pappso::MassSpectrumWidget Class Reference

#include <massspectrumwidget.h>

Inheritance diagram for pappso::MassSpectrumWidget:

Signals
void	mzChanged (double mz) const
void	peakChanged (pappso::DataPointCstSPtr peak_match) const
void	ionChanged (pappso::PeakIonIsotopeMatchCstSPtr ion) const

Public Member Functions
	MassSpectrumWidget (QWidget *parent=0)
	~MassSpectrumWidget ()
void	setQualifiedMassSpectrum (const QualifiedMassSpectrum &spectrum)
void	setMsLevel (unsigned int ms_level)
void	setMassSpectrumCstSPtr (const MassSpectrumCstSPtr &spectrum)
void	setPeptideSp (const PeptideSp &peptide_sp)
void	plot ()
void	rescale ()
void	setPeptideCharge (unsigned int parent_ion_charge)
void	setMaximumIsotopeNumber (unsigned int max_isotope_number)
void	setMaximumIsotopeRank (unsigned int max_isotope_rank)
void	setIonList (const std::list< Enums::PeptideIon > &ion_list)
void	setMs1Precision (PrecisionPtr precision)
void	setMs2Precision (PrecisionPtr precision)
bool	savePdf (const QString &fileName, int width=0, int height=0)
void	toQPaintDevice (QPaintDevice *device, const QSize &size) override
void	highlightPrecursorPeaks ()
QJsonObject	getJsonPsmIsotope () const
Public Member Functions inherited from GraphicDeviceWidget
	GraphicDeviceWidget (QWidget *parent)
virtual	~GraphicDeviceWidget ()
virtual void	toSvgFile (const QString &filename, const QString &title, const QString &description, const QSize &size) final

Protected Member Functions
void	mzChangeEvent (pappso_double mz) const
void	peakChangeEvent (const DataPoint *p_peak_match)

Private Member Functions
void	peptideAnnotate ()
void	setVisibleMassDelta (bool visible)
void	clearData ()
void	computeIsotopeMassList ()

Private Attributes
unsigned int	_tag_nmost_intense = 10
unsigned int	_max_isotope_number = 0
unsigned int	_max_isotope_rank = 1
MassSpectrumCstSPtr	_spectrum_sp
PrecisionPtr	_p_ms1_precision = PrecisionFactory::getDaltonInstance(0.1)
PrecisionPtr	_p_ms2_precision = PrecisionFactory::getDaltonInstance(0.5)
unsigned int	_peptide_charge = 3
unsigned int	_ms_level
PeptideSp	_peptide_sp
std::list< Enums::PeptideIon >	_ion_list
std::list< PeakIonIsotopeMatch >	_peak_ion_isotope_match_list
std::vector< pappso::PeptideNaturalIsotopeAverageSp >	_isotope_mass_list
	list of isotope precursors
QCPSpectrum *	_custom_plot = nullptr
bool	_is_visible_mass_delta
const DataPoint *	_p_mouse_peak = nullptr

Friends
class	QCPSpectrum

Detailed Description

Definition at line 47 of file massspectrumwidget.h.

Constructor & Destructor Documentation

MassSpectrumWidget()

MassSpectrumWidget::MassSpectrumWidget

(

QWidget *

parent = 0

)

Definition at line 41 of file massspectrumwidget.cpp.

                                                      : GraphicDeviceWidget(parent)
{
  qDebug();
 
  _ms_level    = 1;
  _ion_list    = PeptideFragmentIonListBase::getCIDionList();
  _custom_plot = nullptr;
 
  this->setLayout(new QHBoxLayout(this));
 
  this->layout()->setContentsMargins(0, 0, 0, 0);
  setVisibleMassDelta(false);
  qDebug();
}

References GraphicDeviceWidget::GraphicDeviceWidget(), _custom_plot, _ion_list, _ms_level, pappso::PeptideFragmentIonListBase::getCIDionList(), and setVisibleMassDelta().

~MassSpectrumWidget()

MassSpectrumWidget::~MassSpectrumWidget

(

)

Definition at line 55 of file massspectrumwidget.cpp.

