From 284269b12cd2ea4650eff4b752bcfac71817c769 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 10 May 2019 11:02:20 +0200
Subject: [PATCH] refactoring : xic peak renamed
---
src/gui/xic_view/xic_box/xicbox.cpp | 68 ++++++++++++++---------
src/gui/xic_view/xic_box/xicbox.h | 21 ++++---
src/gui/xic_view/xic_widgets/zivywidget.h | 7 ++-
src/gui/xic_view/xicwindow.h | 7 +--
src/output/masschroqml.h | 7 +--
5 files changed, 61 insertions(+), 49 deletions(-)
diff --git a/src/gui/xic_view/xic_box/xicbox.cpp b/src/gui/xic_view/xic_box/xicbox.cpp
index e596f3fff..f5354fcbc 100644
--- a/src/gui/xic_view/xic_box/xicbox.cpp
+++ b/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)
diff --git a/src/gui/xic_view/xic_box/xicbox.h b/src/gui/xic_view/xic_box/xicbox.h
index 7c8fb86e2..a70d3b251 100644
--- a/src/gui/xic_view/xic_box/xicbox.h
+++ b/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;
diff --git a/src/gui/xic_view/xic_widgets/zivywidget.h b/src/gui/xic_view/xic_widgets/zivywidget.h
index 0a0a01985..02022f19d 100644
--- a/src/gui/xic_view/xic_widgets/zivywidget.h
+++ b/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();
diff --git a/src/gui/xic_view/xicwindow.h b/src/gui/xic_view/xicwindow.h
index 80b38a18b..d20888a36 100644
--- a/src/gui/xic_view/xicwindow.h
+++ b/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
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index a81cd8268..9ed29d987 100644
--- a/src/output/masschroqml.h
+++ b/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
--
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