert(ptm_island_sp.get());
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " "
+ << __LINE__;
+ }
}
}
}
--
GitLab
From f5c97f08061830c1d1426ff9305efc21e673795c Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Thu, 29 Oct 2020 12:02:56 +0100
Subject: [PATCH 17/18] Correct best msRun issues (clicked didn't work,
reference didn't used in mcqml file)
---
.../export_masschroq_dialog.ui | 23 ++++++--
.../exportmasschroqdialog.cpp | 53 +++++++++++--------
.../exportmasschroqdialog.h | 1 +
.../masschroqfileparameters.h | 1 -
4 files changed, 51 insertions(+), 27 deletions(-)
diff --git a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
index 086b5333..b648eba5 100644
--- a/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
+++ b/src/gui/export/export_masschroq_dialog/export_masschroq_dialog.ui
@@ -120,7 +120,7 @@
<item>
<widget class="QPushButton" name="pushButton">
<property name="text">
- <string>Best</string>
+ <string>Find Best</string>
</property>
</widget>
</item>
@@ -464,8 +464,8 @@
<slot>doBrowseMsrunDirectory()</slot>
<hints>
<hint type="sourcelabel">
- <x>195</x>
- <y>381</y>
+ <x>214</x>
+ <y>421</y>
</hint>
<hint type="destinationlabel">
<x>736</x>
@@ -473,6 +473,22 @@
</hint>
</hints>
</connection>
+ <connection>
+ <sender>msrun_list_combo_box</sender>
+ <signal>activated(int)</signal>
+ <receiver>ExportMasschroqDialog</receiver>
+ <slot>doUpdateReferenceInSelectedGroup(int)</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>417</x>
+ <y>432</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>817</x>
+ <y>444</y>
+ </hint>
+ </hints>
+ </connection>
</connections>
<slots>
<slot>reject()</slot>
@@ -481,5 +497,6 @@
<slot>doBrowseMsrunDirectory()</slot>
<slot>doFindBestMsrunForAlignment()</slot>
<slot>doShowMsRunsInAlignmentGroup(QModelIndex)</slot>
+ <slot>doUpdateReferenceInSelectedGroup(int)</slot>
</slots>
</ui>
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
index 177f8f25..9458e97b 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.cpp
@@ -157,16 +157,6 @@ ExportMasschroqDialog::getMasschroqFileParameters() const
params.xic_extraction_method =
ui->xic_extraction_method_widget->getXicExtractionMethod();
-
- int index = ui->msrun_list_combo_box->currentIndex();
- if(index != -1)
- {
- MsRunSp msrun_sp =
- qvariant_cast<MsRunSp>(ui->msrun_list_combo_box->itemData(index));
- params.msrun_alignment_reference = msrun_sp;
- }
-
-
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< (int)params.xic_extraction_method;
return params;
@@ -278,17 +268,17 @@ ExportMasschroqDialog::setBestMsrunForAlignment(MsRunSp best_msrun_sp)
mp_main->hideWaitingMessage();
if(best_msrun_sp != nullptr)
{
- qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
- << best_msrun_sp.get()->getXmlId();
+ qDebug() << best_msrun_sp.get();
- for(int index = 0; index < ui->msrun_list_combo_box->count(); index++)
+ int index = 0;
+ for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
{
- MsRunSp msrun_sp =
- qvariant_cast<MsRunSp>(ui->msrun_list_combo_box->itemData(index));
- if(msrun_sp.get() == best_msrun_sp.get())
+ if(ms_run == best_msrun_sp)
{
ui->msrun_list_combo_box->setCurrentIndex(index);
+ msp_selected_group->setMsRunReference(best_msrun_sp);
}
+ index++;
}
}
}
@@ -346,16 +336,33 @@ ExportMasschroqDialog::doShowMsRunsInAlignmentGroup(QModelIndex index)
}
if(msp_selected_group->getMsRunReference() != nullptr)
{
- std::list<MsRunSp>::iterator it;
- it = std::find(msp_selected_group->getMsRunsInAlignmentGroup().begin(),
- msp_selected_group->getMsRunsInAlignmentGroup().end(),
- msp_selected_group->getMsRunReference());
- int idx = std::distance(
- msp_selected_group->getMsRunsInAlignmentGroup().begin(), it);
- ui->msrun_list_combo_box->setCurrentIndex(idx);
+ int index = 0;
+ for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
+ {
+ if(ms_run == msp_selected_group->getMsRunReference())
+ {
+ ui->msrun_list_combo_box->setCurrentIndex(index);
+ }
+ index++;
+ }
}
else
{
ui->msrun_list_combo_box->setCurrentIndex(-1);
}
}
+
+void
+ExportMasschroqDialog::doUpdateReferenceInSelectedGroup(int index)
+{
+ int temp_index = 0;
+ for(MsRunSp ms_run : msp_selected_group->getMsRunsInAlignmentGroup())
+ {
+ if(temp_index == index)
+ {
+ msp_selected_group->setMsRunReference(ms_run);
+ }
+ temp_index++;
+ }
+ qDebug() << index;
+}
diff --git a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
index 94f10f30..1c76f2a8 100644
