From 85964c66c2364ead234cb7c90d0439d8290b7785 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Mon, 24 Jul 2017 08:10:18 +0200
Subject: [PATCH] WIP: building ptm peptide table model
---
src/CMakeLists.txt | 7 +
src/grouping/ptm/ptmsamplescan.cpp | 16 +-
src/grouping/ptm/ptmsamplescan.h | 1 +
.../ptm_peptide_list_view.ui | 11 +-
.../ptmpeptidelistwindow.cpp | 45 +++++
.../ptmpeptidelistwindow.h | 28 ++-
.../ptmpeptidetablemodel.cpp | 190 ++++++++++++++++++
.../ptmpeptidetablemodel.h | 51 ++++-
.../ptmpeptidetableproxymodel.cpp | 13 ++
.../ptmpeptidetableproxymodel.h | 17 +-
10 files changed, 368 insertions(+), 11 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index bdaca3a10..3895ace75 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -128,6 +128,9 @@ SET(XTPCPP_SRCS
./gui/ptm_island_list_view/ptmislandlistwindow.cpp
./gui/ptm_island_list_view/ptmislandtablemodel.cpp
./gui/ptm_island_list_view/ptmislandproxymodel.cpp
+ ./gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+ ./gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+ ./gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
./gui/waiting_message_dialog/waitingmessagedialog.cpp
./gui/workerthread.cpp
./utils/workmonitor.cpp
@@ -148,6 +151,7 @@ SET (GUI_UIS
./gui/protein_list_view/protein_view.ui
./gui/protein_view/protein_detail_view.ui
./gui/ptm_island_list_view/ptm_island_list_view.ui
+ ./gui/ptm_peptide_list_view/ptm_peptide_list_view.ui
./gui/waiting_message_dialog/waiting_message_dialog.ui
)
@@ -174,6 +178,9 @@ SET(XTPCPP_MOC_HDRS
./gui/ptm_island_list_view/ptmislandlistwindow.h
./gui/ptm_island_list_view/ptmislandtablemodel.h
./gui/ptm_island_list_view/ptmislandproxymodel.h
+ ./gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+ ./gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
+ ./gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
./gui/waiting_message_dialog/waitingmessagedialog.h
./gui/workerthread.h
./utils/workmonitor.h
diff --git a/src/grouping/ptm/ptmsamplescan.cpp b/src/grouping/ptm/ptmsamplescan.cpp
index 986bc7f36..f3db43d1d 100644
--- a/src/grouping/ptm/ptmsamplescan.cpp
+++ b/src/grouping/ptm/ptmsamplescan.cpp
@@ -30,6 +30,7 @@
#include "ptmsamplescan.h"
PtmSampleScan::PtmSampleScan(const PeptideMatch * p_peptide_match) {
+ _peptide_match_list.push_back(p_peptide_match);
}
PtmSampleScan::PtmSampleScan(const PtmSampleScan& other){
@@ -37,6 +38,19 @@ PtmSampleScan::PtmSampleScan(const PtmSampleScan& other){
PtmSampleScan::~PtmSampleScan() {
}
+const PeptideMatch * PtmSampleScan::getRepresentativePeptideMatch() const {
+ return _peptide_match_list[0];
+}
bool PtmSampleScan::add(const PeptideMatch * p_peptide_match) {
- return false;
+ if(getRepresentativePeptideMatch()->getHashSampleScan() != p_peptide_match->getHashSampleScan()) {
+ return false;
+ }
+ if(getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getSequence() != p_peptide_match->getPeptideXtpSp().get()->getSequence()) {
+ return false;
+ }
+ if(getRepresentativePeptideMatch()->getPeptideXtpSp().get()->getMass() != p_peptide_match->getPeptideXtpSp().get()->getMass()) {
+ return false;
+ }
+ _peptide_match_list.push_back(p_peptide_match);
+ return true;
}
diff --git a/src/grouping/ptm/ptmsamplescan.h b/src/grouping/ptm/ptmsamplescan.h
index 498933e81..f0446c3cc 100644
--- a/src/grouping/ptm/ptmsamplescan.h
+++ b/src/grouping/ptm/ptmsamplescan.h
@@ -47,6 +47,7 @@ public:
PtmSampleScan(const PtmSampleScan& other);
~PtmSampleScan();
+ const PeptideMatch * getRepresentativePeptideMatch() const;
bool add(const PeptideMatch * p_peptide_match);
private:
std::vector<const PeptideMatch *> _peptide_match_list;
diff --git a/src/gui/ptm_peptide_list_view/ptm_peptide_list_view.ui b/src/gui/ptm_peptide_list_view/ptm_peptide_list_view.ui
index 8e2c18919..f1e7c54d9 100644
--- a/src/gui/ptm_peptide_list_view/ptm_peptide_list_view.ui
+++ b/src/gui/ptm_peptide_list_view/ptm_peptide_list_view.ui
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
- <class>PtmIslandListWindow</class>
- <widget class="QMainWindow" name="PtmIslandListWindow">
+ <class>PtmPeptideListWindow</class>
+ <widget class="QMainWindow" name="PtmPeptideListWindow">
<property name="geometry">
<rect>
<x>0</x>
@@ -14,7 +14,7 @@
<enum>Qt::CustomContextMenu</enum>
</property>
<property name="windowTitle">
- <string>PTM island list</string>
+ <string>PTM peptide list</string>