{
}

Member Function Documentation

clearData()

void MassSpectrumWidget::clearData ( )

private

Definition at line 119 of file massspectrumwidget.cpp.

{
  qDebug();
  _custom_plot->clearData();
  qDebug();
  _custom_plot->clearItems();
  _custom_plot->setSpectrumP(_spectrum_sp.get());
  qDebug();
}

References _custom_plot, and _spectrum_sp.

Referenced by peptideAnnotate(), QCPSpectrum, and setMassSpectrumCstSPtr().

computeIsotopeMassList()

void MassSpectrumWidget::computeIsotopeMassList ( )

private

Definition at line 405 of file massspectrumwidget.cpp.

{
  qDebug() << "_p_ms1_precision->toString()=" << _p_ms1_precision->toString();
  _isotope_mass_list.resize(0);
  // compute isotope masses :
  if(_peptide_sp != nullptr)
    {
      pappso::PeptideNaturalIsotopeList isotope_list(_peptide_sp);
      std::map<unsigned int, pappso::pappso_double> map_isotope_number =
        isotope_list.getIntensityRatioPerIsotopeNumber();
 
      for(unsigned int i = 0; i < map_isotope_number.size(); i++)
        {
 
          unsigned int asked_rank = 0;
          unsigned int given_rank = 0;
          bool more_rank          = true;
          while(more_rank)
            {
              asked_rank++;
              pappso::PeptideNaturalIsotopeAverage isotopeAverageMono(
                isotope_list, asked_rank, i, _peptide_charge, _p_ms1_precision);
              given_rank = isotopeAverageMono.getIsotopeRank();
              if(given_rank < asked_rank)
                {
                  more_rank = false;
                }
              else if(isotopeAverageMono.getIntensityRatio() == 0)
                {
                  more_rank = false;
                }
              else
                {
                  // isotopeAverageMono.makePeptideNaturalIsotopeAverageSp();
                  _isotope_mass_list.push_back(
                    isotopeAverageMono.makePeptideNaturalIsotopeAverageSp());
                }
            }
        }
    }
  qDebug() << "_isotope_mass_list.size()=" << _isotope_mass_list.size();
}

References _isotope_mass_list, _p_ms1_precision, _peptide_charge, _peptide_sp, pappso::PeptideNaturalIsotopeAverage::getIntensityRatio(), pappso::PeptideNaturalIsotopeList::getIntensityRatioPerIsotopeNumber(), pappso::PeptideNaturalIsotopeAverage::getIsotopeRank(), and pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp().

Referenced by peptideAnnotate(), and QCPSpectrum.

getJsonPsmIsotope()

QJsonObject pappso::MassSpectrumWidget::getJsonPsmIsotope

(

)

const

Definition at line 463 of file massspectrumwidget.cpp.

{
  QJsonObject psm_json;
 
  try
    {
 
      if(_peptide_sp.get() != nullptr)
        {
          psm_json.insert("proforma", _peptide_sp.get()->toProForma());
        }
 
      if(_spectrum_sp.get() != nullptr)
        {
          struct data_plot
          {
            pappso::DataPoint point;
            double mz_th;
            int charge;
            int size;
            int isotope_number;
            int isotope_rank;
          };
 
          std::map<pappso::Enums::PeptideIon, std::vector<data_plot>> ion_map;
 
          QJsonObject spectrum_json;
          spectrum_json.insert("mz", pappso::Utils::toJson(_spectrum_sp.get()->xValues()));
          spectrum_json.insert("intensity", pappso::Utils::toJson(_spectrum_sp.get()->yValues()));
 
 
          for(const pappso::PeakIonIsotopeMatch &peakion_match : _peak_ion_isotope_match_list)
            {
              data_plot one_ion_match;
              one_ion_match.charge = (int)peakion_match.getCharge();
              one_ion_match.isotope_number =
                (int)peakion_match.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
              one_ion_match.isotope_rank =
                (int)peakion_match.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeRank();
              one_ion_match.mz_th =
                peakion_match.getPeptideNaturalIsotopeAverageSp().get()->getMz();
              one_ion_match.point = peakion_match.getPeak();
              one_ion_match.size  = (int)peakion_match.getPeptideFragmentIonSp().get()->size();
 
              auto it = ion_map.insert({peakion_match.getPeptideIonType(), {}});
              it.first->second.push_back(one_ion_match);
            }
 
