pretty cool xic area intensity viewer

src/CMakeLists.txt

@@ -28,8 +28,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
 
 #sudo apt-get install libpappsomspp-dev
 #FIND_PACKAGE( Pappsomspp REQUIRED )
- SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR  "/home/olivier/eclipse/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR  "/home/langella/developpement/git/pappsomspp")
  SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
  SET (PAPPSOMSPP_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt5.so")
  SET (PAPPSOMSPP_WIDGET_QT5_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/pappsomspp/widget/libpappsomspp-widget-qt5.so")

src/gui/xic_view/xic_box/xicbox.cpp

@@ -40,18 +40,40 @@
 
 class XicDetectionList: public pappso::XicDetectionSinkInterface {
 public:
+    XicDetectionList () {
+        _max_peak.setArea(0);
+    }
+    void setPeptideEvidenceList(const std::vector<const PeptideEvidence *> & peptide_evidence_list) {
+        for (const PeptideEvidence * p_evidence: peptide_evidence_list) {
+            _rt_list.push_back(p_evidence->getRetentionTime());
+        }
+    }
     void setXicPeak (pappso::XicPeak & xic_peak) override {
         _peak_list.push_back(xic_peak);
+
+        for (pappso::pappso_double rt: _rt_list) {
+            if (xic_peak.containsRt(rt)) {
+                if (xic_peak.getArea() > _max_peak.getArea()) {
+                    _max_peak = xic_peak;
+                }
+            }
+        }
     };
+    const pappso::XicPeak & getMatchedPeak() const {
+        return _max_peak;
+    }
     const std::vector<pappso::XicPeak> & getXicPeakList() const {
         return _peak_list;
     };
     void clear() {
         _peak_list.clear();
+        _max_peak.setArea(0);
     };
 private :
     unsigned int _count=0;
     std::vector<pappso::XicPeak> _peak_list;
+    std::vector<pappso::pappso_double> _rt_list;
+    pappso::XicPeak _max_peak;
 };
 
 
@@ -67,7 +89,10 @@ XicBox::XicBox(XicWindow *parent):
     p_worker->moveToThread(&_xic_thread);
     _xic_thread.start();
 
+
+    //ui->histo_widget->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom );
     //ui->xic_list_widget->setLayout(new QVBoxLayout(ui->xic_list_widget));
+    ui->histo_widget->legend->setVisible(true);
 
 #if QT_VERSION >= 0x050000
     // Qt5 code
@@ -156,8 +181,9 @@ void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
         emit loadXic(_p_peptide_evidence->getMsRunP(), _isotope_mass_list[_xic_widget_list.size()].get()->getMz(), _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
     }
     */
-    _xic_detection_list.clear();
+    _xic_peak_match_list.clear();
     XicDetectionList xic_list;
+    xic_list.setPeptideEvidenceList(_peptide_evidence_list);
     pappso::XicDetectionZivy zivy;
     zivy.setSmoothingHalfEdgeWindows(2);
     zivy.setDetectionThresholdOnMaxmin(3);
@@ -169,7 +195,7 @@ void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
         try {
             xic_list.clear();
             zivy.detect(*(xic_sp_list[i].get()), &xic_list);
-            _xic_detection_list.push_back(xic_list.getXicPeakList());
+            _xic_peak_match_list.push_back(xic_list.getMatchedPeak());
             ui->xic_widget->addXicPeakList(xic_sp_list[i].get(), xic_list.getXicPeakList());
         }
         catch (const pappso::ExceptionNotPossible & e) {
@@ -180,6 +206,39 @@ void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
     qDebug() << "XicBox::setXic plot" ;
     ui->xic_widget->plot();
 
+    QCPBars * observed_intensity = new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis2);
+    observed_intensity->setName("XIC area");
+    //ui->histo_widget->yAxis2->setLabel("intensity");
+
+
+    QVector<double> observed_intensity_data;
+    QVector<QString> labels;
+
+    QVector<double> ticks;
+    double sum = 0;
+    int i = 0;
+    for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: _isotope_mass_list) {
+        sum += _xic_peak_match_list[i].getArea();
+        observed_intensity_data << _xic_peak_match_list[i].getArea();
+        QString isotope_name = QString("+%1").arg(_isotope_mass_list[i].get()->getIsotopeNumber());
+        if (_isotope_mass_list[i].get()->getIsotopeRank() > 1) {
+            isotope_name = QString("+%1 [%2]").arg(_isotope_mass_list[i].get()->getIsotopeNumber()).arg(_isotope_mass_list[i].get()->getIsotopeRank());
+        }
+        isotope_name.append(QString(" (%1%)").arg((int) (_isotope_mass_list[i].get()->getIntensityRatio()*100)));
+        labels << isotope_name;
+        ticks << i;
+        i++;
+    }
+
+    observed_intensity->setPen(QPen(QColor("red")));
+    //_graph_peak_surface_list.back()->setScatterStyle(QCPScatterStyle::ssDot);
+    // observed_intensity->setBrush(QBrush(QColor(170, 255, 0, 0)));
+
+    observed_intensity->setData(ticks, observed_intensity_data);
+
+    ui->histo_widget->yAxis2->setVisible(true);
+    ui->histo_widget->yAxis2->setRange(0, sum);
+    ui->histo_widget->replot();
     qDebug() << "XicBox::setXic end";
 
 }
@@ -198,14 +257,16 @@ void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverage
     QCPBars * theoretical_ratio = new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis);
     theoretical_ratio->setName("theoretical ratio");
     ui->histo_widget->xAxis->setLabel("isotopes");
-    ui->histo_widget->yAxis->setLabel("intensity");
+    //ui->histo_widget->yAxis->setLabel("th. ratio");
 
     QVector<double> theoretical_ratio_data;
 
     QVector<double> ticks;
     QVector<QString> labels;
     int i = 0;
+    double sum = 0;
     for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: _isotope_mass_list) {
+        sum += natural_isotope_average.get()->getIntensityRatio();
         theoretical_ratio_data << natural_isotope_average.get()->getIntensityRatio();
         QString isotope_name = QString("+%1").arg(_isotope_mass_list[i].get()->getIsotopeNumber());
         if (_isotope_mass_list[i].get()->getIsotopeRank() > 1) {
@@ -232,7 +293,7 @@ void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverage
     theoretical_ratio->setData(ticks, theoretical_ratio_data);
 
 
-    ui->histo_widget->yAxis->setRange(0, 1);
+    ui->histo_widget->yAxis->setRange(0, sum);
     ui->histo_widget->xAxis->setRange(-0.8, _isotope_mass_list.size());
     ui->histo_widget->replot();
 }

src/gui/xic_view/xic_box/xicbox.h

@@ -69,7 +69,7 @@ private:
     std::vector<pappso::PeptideNaturalIsotopeAverageSp> _isotope_mass_list;
     pappso::XicSp _xic_sp;
     std::vector<pappso::XicWidget *> _xic_widget_list;
-    std::vector<std::vector<pappso::XicPeak>> _xic_detection_list;
+    std::vector<pappso::XicPeak> _xic_peak_match_list;
 };