refactoring : xic peak renamed

src/gui/xic_view/xic_box/xicbox.cpp

@@ -33,14 +33,14 @@
 #include <pappsomspp/exception/exceptionnotfound.h>
 #include "../xicworkerthread.h"
 #include "../../project_view/projectwindow.h"
-#include <pappsomspp/processing/detection/xicdetectionzivy.h>
+#include <pappsomspp/processing/detection/tracedetectionzivy.h>
 #include <pappsomspp/exception/exceptionnotpossible.h>
 
 
 bool
-XicBoxNaturalIsotope::contains(const pappso::XicPeakCstSPtr &peak) const
+XicBoxNaturalIsotope::contains(const pappso::TracePeakCstSPtr &peak) const
 {
-  for(const pappso::XicPeakCstSPtr &peak_i : detected_peak_list)
+  for(const pappso::TracePeakCstSPtr &peak_i : detected_peak_list)
     {
       if(peak_i.get() == peak.get())
         {
@@ -67,9 +67,9 @@ class XicDetectionList : public pappso::TraceDetectionSinkInterface
       }
   }
   void
-  setXicPeak(pappso::XicPeak &xic_peak) override
+  setTracePeak(pappso::TracePeak &xic_peak) override
   {
-    pappso::XicPeakCstSPtr peak_sp = xic_peak.makeXicPeakCstSPtr();
+    pappso::TracePeakCstSPtr peak_sp = xic_peak.makeTracePeakCstSPtr();
     _peak_list.push_back(peak_sp);
 
     for(pappso::pappso_double rt : _rt_list)
@@ -84,12 +84,12 @@ class XicDetectionList : public pappso::TraceDetectionSinkInterface
           }
       }
   };
-  const pappso::XicPeakCstSPtr &
+  const pappso::TracePeakCstSPtr &
   getMatchedPeak() const
   {
     return _max_peak;
   }
-  const std::vector<pappso::XicPeakCstSPtr> &
+  const std::vector<pappso::TracePeakCstSPtr> &
   getXicPeakList() const
   {
     return _peak_list;
@@ -103,9 +103,9 @@ class XicDetectionList : public pappso::TraceDetectionSinkInterface
 
   private:
   unsigned int _count = 0;
-  std::vector<pappso::XicPeakCstSPtr> _peak_list;
+  std::vector<pappso::TracePeakCstSPtr> _peak_list;
   std::vector<pappso::pappso_double> _rt_list;
-  pappso::XicPeakCstSPtr _max_peak;
+  pappso::TracePeakCstSPtr _max_peak;
 };
 
 
@@ -139,13 +139,17 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
   connect(p_worker, &XicWorkerThread::operationFailed, this, &XicBox::error);
 
 
-  connect(this, &XicBox::computeIsotopeMassList, p_worker,
+  connect(this,
+          &XicBox::computeIsotopeMassList,
+          p_worker,
           &XicWorkerThread::doComputeIsotopeMassList);
-  connect(p_worker, &XicWorkerThread::isotopeMassListComputed, this,
+  connect(p_worker,
+          &XicWorkerThread::isotopeMassListComputed,
+          this,
           &XicBox::setIsotopeMassList);
 
-  connect(_p_xic_window, &XicWindow::reExtractXicNeeded, this,
-          &XicBox::reExtractXic);
+  connect(
+    _p_xic_window, &XicWindow::reExtractXicNeeded, this, &XicBox::reExtractXic);
   /*  connect(ui->xic_widget,
           qOverload<std::vector<std::pair<pappso::XicCstSPtr,
   pappso::XicPeakSp>>>( &pappso::XicWidget::xicPeakListChanged), this,
@@ -156,7 +160,9 @@ XicBox::XicBox(XicWindow *parent) : QWidget(parent), ui(new Ui::XicBox)
           this,
           &XicBox::onXicWidgetClick);
 */
-  connect(_p_xic_window, &XicWindow::rtUnitChangeNeeded, this,
+  connect(_p_xic_window,
+          &XicWindow::rtUnitChangeNeeded,
+          this,
           &XicBox::onRtUnitChanged);
 #else
 // Qt4 code
@@ -194,7 +200,7 @@ XicBox::onXicWidgetClick(double rt, double intensity)
 {
   qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
   ui->xic_widget->clearXicPeakBorders();
-  std::vector<pappso::XicPeakCstSPtr> draw_peak_borders;
+  std::vector<pappso::TracePeakCstSPtr> draw_peak_borders;
   for(XicBoxNaturalIsotope peak : _natural_isotope_list)
     {
       qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
@@ -264,13 +270,15 @@ XicBox::setPeptideEvidence(const PeptideEvidence *p_peptide_evidence)
   _p_xic_window->getProjectWindow()
     ->getProjectP()
     ->getSameXicPeptideEvidenceList(
-      _peptide_evidence_list, _msrun_sp.get(),
+      _peptide_evidence_list,
+      _msrun_sp.get(),
       _p_peptide_evidence->getPeptideXtpSp().get(),
       _p_peptide_evidence->getCharge());
 
   emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
                               _p_peptide_evidence->getCharge(),
-                              _p_xic_window->getXicExtractPrecision(), 0.8);
+                              _p_xic_window->getXicExtractPrecision(),
+                              0.8);
 }
 
 void
@@ -295,7 +303,8 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
   _p_xic_window->getProjectWindow()
     ->getProjectP()
     ->getSameXicPeptideEvidenceList(
-      _peptide_evidence_list, _msrun_sp.get(),
+      _peptide_evidence_list,
+      _msrun_sp.get(),
       _p_peptide_evidence->getPeptideXtpSp().get(),
       _p_peptide_evidence->getCharge());
   //_p_xic_window->getProjectWindow()->getProjectP()->getSameXicPeptideEvidenceList(p_peptide_evidence,
@@ -303,7 +312,8 @@ XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence *p_peptide_evidence,
 
   emit computeIsotopeMassList(_p_peptide_evidence->getPeptideXtpSp(),
                               _p_peptide_evidence->getCharge(),
-                              _p_xic_window->getXicExtractPrecision(), 0.8);
+                              _p_xic_window->getXicExtractPrecision(),
+                              0.8);
 }
 
 void
@@ -373,7 +383,7 @@ XicBox::setXic(std::vector<pappso::XicCstSPtr> xic_sp_list)
   XicDetectionList xic_list;
   xic_list.setPeptideEvidenceList(_peptide_evidence_list);
 
-  std::vector<pappso::XicPeakCstSPtr> draw_peak_borders;
+  std::vector<pappso::TracePeakCstSPtr> draw_peak_borders;
 
   for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
     {
@@ -401,7 +411,7 @@ XicBox::setXic(std::vector<pappso::XicCstSPtr> xic_sp_list)
 
 void
 XicBox::drawObservedAreaBars(
-  const std::vector<pappso::XicPeakCstSPtr> &observed_peak_to_draw_list)
+  const std::vector<pappso::TracePeakCstSPtr> &observed_peak_to_draw_list)
 {
   if(_isotope_ratio_graph_observed_intensity == nullptr)
     {
@@ -428,8 +438,8 @@ XicBox::drawObservedAreaBars(
   qDebug() << "XicBox::setXic plot _isotope_mass_list";
   for(const XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)
     {
-      pappso::XicPeakCstSPtr peak_to_draw;
-      for(pappso::XicPeakCstSPtr observed_peak : observed_peak_to_draw_list)
+      pappso::TracePeakCstSPtr peak_to_draw;
+      for(pappso::TracePeakCstSPtr observed_peak : observed_peak_to_draw_list)
         {
           if(xic_isotope.contains(observed_peak))
             {
@@ -496,7 +506,9 @@ XicBox::setIsotopeMassList(
         {nullptr, natural_isotope_average, nullptr, nullptr});
     }
 
-  emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
+  emit loadXic(_msrun_sp,
+               mass_list,
+               _p_xic_window->getXicExtractPrecision(),
                pappso::XicExtractMethod::max);
 
   // histogram
@@ -570,7 +582,9 @@ XicBox::reExtractXic()
       mass_list.push_back(
         xic_isotope.peptide_natural_isotope_sp.get()->getMz());
     }
-  emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(),
+  emit loadXic(_msrun_sp,
+               mass_list,
+               _p_xic_window->getXicExtractPrecision(),
                _p_xic_window->getXicExtractionMethod());
   qDebug() << "XicBox::reExtractXic end";
 }
@@ -583,7 +597,7 @@ XicBox::setRetentionTime(double rt)
 }
 void
 XicBox::setXicPeakList(
-  std::vector<std::pair<pappso::XicCstSPtr, pappso::XicPeakCstSPtr>>
+  std::vector<std::pair<pappso::XicCstSPtr, pappso::TracePeakCstSPtr>>
     xic_peak_list)
 {
   qDebug() << "XicBox::setXicPeakList begin";
@@ -593,7 +607,7 @@ XicBox::setXicPeakList(
       xic_isotope.one_peak_sp = nullptr;
     }
 