          QJsonObject psm_ion_json;
          for(auto &cle_valeur : ion_map)
            {
              std::vector<data_plot> &current_vector = cle_valeur.second;
 
              std::sort(
                current_vector.begin(),
                current_vector.end(),
                [](const data_plot &a, const data_plot &b) { return a.point.x < b.point.x; });
              QJsonArray current_ion_json_arr;
 
              for(const data_plot &one_point : current_vector)
                {
                  QJsonObject current_ion;
                  current_ion.insert("mz", one_point.point.x);
                  current_ion.insert("mzth", one_point.mz_th);
                  current_ion.insert("intensity", one_point.point.y);
                  current_ion.insert("size", one_point.size);
                  current_ion.insert("charge", one_point.charge);
                  current_ion.insert("isotope", one_point.isotope_number);
                  current_ion.insert("rank", one_point.isotope_rank);
 
                  current_ion_json_arr.push_back(current_ion);
                }
 
 
              psm_ion_json.insert(pappso::Utils::toString(cle_valeur.first), current_ion_json_arr);
            }
 
          psm_json.insert("ion-series", psm_ion_json);
          psm_json.insert("spectra", spectrum_json);
        }
    }
  catch(const pappso::PappsoException &error)
    {
      throw pappso::PappsoException(
        QObject::tr("Unable to build JSON PSM object:\n%1").arg(error.qwhat()));
    }
  return psm_json;
}

References _peak_ion_isotope_match_list, _peptide_sp, _spectrum_sp, pappso::a, pappso::b, pappso::PappsoException::qwhat(), pappso::Utils::toJson(), and pappso::Utils::toString().

highlightPrecursorPeaks()

void pappso::MassSpectrumWidget::highlightPrecursorPeaks

(

)

Definition at line 449 of file massspectrumwidget.cpp.

{
 
  if(_ms_level > 1)
    {
      pappso_double precursor_mz_1 = _peptide_sp->getMz(1);
      _custom_plot->highlightPrecursorPeaks(precursor_mz_1, 1, _p_ms2_precision);
      pappso_double precursor_mz_charge = _peptide_sp->getMz(_peptide_charge);
      _custom_plot->highlightPrecursorPeaks(precursor_mz_charge, _peptide_charge, _p_ms2_precision);
    }
}

References _custom_plot, _ms_level, _p_ms2_precision, _peptide_charge, and _peptide_sp.

ionChanged

void pappso::MassSpectrumWidget::ionChanged ( pappso::PeakIonIsotopeMatchCstSPtr ion ) const

signal

Referenced by peakChangeEvent().

mzChanged

void pappso::MassSpectrumWidget::mzChanged ( double mz ) const

signal

Referenced by mzChangeEvent().

mzChangeEvent()

void MassSpectrumWidget::mzChangeEvent ( pappso_double mz ) const

protected

Definition at line 360 of file massspectrumwidget.cpp.

{
  emit mzChanged(mz);
}

References mzChanged().

Referenced by QCPSpectrum.

peakChanged

void pappso::MassSpectrumWidget::peakChanged ( pappso::DataPointCstSPtr peak_match ) const

signal

Referenced by peakChangeEvent().

peakChangeEvent()

void MassSpectrumWidget::peakChangeEvent ( const DataPoint * p_peak_match )

protected

Definition at line 366 of file massspectrumwidget.cpp.

