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Commit 53fafb57 authored by Langella Olivier's avatar Langella Olivier
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display isotope ratio on clicked peaks

parent 434fa620
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src/gui/xic_view/xic_box/xicbox.cpp
+ 81
− 42
View file @ 53fafb57
......@@ -36,6 +36,14 @@
#include <pappsomspp/exception/exceptionnotpossible.h>
bool XicBoxNaturalIsotope::contains(const pappso::XicPeakSp & peak) const {
for (const pappso::XicPeakSp & peak_i:detected_peak_list) {
if (peak_i.get() == peak.get()) {
return true;
}
}
return false;
}
class XicDetectionList: public pappso::XicDetectionSinkInterface {
public:
......@@ -146,10 +154,19 @@ XicBox::~XicBox()
void XicBox::onXicWidgetClick(double rt, double intensity) {
qDebug() << __FILE__ << " " <<__FUNCTION__ << " " << __LINE__;
ui->xic_widget->clearXicPeakBorders();
for (pappso::XicPeakSp xic_peak_sp:_xic_peak_current_list) {
std::vector <pappso::XicPeakSp> draw_peak_borders;
for (XicBoxNaturalIsotope peak:_natural_isotope_list) {
qDebug() << __FILE__ << " " <<__FUNCTION__ << " " << __LINE__;
ui->xic_widget->drawXicPeakBorders(xic_peak_sp);
draw_peak_borders.push_back(peak.one_peak_sp);
if (peak.one_peak_sp.get() != nullptr) {
ui->xic_widget->drawXicPeakBorders(peak.one_peak_sp);
}
}
if (_peptide_evidence_list.size() == 0) {
drawObservedAreaBars(draw_peak_borders);
}
}
void XicBox::remove() {
......@@ -216,26 +233,29 @@ void XicBox::setPeptideEvidenceInMsRun(const PeptideEvidence * p_peptide_evidenc
void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
qDebug() << "XicBox::setXic begin " << xic_sp_list.size();
ui->xic_widget->clear();
for (int i=0; i < xic_sp_list.size(); i++) {
_natural_isotope_list[i].xic_sp = xic_sp_list[i];
}
//pappso::XicWidget * xic_widget = new pappso::XicWidget(this);
//ui->xic_list_widget->layout()->addWidget(xic_widget);
for (int i=0; i < xic_sp_list.size(); i++) {
qDebug() << "XicBox::setXic xic " << xic_sp_list[i].get();
if (xic_sp_list[i].get() == nullptr) {
throw new pappso::PappsoException("Error in XicBox::setXic:\n xic_sp_list[i].get() == nullptr");
for (XicBoxNaturalIsotope & xic_isotope :_natural_isotope_list) {
//qDebug() << "XicBox::setXic xic " << xic_isotope.xic_sp.get();
if (xic_isotope.xic_sp.get() == nullptr) {
throw new pappso::PappsoException("Error in XicBox::setXic:\n xic_isotope.xic_sp.get() == nullptr");
}
qDebug() << "XicBox::setXic xic_sp_list[i].size() " << xic_sp_list[i].get()->size();
ui->xic_widget->addXicSp(xic_sp_list[i]);
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());
qDebug() << "XicBox::setXic xic_isotope.xic_sp.size() " << xic_isotope.xic_sp.get()->size();
ui->xic_widget->addXicSp(xic_isotope.xic_sp);
QString isotope_name = QString("+%1").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1) {
isotope_name = QString("+%1 [%2]").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber()).arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
}
isotope_name.append(QString(" (%1%)").arg((int) (_isotope_mass_list[i].get()->getIntensityRatio()*100)));
ui->xic_widget->setName(xic_sp_list[i].get(), isotope_name);
isotope_name.append(QString(" (%1%)").arg((int) (xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio()*100)));
ui->xic_widget->setName(xic_isotope.xic_sp.get(), isotope_name);
if (_isotope_mass_list[i].get()->getIsotopeNumber() == 0) {
if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber() == 0) {
for (const PeptideEvidence * peptide_evidence:_peptide_evidence_list) {
qDebug() << "XicBox::setXic peptide_evidence " << peptide_evidence->getRetentionTime();
ui->xic_widget->addMsMsEvent(xic_sp_list[i].get(), peptide_evidence->getRetentionTime());
ui->xic_widget->addMsMsEvent(xic_isotope.xic_sp.get(), peptide_evidence->getRetentionTime());
}
}
}
......@@ -247,17 +267,19 @@ 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_peak_match_list.clear();
