first protein table view

src/core/project.cpp

@@ -78,5 +78,10 @@ void Project::readXpipFile(QFileInfo xpip_fileinfo) {
 }
 
 
-void Project::addProteinSp(pappso::ProteinSp makeProteinSp) {
+void Project::addProteinSp(pappso::ProteinSp protein_sp) {
+  _protein_list.push_back(protein_sp);
 }
+
+    std::vector<pappso::ProteinSp> & Project::getProteinList() {
+      return _protein_list;
+    }
\ No newline at end of file

src/core/project.h

@@ -39,9 +39,12 @@ public:
     
     ProjectSp makeProjectSp() const;
     void readXpipFile(QFileInfo xpip_source);
-    void addProteinSp(pappso::ProteinSp makeProteinSp);
+    void addProteinSp(pappso::ProteinSp protein_sp);
+    std::vector<pappso::ProteinSp> & getProteinList();
     
-    pappso::GrpExperiment * _p_grp_experiment= nullptr; 
+    pappso::GrpExperiment * _p_grp_experiment= nullptr;
+private :
+  std::vector<pappso::ProteinSp> _protein_list;
 };
 
 #endif // PROJECT_H

src/files/xpipfile.cpp

@@ -24,6 +24,12 @@
 XpipFile::XpipFile(const QUrl & xpip_source) : _xpip_source(xpip_source)
 {
 
+}
+
+
+    XpipFile::XpipFile(const QFileInfo & xpip_source): _xpip_source(xpip_source.absoluteFilePath())
+{
+
 }
 
 XpipFile::~XpipFile()

src/files/xpipfile.h

@@ -23,12 +23,14 @@
 #define XPIPFILE_H
 
 #include <QUrl>
+#include <QFileInfo>
 #include "../core/project.h"
 
 class XpipFile
 {
 public:
     XpipFile(const QUrl & xpip_source);
+    XpipFile(const QFileInfo & xpip_source);
     ~XpipFile();
     
     ProjectSp getProjectSp() const;

src/gui/main.ui

@@ -20,7 +20,7 @@
      <x>0</x>
      <y>0</y>
      <width>286</width>
-     <height>22</height>
+     <height>19</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuFile">
@@ -39,5 +39,25 @@
   </action>
  </widget>
  <resources/>
- <connections/>
+ <connections>
+  <connection>
+   <sender>actionLoad</sender>
+   <signal>triggered()</signal>
+   <receiver>Main</receiver>
+   <slot>selectXpipFile()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>-1</x>
+     <y>-1</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>142</x>
+     <y>185</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+ <slots>
+  <slot>selectXpipFile()</slot>
+ </slots>
 </ui>

src/gui/mainwindow.cpp

@@ -22,9 +22,12 @@
 ******************************************************************************/
 
 #include <QDockWidget>
+#include <QSettings>
+#include <QFileDialog>
 #include "mainwindow.h"
 
 #include "ui_main.h"
+#include "files/xpipfile.h"
 
 
 MainWindow::MainWindow(QWidget *parent):
@@ -69,3 +72,26 @@ MainWindow::~MainWindow()
     delete ui;
 
 }
+
+
+void MainWindow::selectXpipFile() {
+
+    QSettings settings;
+    QString default_location = settings.value("path/xpipfile", "").toString();
+
+    QString filename = QFileDialog::getOpenFileName(this,
+                       tr("Open XPIP File"), default_location,
+                       tr("xpip files (*.xpip);;all files (*)"));
+
+    if (filename.isEmpty()) {
+        return;
+    }
+    QFileInfo new_xpip_file;
+    new_xpip_file.setFile(filename);
+    
+    XpipFile xpip_file(new_xpip_file);
+    
+    _project_sp = xpip_file.getProjectSp();
+    _protein_list_window->setProject(_project_sp.get());
+    
+}

src/gui/mainwindow.h

@@ -34,6 +34,7 @@
 #include <pwiz/data/msdata/MSDataFile.hpp>
 #include "../utils/readspectrum.h"
 #include "protein_list_view/proteinlistwindow.h"
+#include "core/project.h"
 
 
 
@@ -45,7 +46,7 @@ class Main;
 class PwizLoaderThread : public QObject
 {
     Q_OBJECT
-    public:
+public:
 
 public slots:
     void doMsDataFileLoad(const QString & parameter) {
@@ -58,7 +59,7 @@ signals:
     void msDataReady(pwiz::msdata::MSDataFile * p_ms_data_file);
 };
 
-class MainWindow: public QMainWindow {	
+class MainWindow: public QMainWindow {
     Q_OBJECT
     QThread workerThread;
 
@@ -68,6 +69,7 @@ public:
     ~MainWindow();
 
 public slots:
+    void selectXpipFile();
     //void peptideEdited(QString peptideStr);
     // void setColor(const QColor &color);
     // void setShape(Shape shape);
@@ -76,10 +78,13 @@ signals:
 
 private:
     Ui::Main *ui;
-    
-    
+
+
     ProteinListWindow * _protein_list_window=nullptr;
 