{
  qDebug() << "p_peak_match=" << p_peak_match;
  if(_p_mouse_peak != p_peak_match)
    {
      _p_mouse_peak = p_peak_match;
      DataPointCstSPtr peak_shp;
      // emit peakChanged(peak_shp);
      if(_p_mouse_peak != nullptr)
        {
          qDebug() << "_p_mouse_peak->x=" << _p_mouse_peak->x;
          peak_shp = _p_mouse_peak->makeDataPointCstSPtr();
          emit peakChanged(peak_shp);
          // try to find matched ion (if it exists)
          bool found = false;
          for(const PeakIonIsotopeMatch &peak_ion_match : _peak_ion_isotope_match_list)
            {
              if(peak_ion_match.getPeak().x == _p_mouse_peak->x)
                {
                  // found
                  emit ionChanged(std::make_shared<const PeakIonIsotopeMatch>(
                    PeakIonIsotopeMatch(peak_ion_match)));
                  found = true;
                }
            }
          if(!found)
            {
              emit ionChanged(std::shared_ptr<const PeakIonIsotopeMatch>());
            }
        }
      else
        {
          qDebug() << "no peak";
          emit peakChanged(peak_shp);
        }
    }
}

References _p_mouse_peak, _peak_ion_isotope_match_list, ionChanged(), and peakChanged().

Referenced by QCPSpectrum.

peptideAnnotate()

void MassSpectrumWidget::peptideAnnotate ( )

private

Definition at line 185 of file massspectrumwidget.cpp.

{
  qDebug() << " _max_isotope_number=" << _max_isotope_number;
  clearData();
  _peak_ion_isotope_match_list.clear();
  if((_spectrum_sp == nullptr) || (_peptide_sp == nullptr))
    {
    }
  else
    {
      if(_ms_level > 1)
        {
          qDebug();
          PeptideIsotopeSpectrumMatch psm_match(*(_spectrum_sp.get()),
                                                _peptide_sp,
                                                _peptide_charge,
                                                _p_ms2_precision,
                                                _ion_list,
                                                _max_isotope_number,
                                                _max_isotope_rank);
 
          _peak_ion_isotope_match_list = psm_match.getPeakIonIsotopeMatchList();
          qDebug() << "_peak_ion_isotope_match_list.size()=" << _peak_ion_isotope_match_list.size();
        }
      else
        {
        }
      computeIsotopeMassList();
    }
  qDebug();
}

References _ion_list, _max_isotope_number, _max_isotope_rank, _ms_level, _p_ms2_precision, _peak_ion_isotope_match_list, _peptide_charge, _peptide_sp, _spectrum_sp, clearData(), computeIsotopeMassList(), and pappso::PeptideIsotopeSpectrumMatch::getPeakIonIsotopeMatchList().

Referenced by plot(), and QCPSpectrum.

plot()

void MassSpectrumWidget::plot

(

)

Definition at line 265 of file massspectrumwidget.cpp.

{
 
  qDebug() << "_ms_level=" << _ms_level;
  peptideAnnotate();
  if(_ms_level == 1)
    {
      qDebug();
      if(_spectrum_sp != nullptr)
        {
          qDebug();
          if(_isotope_mass_list.size() > 0)
            {
 
              qDebug() << "_isotope_mass_list.size()=" << _isotope_mass_list.size();
              std::sort(_isotope_mass_list.begin(),
                        _isotope_mass_list.end(),
                        [](const PeptideNaturalIsotopeAverageSp &a,
                           const PeptideNaturalIsotopeAverageSp &b) {
                          return a.get()->getMz() < b.get()->getMz();
                        });
 
              if(_isotope_mass_list.size() > 0)
                {
                  PeptideNaturalIsotopeAverageSp precursor_peptide = _isotope_mass_list.at(0);
                  qDebug() << "precursor_peptide.get()->getMz()="
                           << precursor_peptide.get()->getMz();
                  MzRange precursor_mass(precursor_peptide.get()->getMz(), _p_ms1_precision);
                  DataPoint monoisotope_peak;
                  monoisotope_peak.y = 0;
 