</property>
<widget class="QWidget" name="centralwidget">
<property name="contextMenuPolicy">
@@ -22,7 +22,7 @@
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
- <widget class="QTableView" name="ptm_island_tableview">
+ <widget class="QTableView" name="ptm_peptide_tableview">
<property name="contextMenuPolicy">
<enum>Qt::DefaultContextMenu</enum>
</property>
@@ -79,7 +79,7 @@
<x>0</x>
<y>0</y>
<width>826</width>
- <height>23</height>
+ <height>25</height>
</rect>
</property>
</widget>
@@ -95,4 +95,3 @@
<slot>doSearchOn(QString)</slot>
</slots>
</ui>
-
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
index 3309a7dbe..69d462d69 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.cpp
@@ -28,3 +28,48 @@
******************************************************************************/
#include "ptmpeptidelistwindow.h"
+#include "../ptm_island_list_view/ptmislandlistwindow.h"
+
+#include "ui_ptm_peptide_list_view.h"
+
+PtmPeptideListWindow::PtmPeptideListWindow(PtmIslandListWindow * parent):QMainWindow(parent),
+ ui(new Ui::PtmPeptideListWindow) {
+ _p_ptm_island_list_window = parent;
+
+ ui->setupUi(this);
+ /*
+ */
+ _ptm_table_model_p = new PtmPeptideTableModel(this);
+
+
+ _ptm_proxy_model_p = new PtmPeptideTableProxyModel(this, _ptm_table_model_p);
+ _ptm_proxy_model_p->setSourceModel(_ptm_table_model_p);
+ _ptm_proxy_model_p->setDynamicSortFilter(true);
+ ui->ptm_peptide_tableview->setModel( _ptm_proxy_model_p );
+ ui->ptm_peptide_tableview->setSortingEnabled(true);
+ ui->ptm_peptide_tableview->setAlternatingRowColors(true);
+
+
+
+#if QT_VERSION >= 0x050000
+ // Qt5 code
+ /*
+ connect(&workerThread, &QThread::finished, worker, &QObject::deleteLater);
+ connect(this, &PtSpectrumViewer::operateMsDataFile, worker, &PwizLoaderThread::doMsDataFileLoad);
+ connect(worker, &PwizLoaderThread::msDataReady, this, &PtSpectrumViewer::handleMsDataFile);
+ */
+#else
+// Qt4 code
+ //connect (this, SIGNAL(ptmIslandDataChanged()), _ptm_table_model_p, SLOT(onPtmIslandDataChanged()));
+
+ //connect (_project_window, SIGNAL(identificationPtmGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationPtmGroupGrouped(IdentificationGroup *)));
+ //connect (_project_window, SIGNAL(identificationGroupGrouped(IdentificationGroup *)), this,SLOT(doIdentificationGroupGrouped(IdentificationGroup *)));
+ connect(ui->ptm_peptide_tableview, SIGNAL(clicked(const QModelIndex &)), _ptm_table_model_p, SLOT(onTableClicked(const QModelIndex &)));
+
+#endif
+}
+PtmPeptideListWindow::~PtmPeptideListWindow() {
+}
+void PtmPeptideListWindow::setPtmIsland(PtmIsland * p_ptm_island) {
+ _p_ptm_island = _p_ptm_island;
+}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
index e6bc83630..5a6af5cf6 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidelistwindow.h
@@ -30,8 +30,32 @@
#ifndef PTMPEPTIDELISTWINDOW_H
#define PTMPEPTIDELISTWINDOW_H
-class PtmPeptideListWindow
-{
+#include <QMainWindow>
+#include "../../grouping/ptm/ptmisland.h"
+#include "ptmpeptidetablemodel.h"
+#include "ptmpeptidetableproxymodel.h"
+
+class PtmIslandListWindow;
+
+namespace Ui {
+class PtmPeptideListWindow;
+}
+
+class PtmPeptideListWindow: public QMainWindow {
+ Q_OBJECT
+public:
+
+ explicit PtmPeptideListWindow(PtmIslandListWindow * parent = 0);
+ ~PtmPeptideListWindow();
+ void setPtmIsland(PtmIsland * p_ptm_island);
+
+private:
+ PtmIsland * _p_ptm_island=nullptr;
+ Ui::PtmPeptideListWindow *ui;
+ PtmPeptideTableModel * _ptm_table_model_p = nullptr;
+ PtmPeptideTableProxyModel * _ptm_proxy_model_p = nullptr;
+ PtmIslandListWindow * _p_ptm_island_list_window;
+
};
#endif // PTMPEPTIDELISTWINDOW_H
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
index 6ce26eecb..1ad88b010 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.cpp
@@ -27,3 +27,193 @@
******************************************************************************/
#include "ptmpeptidetablemodel.h"
+#include "ptmpeptidelistwindow.h"
+#include <QDebug>
+
+PtmPeptideTableModel::PtmPeptideTableModel(PtmPeptideListWindow * p_ptm_peptide_list_window) {
+}
+
+PtmPeptideTableModel::~PtmPeptideTableModel() {
+}
+
+const QString PtmPeptideTableModel::getTitle(PtmPeptideListColumn column) {
+ qDebug() << "PtmPeptideTableModel::getTitle begin ";
+ return PtmPeptideTableModel::getTitle((std::int8_t) column);
+ //qDebug() << "ProteinTableModel::getTitle end ";
+}