+private :
+    ProjectSp _project_sp=nullptr;
+
 };
 
 #endif // MAINWINDOW_H

src/gui/protein_list_view/proteinlistwindow.cpp

@@ -24,7 +24,6 @@
 #include "proteinlistwindow.h"
 
 #include "ui_protein_view.h"
-#include "proteintablemodel.h"
 
 
 ProteinListWindow::ProteinListWindow(QWidget *parent):
@@ -51,8 +50,8 @@ ProteinListWindow::ProteinListWindow(QWidget *parent):
     /*
     */
 
-    ProteinTableModel * p_myModel = new ProteinTableModel(0);
-    ui->tableView->setModel( p_myModel );
+    _protein_table_model_p = new ProteinTableModel(0);
+    ui->tableView->setModel( _protein_table_model_p );
 }
 
 ProteinListWindow::~ProteinListWindow()
@@ -60,4 +59,9 @@ ProteinListWindow::~ProteinListWindow()
     //if (_p_ms_data_file != nullptr) delete _p_ms_data_file;
     delete ui;
 
-}
\ No newline at end of file
+}
+
+
+    void ProteinListWindow::setProject(Project* project_p) {
+      _protein_table_model_p->setProject(project_p);
+    }
\ No newline at end of file

src/gui/protein_list_view/proteinlistwindow.h

@@ -26,6 +26,7 @@
 
 
 #include <QMainWindow>
+#include "proteintablemodel.h"
 
 //http://doc.qt.io/qt-4.8/qt-itemviews-chart-mainwindow-cpp.html
 namespace Ui {
@@ -39,6 +40,7 @@ public:
 
     explicit ProteinListWindow(QWidget * parent = 0);
     ~ProteinListWindow();
+    void setProject(Project* project_p);
 
 public slots:
     //void peptideEdited(QString peptideStr);
@@ -49,6 +51,7 @@ signals:
 
 private:
     Ui::ProteinView *ui;
+    ProteinTableModel * _protein_table_model_p = nullptr;
 
 };
 

src/gui/protein_list_view/proteintablemodel.cpp

@@ -35,8 +35,21 @@ ProteinTableModel::ProteinTableModel(QObject *parent)
     //emit dataChanged(topLeft, topLeft);
 }
 
+
+void ProteinTableModel::setProject(Project * p_project) {
+  qDebug() << "ProteinTableModel::setProject begin " << p_project->getProteinList().size();
+    _p_project = p_project;
+    
+    QModelIndex topLeft = createIndex(0,0);
+    emit headerDataChanged(Qt::Horizontal, 0,3);
+    emit dataChanged(topLeft, topLeft);
+}
+
 int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
-    return 2;
+    if (_p_project != nullptr) {
+        return _p_project->getProteinList().size();
+    }
+    return 0;
 }
 int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
     return 3;
@@ -67,6 +80,11 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
              .arg(row).arg(col).arg(role);
     if (role == Qt::DisplayRole)
     {
+        if (col == 2) {
+            if (_p_project != nullptr) {
+                return _p_project->getProteinList().at(row).get()->getDescription();
+            }
+        }
         return QString("Row%1, Column%2")
                .arg(index.row() + 1)
                .arg(index.column() +1);

src/gui/protein_list_view/proteintablemodel.h

@@ -25,6 +25,7 @@
 #define PROTEINTABLEMODEL_H
 
 #include <QAbstractTableModel>
+#include "../../core/project.h"
 
 class ProteinTableModel: public QAbstractTableModel
 {
@@ -35,6 +36,12 @@ public:
     int columnCount(const QModelIndex &parent = QModelIndex()) const override;
     QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
     QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override;
+
+
+    void setProject(Project * p_project);
+
+private :
+    Project * _p_project = nullptr;
 };
 
 #endif // PROTEINTABLEMODEL_H

src/input/xpipsaxhandler.cpp

@@ -41,9 +41,9 @@ bool XpipSaxHandler::startElement(const QString & namespaceURI, const QString &
 
     try {
         //startElement_group
-        if (qName == "group")
+        if (qName == "protein")
         {
-            //is_ok = startElement_group(attributes);
+            is_ok = startElement_protein(attributes);
         }
         _current_text.clear();
     }
@@ -64,10 +64,13 @@ bool XpipSaxHandler::endElement(const QString & namespaceURI, const QString & lo
     bool is_ok = true;
     // endElement_peptide_list
     try {
-        if (qName == "group")
+        if (qName == "protein")
         {
-            //is_ok = endElement_group();
+            is_ok = endElement_protein();
         }
+        else if (qName == "sequence") {
+	  is_ok = endElement_sequence();
+	}
 
         // end of detection_moulon
         // else if ((_tag_stack.size() > 1) &&