                  for(const DataPoint &peak : *(_spectrum_sp.get()))
                    {
                      if(precursor_mass.contains(peak.x))
                        {
                          if(peak.y > monoisotope_peak.y)
                            {
                              qDebug() << "SpectrumWidget::plot  "
                                          "(peak.intensity > "
                                          "monoisotope_peak.intensity) ";
                              monoisotope_peak = peak;
                            }
                        }
                    }
                  if(monoisotope_peak.y > 0)
                    {
                      qDebug() << "addMs1IsotopePattern";
                      _custom_plot->addMs1IsotopePattern(_isotope_mass_list, monoisotope_peak.y);
                    }
                }
            }
        }
    }
  else
    {
      qDebug() << "_peak_ion_isotope_match_list.size()=" << _peak_ion_isotope_match_list.size();
      _peak_ion_isotope_match_list.sort(
        [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
          return a.getPeak().y > b.getPeak().y;
        });
      unsigned int i = 0;
      for(const PeakIonIsotopeMatch &peak_ion_match : _peak_ion_isotope_match_list)
        {
          _custom_plot->addPeakIonIsotopeMatch(peak_ion_match);
 
          _custom_plot->addMassDelta(peak_ion_match);
          //_p_delta_graph->addData(peak_ion_match.getPeak().x,
          // peak_ion_match.getPeak().y);
          if(i < _tag_nmost_intense)
            {
              QCPItemText *text_label = new QCPItemText(_custom_plot);
              text_label->setVisible(true);
              //_custom_plot->addItem(text_label);
              text_label->setPositionAlignment(Qt::AlignBottom | Qt::AlignHCenter);
              text_label->position->setType(QCPItemPosition::ptPlotCoords);
              text_label->position->setCoords(
                peak_ion_match.getPeak().x,
                peak_ion_match.getPeak().y); // place position at center/top of axis rect
              text_label->setFont(QFont(font().family(), 8));
              text_label->setText(
                peak_ion_match.getPeptideFragmentIonSp().get()->getCompletePeptideIonName(
                  peak_ion_match.getCharge()));
              // text_label->setPen(QPen(PeptideFragmentIon::getPeptideIonColor(peak_ion_match.getPeptideIonType()),
              // 1)); // show black border around text
              text_label->setColor(
                QColor(PeptideFragmentIon::getPeptideIonColor(peak_ion_match.getPeptideIonType())));
            }
          i++;
        }
    }
 
  _custom_plot->replot();
  qDebug();
}

References _custom_plot, _isotope_mass_list, _ms_level, _p_ms1_precision, _peak_ion_isotope_match_list, _spectrum_sp, _tag_nmost_intense, pappso::a, pappso::b, pappso::MzRange::contains(), pappso::PeptideNaturalIsotopeAverage::getMz(), pappso::PeptideFragmentIon::getPeptideIonColor(), peptideAnnotate(), and pappso::DataPoint::y.

rescale()

void MassSpectrumWidget::rescale

(

)

Definition at line 238 of file massspectrumwidget.cpp.

{
  qDebug();
 
  _custom_plot->rescale();
 
  /*
  if (_p_delta_axis_rect != nullptr) {
      _p_delta_axis_rect->axis(QCPAxis::AxisType::atLeft)->rescale();
  }
  */
  _custom_plot->replot();
  qDebug();
}

References _custom_plot.

savePdf()

bool MassSpectrumWidget::savePdf	(	const QString &	fileName,
		int	width = 0,
		int	height = 0 )

Definition at line 60 of file massspectrumwidget.cpp.

{
 
  if(_custom_plot != nullptr)
    {
      return _custom_plot->savePdf(fileName, width, height);
    }
  else
    {
      return false;
    }
}

References _custom_plot.

setIonList()

void MassSpectrumWidget::setIonList

(

const std::list< Enums::PeptideIon > &

ion_list

)

Definition at line 135 of file massspectrumwidget.cpp.

{
  _ion_list = ion_list;
}

References _ion_list.

setMassSpectrumCstSPtr()

void MassSpectrumWidget::setMassSpectrumCstSPtr

(

const MassSpectrumCstSPtr &

spectrum

)

Definition at line 228 of file massspectrumwidget.cpp.