+const QString PtmPeptideTableModel::getDescription(PtmPeptideListColumn column) {
+ qDebug() << "PtmPeptideTableModel::columnCount begin ";
+ return PtmPeptideTableModel::getDescription((std::int8_t) column);
+ //qDebug() << "ProteinTableModel::columnCount end ";
+}
+
+const QString PtmPeptideTableModel::getTitle(std::int8_t column) {
+ switch (column) {
+
+ case (std::int8_t) PtmPeptideListColumn::peptide_ptm_grouping_id:
+ return "peptide ID";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::sample:
+ return "sample";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::scan:
+ return "scan";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::rt:
+ return "RT";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::charge:
+ return "charge";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::sequence:
+ return "sequence";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::modifs:
+ return "modifs";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::label:
+ return "label";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::start:
+ return "start";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::length:
+ return "length";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::used:
+ return "used";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::subgroups:
+ return "subgroups";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::Evalue:
+ return "Evalue";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::theoretical_mhplus:
+ return "theoretical MH+";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::delta_mhplus:
+ return "delta MH+";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::hyperscore:
+ return "hyperscore";
+
+ }
+ return "";
+}
+
+const QString PtmPeptideTableModel::getDescription(std::int8_t column) {
+ switch (column) {
+
+ case (std::int8_t) PtmPeptideListColumn::peptide_ptm_grouping_id:
+ return "unique PTM peptide identifier within this PTM grouping experiment";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::sample:
+ return "MS sample name";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::scan:
+ return "scan number";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::rt:
+ return "retention time in seconds";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::charge:
+ return "peptide charge";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::sequence:
+ return "peptide sequence";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::modifs:
+ return "peptide modifications";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::label:
+ return "peptide label";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::start:
+ return "peptide start position on protein";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::length:
+ return "peptide length";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::used:
+ return "number of subgroups in which this peptide is used";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::subgroups:
+ return "list of subgroups in which this peptide is used";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::Evalue:
+ return "peptide Evalue";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::theoretical_mhplus:
+ return "peptide theoretical MH+";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::delta_mhplus:
+ return "peptide mass difference betwenn observed mass and theoretical mass";
+ break;
+ case (std::int8_t) PtmPeptideListColumn::hyperscore:
+ return "X!Tandem hyperscore";
+
+ }
+ return "";
+}
+
+int PtmPeptideTableModel::rowCount(const QModelIndex &parent ) const {
+ qDebug() << "PtmPeptideTableModel::rowCount begin ";
+ return _ptm_sample_scan_list.size();
+}
+int PtmPeptideTableModel::columnCount(const QModelIndex &parent ) const {
+ //qDebug() << "ProteinTableModel::columnCount begin ";
+ return 6;
+}
+QVariant PtmPeptideTableModel::headerData(int section, Qt::Orientation orientation, int role) const
+{
+ if (orientation == Qt::Horizontal)
+ {
+ switch (role) {
+ case Qt::DisplayRole :
+ return QVariant(getTitle(section));
+ break;
+ case Qt::ToolTipRole :
+ return QVariant(getDescription(section));
+ break;
+
+ }
+ }
+ return QVariant();
+}
+QVariant PtmPeptideTableModel::data(const QModelIndex &index, int role ) const {
+ // generate a log message when this method gets called
+ int row = index.row();
+ int col = index.column();
+