XicDetectionList xic_list;
xic_list.setPeptideEvidenceList(_peptide_evidence_list);
std::vector <pappso::XicPeakSp> draw_peak_borders;
for (int i=0; i < xic_sp_list.size(); i++) {
for (XicBoxNaturalIsotope & xic_isotope :_natural_isotope_list) {
try {
xic_list.clear();
_p_xic_window->xicDetect(*(xic_sp_list[i].get()), &xic_list);
_xic_peak_match_list.push_back(xic_list.getMatchedPeak());
ui->xic_widget->addXicPeakList(xic_sp_list[i].get(), xic_list.getXicPeakList());
_p_xic_window->xicDetect(*(xic_isotope.xic_sp.get()), &xic_list);
xic_isotope.matched_peak_sp = xic_list.getMatchedPeak();
xic_isotope.detected_peak_list = xic_list.getXicPeakList();
ui->xic_widget->addXicPeakList(xic_isotope.xic_sp.get(), xic_list.getXicPeakList());
draw_peak_borders.push_back(xic_isotope.matched_peak_sp);
}
catch (const pappso::ExceptionNotPossible & e) {
qDebug() << e.qwhat();
......@@ -266,7 +288,11 @@ void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
qDebug() << "XicBox::setXic plot" ;
ui->xic_widget->plot();
drawObservedAreaBars(draw_peak_borders);
}
void XicBox::drawObservedAreaBars(const std::vector<pappso::XicPeakSp> & observed_peak_to_draw_list) {
if (_isotope_ratio_graph_observed_intensity == nullptr) {
qDebug() << "XicBox::setXic plot new QCPBars" ;
_isotope_ratio_graph_observed_intensity = new QCPBars(ui->histo_widget->xAxis, ui->histo_widget->yAxis2);
......@@ -287,17 +313,23 @@ void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
int i = 0;
qDebug() << "XicBox::setXic plot _isotope_mass_list" ;
for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: _isotope_mass_list) {
if (_xic_peak_match_list[i].get() == nullptr) {
for (const XicBoxNaturalIsotope & xic_isotope : _natural_isotope_list) {
pappso::XicPeakSp peak_to_draw;
for (pappso::XicPeakSp observed_peak : observed_peak_to_draw_list) {
if (xic_isotope.contains(observed_peak)) {
peak_to_draw = observed_peak;
}
}
if (peak_to_draw.get() == nullptr) {
}
else {
sum += _xic_peak_match_list[i].get()->getArea();
observed_intensity_data << _xic_peak_match_list[i].get()->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());
sum += peak_to_draw.get()->getArea();
observed_intensity_data << peak_to_draw.get()->getArea();
QString isotope_name = QString("+%1").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1) {
isotope_name = QString("+%1 [%2]").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber()).arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
}
isotope_name.append(QString(" (%1%)").arg((int) (_isotope_mass_list[i].get()->getIntensityRatio()*100)));
isotope_name.append(QString(" (%1%)").arg((int) (xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio()*100)));
labels << isotope_name;
ticks << i;
}
......@@ -321,11 +353,12 @@ void XicBox::setXic(std::vector< pappso::XicSp> xic_sp_list) {
void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverageSp> isotope_mass_list) {
_isotope_mass_list = isotope_mass_list;
_natural_isotope_list.clear();
std::vector<pappso::mz> mass_list;
for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: _isotope_mass_list) {
for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: isotope_mass_list) {
mass_list.push_back(natural_isotope_average.get()->getMz());
_natural_isotope_list.push_back({nullptr, natural_isotope_average, nullptr, nullptr});
}
emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
......@@ -342,14 +375,14 @@ void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverage
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) {
isotope_name = QString("+%1 [%2]").arg(_isotope_mass_list[i].get()->getIsotopeNumber()).arg(_isotope_mass_list[i].get()->getIsotopeRank());
for (const XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
sum += xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio();
theoretical_ratio_data << xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio();