{
  qDebug();
  _spectrum_sp = spectrum;
 
  clearData();
  qDebug();
}

References _spectrum_sp, and clearData().

Referenced by setQualifiedMassSpectrum().

setMaximumIsotopeNumber()

void MassSpectrumWidget::setMaximumIsotopeNumber

(

unsigned int

max_isotope_number

)

Definition at line 174 of file massspectrumwidget.cpp.

{
  _max_isotope_number = max_isotope_number;
}

References _max_isotope_number.

setMaximumIsotopeRank()

void MassSpectrumWidget::setMaximumIsotopeRank

(

unsigned int

max_isotope_rank

)

Definition at line 180 of file massspectrumwidget.cpp.

{
  _max_isotope_rank = max_isotope_rank;
}

References _max_isotope_rank.

setMs1Precision()

void MassSpectrumWidget::setMs1Precision

(

PrecisionPtr

precision

)

Definition at line 159 of file massspectrumwidget.cpp.

{
  qDebug() << "precision->toString()=" << precision->toString();
  _p_ms1_precision = precision;
  //_precision._precision = precision._precision;
}

References _p_ms1_precision, and pappso::PrecisionBase::toString().

setMs2Precision()

void MassSpectrumWidget::setMs2Precision

(

PrecisionPtr

precision

)

Definition at line 166 of file massspectrumwidget.cpp.

{
  qDebug() << "precision->toString()=" << precision->toString();
  _p_ms2_precision = precision;
  //_precision._precision = precision._precision;
}

References _p_ms2_precision, and pappso::PrecisionBase::toString().

setMsLevel()

void MassSpectrumWidget::setMsLevel

(

unsigned int

ms_level

)

Definition at line 141 of file massspectrumwidget.cpp.

{
  qDebug() << "ms_level=" << ms_level;
  _ms_level = ms_level;
 
 
  if(_ms_level == 1)
    {
      setVisibleMassDelta(false);
    }
  else
    {
      setVisibleMassDelta(true);
    }
 
  //_precision._precision = precision._precision;
}

References _ms_level, and setVisibleMassDelta().

Referenced by setQualifiedMassSpectrum().

setPeptideCharge()

void MassSpectrumWidget::setPeptideCharge

(

unsigned int

parent_ion_charge

)

Definition at line 130 of file massspectrumwidget.cpp.

{
  _peptide_charge = parent_ion_charge;
}

References _peptide_charge.

setPeptideSp()

void MassSpectrumWidget::setPeptideSp

(

const PeptideSp &

peptide_sp

)

Definition at line 218 of file massspectrumwidget.cpp.

{
  qDebug();
  _peptide_sp = peptide_sp;
 
  // clearData();
  qDebug();
}

References _peptide_sp.

setQualifiedMassSpectrum()

void MassSpectrumWidget::setQualifiedMassSpectrum

(

const QualifiedMassSpectrum &

spectrum

)

Definition at line 254 of file massspectrumwidget.cpp.

{
  qDebug() << "spectrum.getPrecursorCharge()=" << spectrum.getPrecursorCharge();
 
  setMsLevel(spectrum.getMsLevel());
  setMassSpectrumCstSPtr(spectrum.getMassSpectrumCstSPtr());
 
  qDebug();
}

References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getMsLevel(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), setMassSpectrumCstSPtr(), and setMsLevel().

setVisibleMassDelta()

void MassSpectrumWidget::setVisibleMassDelta ( bool visible )

private

Definition at line 87 of file massspectrumwidget.cpp.