-  for(std::pair<pappso::XicCstSPtr, pappso::XicPeakCstSPtr> &pair_xic_peak :
+  for(std::pair<pappso::XicCstSPtr, pappso::TracePeakCstSPtr> &pair_xic_peak :
       xic_peak_list)
     {
       for(XicBoxNaturalIsotope &xic_isotope : _natural_isotope_list)

src/gui/xic_view/xic_box/xicbox.h

@@ -40,20 +40,20 @@
 
 namespace Ui
 {
-  class XicBox;
+class XicBox;
 }
 
 
 struct XicBoxNaturalIsotope
 {
 
-  bool contains(const pappso::XicPeakCstSPtr &peak) const;
+  bool contains(const pappso::TracePeakCstSPtr &peak) const;
 
   pappso::XicCstSPtr xic_sp;
   pappso::PeptideNaturalIsotopeAverageSp peptide_natural_isotope_sp;
-  pappso::XicPeakCstSPtr matched_peak_sp;
-  pappso::XicPeakCstSPtr one_peak_sp;
-  std::vector<pappso::XicPeakCstSPtr> detected_peak_list;
+  pappso::TracePeakCstSPtr matched_peak_sp;
+  pappso::TracePeakCstSPtr one_peak_sp;
+  std::vector<pappso::TracePeakCstSPtr> detected_peak_list;
 };
 
 class XicBox : public QWidget
@@ -67,9 +67,12 @@ class XicBox : public QWidget
                                  MsRunSp msrun_sp);
 
   signals:
-  void loadXic(MsRunSp p_msrun, std::vector<pappso::pappso_double> mz_list,
-               pappso::PrecisionPtr precision, pappso::XicExtractMethod method);
-  void computeIsotopeMassList(pappso::PeptideSp peptide_sp, unsigned int charge,
+  void loadXic(MsRunSp p_msrun,
+               std::vector<pappso::pappso_double> mz_list,
+               pappso::PrecisionPtr precision,
+               pappso::XicExtractMethod method);
+  void computeIsotopeMassList(pappso::PeptideSp peptide_sp,
+                              unsigned int charge,
                               pappso::PrecisionPtr precision,
                               double minimum_isotope_pattern_ratio);
   private slots:
@@ -87,7 +90,7 @@ class XicBox : public QWidget
 
   private:
   void drawObservedAreaBars(
-    const std::vector<pappso::XicPeakCstSPtr> &observed_peak_to_draw);
+    const std::vector<pappso::TracePeakCstSPtr> &observed_peak_to_draw);
 
   private:
   Ui::XicBox *ui;

src/gui/xic_view/xic_widgets/zivywidget.h

@@ -30,17 +30,18 @@
 #pragma once
 
 #include <QWidget>
-#include <pappsomspp/processing/detection/xicdetectionzivy.h>
+#include <pappsomspp/processing/detection/tracedetectionzivy.h>
 
 namespace Ui
 {
-  class ZivyWidget;
+class ZivyWidget;
 }
 
 
 struct ZivyParams
 {
-  std::shared_ptr<pappso::TraceDetectionInterface> newTraceDetectionZivySPtr() const;
+  std::shared_ptr<pappso::TraceDetectionInterface>
+  newTraceDetectionZivySPtr() const;
   void saveSettings() const;
   void loadSettings();
 

src/gui/xic_view/xicwindow.h

@@ -27,13 +27,12 @@
  *implementation
  ******************************************************************************/
 
-#ifndef XICWINDOW_H
-#define XICWINDOW_H
+#pragma once
 
 #include <QMainWindow>
 #include <QAbstractButton>
 #include <pappsomspp/xic/xic.h>
-#include <pappsomspp/processing/detection/xicdetectionzivy.h>
+#include <pappsomspp/processing/detection/tracedetectionzivy.h>
 
 #include "../../core/peptideevidence.h"
 #include "xic_widgets/zivydialog.h"
@@ -97,5 +96,3 @@ class XicWindow : public QMainWindow
 
   ZivyDialog *_p_zivy_dialog;
 };
-
-#endif // XICWINDOW_H

src/output/masschroqml.h

@@ -28,13 +28,12 @@
  *implementation
  ******************************************************************************/
 
-#ifndef MASSCHROQML_H
-#define MASSCHROQML_H
+#pragma once
 
 #include <QXmlStreamWriter>
 #include <QFile>
 #include <QString>
-#include <pappsomspp/processing/detection/xicdetectionzivy.h>
+#include <pappsomspp/processing/detection/tracedetectionzivy.h>
 #include "../core/project.h"
 #include "../grouping/groupinggroup.h"
 #include "../gui/xic_view/xic_widgets/zivywidget.h"
@@ -70,5 +69,3 @@ class MassChroQml
   IdentificationGroup *_p_identification_group;
   ZivyParams _detect_zivy;
 };
-
-#endif // MASSCHROQML_H