QString isotope_name = QString("+%1").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber());
if (xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank() > 1) {
isotope_name = QString("+%1 [%2]").arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeNumber()).arg(xic_isotope.peptide_natural_isotope_sp.get()->getIsotopeRank());
}
isotope_name.append(QString(" (%1%)").arg((int) (_isotope_mass_list[i].get()->getIntensityRatio()*100)));
isotope_name.append(QString(" (%1%)").arg((int) (xic_isotope.peptide_natural_isotope_sp.get()->getIntensityRatio()*100)));
labels << isotope_name;
ticks << i;
i++;
......@@ -371,7 +404,7 @@ void XicBox::setIsotopeMassList(std::vector<pappso::PeptideNaturalIsotopeAverage
ui->histo_widget->yAxis->setRange(0, sum);
ui->histo_widget->xAxis->setRange(-0.8, _isotope_mass_list.size());
ui->histo_widget->xAxis->setRange(-0.8, _natural_isotope_list.size());
ui->histo_widget->replot();
}
......@@ -381,8 +414,8 @@ void XicBox::reExtractXic() {
ui->xic_widget->clear();
std::vector<pappso::mz> mass_list;
for (pappso::PeptideNaturalIsotopeAverageSp & natural_isotope_average: _isotope_mass_list) {
mass_list.push_back(natural_isotope_average.get()->getMz());
for (const XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
mass_list.push_back(xic_isotope.peptide_natural_isotope_sp.get()->getMz());
}
emit loadXic(_msrun_sp, mass_list, _p_xic_window->getXicExtractPrecision(), XicExtractMethod::max);
qDebug() << "XicBox::reExtractXic end";
......@@ -394,15 +427,21 @@ void XicBox::setRetentionTime(double rt) {
}
void XicBox::setXicPeakList(std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list) {
qDebug() << "XicBox::setXicPeakList begin";
_xic_peak_current_list.clear();
QString html ;
for (XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
xic_isotope.one_peak_sp = nullptr;
}
for (std::pair<pappso::XicSp, pappso::XicPeakSp> & pair_xic_peak: xic_peak_list) {
for (XicBoxNaturalIsotope & xic_isotope: _natural_isotope_list) {
if (xic_isotope.xic_sp.get() == pair_xic_peak.first.get()) {
xic_isotope.one_peak_sp = pair_xic_peak.second;
}
}
html.append(tr("<p>%1<br/>area: %2<br/>rt begin: %3<br/>rt max: %4<br/>rt end: %5<br/></p>").arg(ui->xic_widget->getName(pair_xic_peak.first.get())).arg(pair_xic_peak.second.get()->getArea()).arg(pair_xic_peak.second.get()->getLeftBoundary().rt)
.arg(pair_xic_peak.second.get()->getMaxXicElement().rt)
.arg(pair_xic_peak.second.get()->getRightBoundary().rt)
);
_xic_peak_current_list.push_back(pair_xic_peak.second);
}
ui->xic_widget->setToolTip(html);
......
src/gui/xic_view/xic_box/xicbox.h
+ 16
− 4
View file @ 53fafb57
......@@ -43,6 +43,18 @@ namespace Ui {
class XicBox;
}
struct XicBoxNaturalIsotope {
bool contains(const pappso::XicPeakSp & peak) const;
pappso::XicSp xic_sp;
pappso::PeptideNaturalIsotopeAverageSp peptide_natural_isotope_sp;
pappso::XicPeakSp matched_peak_sp;
pappso::XicPeakSp one_peak_sp;
std::vector <pappso::XicPeakSp> detected_peak_list;
};
class XicBox: public QWidget
{
Q_OBJECT
......@@ -67,6 +79,9 @@ private slots:
void setXicPeakList(std::vector<std::pair<pappso::XicSp, pappso::XicPeakSp>> xic_peak_list);
void onRtUnitChanged();
void onXicWidgetClick(double rt, double intensity);
private:
void drawObservedAreaBars(const std::vector<pappso::XicPeakSp> & observed_peak_to_draw);
private:
Ui::XicBox *ui;
......@@ -75,11 +90,8 @@ private:
const PeptideEvidence * _p_peptide_evidence;
MsRunSp _msrun_sp;
std::vector<const PeptideEvidence *> _peptide_evidence_list;
std::vector<pappso::PeptideNaturalIsotopeAverageSp> _isotope_mass_list;
pappso::XicSp _xic_sp;
std::vector<XicBoxNaturalIsotope> _natural_isotope_list;
std::vector<pappso::XicWidget *> _xic_widget_list;
std::vector<pappso::XicPeakSp> _xic_peak_match_list;
std::vector<pappso::XicPeakSp> _xic_peak_current_list;
QCPBars * _isotope_ratio_graph_observed_intensity= nullptr;
......
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