+ if (row >= _ptm_sample_scan_list.size()) return QVariant();
+ switch(role) {
+ case Qt::DisplayRole:
+ switch (col) {
+
+ case (std::int8_t)PtmPeptideListColumn::peptide_ptm_grouping_id:
+ return QVariant();
+ break;
+ case (std::int8_t)PtmPeptideListColumn::sample:
+ return _ptm_sample_scan_list.at(row).get()->getRepresentativePeptideMatch()->getIdentificationDataSource()->getSampleName();
+ break;
+ case (std::int8_t)PtmPeptideListColumn::scan:
+ //return QVariant ((quint32) _p_protein_match->getPeptideMatchList().at(row)->getScan());
+ break;
+ case (std::int8_t)PtmPeptideListColumn::rt:
+ //return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getRetentionTime());
+ break;
+ case (std::int8_t)PtmPeptideListColumn::charge:
+ //return QVariant ((qreal) _p_protein_match->getPeptideMatchList().at(row)->getCharge());
+ break;
+ case (std::int8_t)PtmPeptideListColumn::sequence:
+ //return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getSequence();
+ break;
+ case (std::int8_t)PtmPeptideListColumn::modifs:
+ //return _p_protein_match->getPeptideMatchList().at(row)->getPeptideXtpSp().get()->getModifString();
+ break;
+
+ }
+ }
+ return QVariant();
+}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
index d1eed50da..96d744c52 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetablemodel.h
@@ -29,8 +29,57 @@
#ifndef PTMPEPTIDETABLEMODEL_H
#define PTMPEPTIDETABLEMODEL_H
-class PtmPeptideTableModel
+#include <QAbstractTableModel>
+#include "../../grouping/ptm/ptmsamplescan.h"
+
+
+
+/** \def PtmPeptideListColumn list of available fields to display in ptm peptide list
+ *
+ */
+
+enum class PtmPeptideListColumn: std::int8_t {
+ peptide_ptm_grouping_id=0, ///< peptide PTM grouping id
+ sample=1,
+ scan=2,
+ rt=3,
+ charge=4,
+ sequence=5,
+ modifs=6,
+ label=7,
+ start=8,
+ length=9,
+ used=10,
+ subgroups=11,
+ Evalue=12,
+ theoretical_mhplus=13,
+ delta_mhplus=14,
+ hyperscore=15
+
+};
+
+
+class PtmPeptideListWindow;
+class PtmPeptideTableModel: public QAbstractTableModel
{
+ Q_OBJECT
+public:
+ PtmPeptideTableModel(PtmPeptideListWindow * p_ptm_peptide_list_window);
+ virtual int rowCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual int columnCount(const QModelIndex &parent = QModelIndex()) const override;
+ virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
+ virtual QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+ static const QString getTitle(PtmPeptideListColumn column);
+ static const QString getDescription(PtmPeptideListColumn column);
+
+ ~PtmPeptideTableModel();
+
+private :
+ static const QString getTitle(std::int8_t column);
+ static const QString getDescription(std::int8_t column);
+
+private:
+ std::vector<PtmSampleScanSp> _ptm_sample_scan_list;
};
#endif // PTMPEPTIDETABLEMODEL_H
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
index b6b394c4a..9be577329 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.cpp
@@ -27,3 +27,16 @@
******************************************************************************/
#include "ptmpeptidetableproxymodel.h"
+#include "ptmpeptidetablemodel.h"
+#include "ptmpeptidelistwindow.h"
+
+PtmPeptideTableProxyModel::PtmPeptideTableProxyModel(PtmPeptideListWindow * p_ptm_peptide_list_window, PtmPeptideTableModel* ptm_table_model_p)
+{
+ _p_ptm_peptide_list_window = p_ptm_peptide_list_window;
+ _p_ptm_table_model = ptm_table_model_p;
+}
+
+PtmPeptideTableProxyModel::~PtmPeptideTableProxyModel()
+{
+
+}
diff --git a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
index 5e0a9f676..c680c57b9 100644
--- a/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
+++ b/src/gui/ptm_peptide_list_view/ptmpeptidetableproxymodel.h
@@ -29,8 +29,23 @@
#ifndef PTMPEPTIDETABLEPROXYMODEL_H
#define PTMPEPTIDETABLEPROXYMODEL_H
-class PtmPeptideTableProxyModel
+#include <QAbstractTableModel>
+#include <QSortFilterProxyModel>
+
+
+class PtmPeptideListWindow;
+class PtmPeptideTableModel;
+
+class PtmPeptideTableProxyModel: public QSortFilterProxyModel
{
+ Q_OBJECT
+public:
+ PtmPeptideTableProxyModel(PtmPeptideListWindow * p_ptm_peptide_list_window, PtmPeptideTableModel* ptm_table_model_p);
+ ~PtmPeptideTableProxyModel();
+
+private:
+ PtmPeptideListWindow * p_ptm_peptide_list_window;
+ PtmPeptideTableModel* ptm_table_model_p;
};
#endif // PTMPEPTIDETABLEPROXYMODEL_H
--
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