--- a/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
+++ b/src/gui/export/export_masschroq_dialog/exportmasschroqdialog.h
@@ -76,6 +76,7 @@ class ExportMasschroqDialog : public QDialog
void doBrowseMsrunDirectory();
void doFindBestMsrunForAlignment();
void doShowMsRunsInAlignmentGroup(QModelIndex index);
+ void doUpdateReferenceInSelectedGroup(int index);
private:
Ui::ExportMasschroqDialog *ui;
diff --git a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
index 55b61563..9015506e 100644
--- a/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
+++ b/src/gui/export/export_masschroq_dialog/masschroqfileparameters.h
@@ -61,6 +61,5 @@ struct MasschroqFileParameters
pappso::XicExtractMethod xic_extraction_method; // sum or max
- MsRunSp msrun_alignment_reference;
std::vector<MsRunAlignmentGroupSp> alignment_groups;
};
--
GitLab
From 490c6adaba7a2324b1ed6e57d63807b987dc7aab Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Mon, 2 Nov 2020 09:37:22 +0100
Subject: [PATCH 18/18] Correct TDF folder loading issue : Identification
didn't work with the folder
---
src/core/tandem_run/tandembatchprocess.cpp | 21 ++++++++++++++++---
src/gui/tandem_run_dialog/tandemrundialog.cpp | 10 +++++----
2 files changed, 24 insertions(+), 7 deletions(-)
diff --git a/src/core/tandem_run/tandembatchprocess.cpp b/src/core/tandem_run/tandembatchprocess.cpp
index 7497799a..74abc820 100644
--- a/src/core/tandem_run/tandembatchprocess.cpp
+++ b/src/core/tandem_run/tandembatchprocess.cpp
@@ -263,7 +263,14 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
p_out->writeStartElement("note");
p_out->writeAttribute("type", "input");
p_out->writeAttribute("label", "spectrum, path");
- p_out->writeCharacters(mz_file);
+ if(mz_file_info.isDir())
+ {
+ p_out->writeCharacters(mz_file + "/analysis.tdf");
+ }
+ else
+ {
+ p_out->writeCharacters(mz_file);
+ }
p_out->writeEndElement();
//<note type="heading">Protein general</note>
@@ -292,8 +299,18 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
p_out->writeAttribute("label", "output, path");
if(mz_file_info.completeSuffix() == "tdf")
{
+
QString output_name =
QFileInfo(mz_file_info.absoluteDir().dirName()).baseName();
+ qDebug() << output_name;
+ p_out->writeCharacters(QString("%1/%2.xml")
+ .arg(_tandem_run_batch._output_directory)
+ .arg(output_name));
+ }
+ else if(mz_file_info.isDir())
+ {
+ QString output_name = QFileInfo(mz_file_info).baseName();
+ qDebug() << output_name;
p_out->writeCharacters(QString("%1/%2.xml")
.arg(_tandem_run_batch._output_directory)
.arg(output_name));
@@ -316,8 +333,6 @@ TandemBatchProcess::writeXmlInputFile(QXmlStreamWriter *p_out,
void
TandemBatchProcess::runOne(const QString &mz_file)
{
-
-
QTemporaryFile xml_input_file;
xml_input_file.setAutoRemove(true);
if(xml_input_file.open())
diff --git a/src/gui/tandem_run_dialog/tandemrundialog.cpp b/src/gui/tandem_run_dialog/tandemrundialog.cpp
index c4c2e32f..ee4d5c24 100644
--- a/src/gui/tandem_run_dialog/tandemrundialog.cpp
+++ b/src/gui/tandem_run_dialog/tandemrundialog.cpp
@@ -405,9 +405,10 @@ TandemRunDialog::selectTdfFolder()
{
QSettings settings;
QString default_tdf_location =
- settings.value("path/tandemrun_tdf_directory", "").toString();
+ settings.value("path/tandemrun_tdf_directory", "/").toString();
QFileDialog directories_dialog;
- directories_dialog.setOption(QFileDialog::ShowDirsOnly, true);
+ directories_dialog.setDirectory(default_tdf_location);
+ directories_dialog.setFileMode(QFileDialog::DirectoryOnly);
directories_dialog.setOption(QFileDialog::DontUseNativeDialog, true);
directories_dialog.setWindowTitle("Select the timsTOF folders");
QListView *lView = directories_dialog.findChild<QListView *>("listView");
@@ -424,13 +425,15 @@ TandemRunDialog::selectTdfFolder()
directories_names = directories_dialog.selectedFiles();
}
- if(directories_names.size() > 0)
+ if(directories_names.size() > 1)
{
settings.setValue("path/tandemrun_tdf_directory",
QFileInfo(directories_names[0]).absolutePath());
+ directories_names.pop_front();
}
for(QString directory_name : directories_names)
{
+ // qDebug() << directory_name+"/analysis.tdf";
if(!QFileInfo(directory_name + "/analysis.tdf").exists())
{
throw pappso::PappsoException(
@@ -444,7 +447,6 @@ TandemRunDialog::selectTdfFolder()
QStringList file_list = _p_mz_file_list->stringList();
file_list.append(directories_names);
_p_mz_file_list->setStringList(file_list);
-
}
catch(pappso::PappsoException &error)
{
--
GitLab