{
  qDebug();
  if(_custom_plot != nullptr)
    {
      if(visible == _is_visible_mass_delta)
        return;
      delete _custom_plot;
    }
  _is_visible_mass_delta = visible;
  while(auto item = this->layout()->takeAt(0))
    {
      delete item->widget();
    }
  qDebug();
  _custom_plot = new QCPSpectrum(this, visible);
  this->layout()->addWidget(_custom_plot);
  qDebug();
  _custom_plot->xAxis->setLabel("m/z");
  _custom_plot->yAxis->setLabel("intensity");
  qDebug();
  _custom_plot->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom);
  _custom_plot->axisRect()->setRangeDrag(Qt::Horizontal);
  _custom_plot->axisRect()->setRangeZoom(Qt::Horizontal);
  qDebug();
  // legend->setVisible(false);
  // legend->setFont(QFont("Helvetica",9));
  // set locale to english, so we get english decimal separator:
  // setLocale(QLocale(QLocale::English, QLocale::UnitedKingdom));
  qDebug();
}

References _custom_plot, _is_visible_mass_delta, and QCPSpectrum.

Referenced by MassSpectrumWidget(), QCPSpectrum, and setMsLevel().

toQPaintDevice()

void MassSpectrumWidget::toQPaintDevice ( QPaintDevice * device, const QSize & size )

overridevirtual

Implements GraphicDeviceWidget.

Definition at line 75 of file massspectrumwidget.cpp.

{
 
  if(_custom_plot != nullptr)
    {
      QCPPainter painter;
      painter.begin(device);
      _custom_plot->toPainter(&painter, size.width(), size.height());
      painter.end();
    }
}

References _custom_plot.

Friends And Related Symbol Documentation

QCPSpectrum

friend class QCPSpectrum

friend

Definition at line 85 of file massspectrumwidget.h.

References clearData(), computeIsotopeMassList(), mzChangeEvent(), peakChangeEvent(), peptideAnnotate(), QCPSpectrum, and setVisibleMassDelta().

Referenced by QCPSpectrum, and setVisibleMassDelta().

Member Data Documentation

_custom_plot

QCPSpectrum* pappso::MassSpectrumWidget::_custom_plot = nullptr

private

Definition at line 113 of file massspectrumwidget.h.

Referenced by MassSpectrumWidget(), clearData(), highlightPrecursorPeaks(), plot(), rescale(), savePdf(), setVisibleMassDelta(), and toQPaintDevice().

_ion_list

std::list<Enums::PeptideIon> pappso::MassSpectrumWidget::_ion_list

private

Definition at line 105 of file massspectrumwidget.h.

Referenced by MassSpectrumWidget(), peptideAnnotate(), and setIonList().

_is_visible_mass_delta

bool pappso::MassSpectrumWidget::_is_visible_mass_delta

private

Definition at line 114 of file massspectrumwidget.h.

Referenced by setVisibleMassDelta().

_isotope_mass_list

std::vector<pappso::PeptideNaturalIsotopeAverageSp> pappso::MassSpectrumWidget::_isotope_mass_list

private

list of isotope precursors

Definition at line 111 of file massspectrumwidget.h.

Referenced by computeIsotopeMassList(), and plot().

_max_isotope_number

unsigned int pappso::MassSpectrumWidget::_max_isotope_number = 0

private

Definition at line 97 of file massspectrumwidget.h.

Referenced by peptideAnnotate(), and setMaximumIsotopeNumber().

_max_isotope_rank

unsigned int pappso::MassSpectrumWidget::_max_isotope_rank = 1

private

Definition at line 98 of file massspectrumwidget.h.

Referenced by peptideAnnotate(), and setMaximumIsotopeRank().

_ms_level

unsigned int pappso::MassSpectrumWidget::_ms_level

private

Definition at line 103 of file massspectrumwidget.h.

Referenced by MassSpectrumWidget(), highlightPrecursorPeaks(), peptideAnnotate(), plot(), and setMsLevel().

_p_mouse_peak

const DataPoint* pappso::MassSpectrumWidget::_p_mouse_peak = nullptr

private

Definition at line 116 of file massspectrumwidget.h.

Referenced by peakChangeEvent().

_p_ms1_precision

PrecisionPtr pappso::MassSpectrumWidget::_p_ms1_precision = PrecisionFactory::getDaltonInstance(0.1)

private

Definition at line 100 of file massspectrumwidget.h.

Referenced by computeIsotopeMassList(), plot(), and setMs1Precision().

_p_ms2_precision

PrecisionPtr pappso::MassSpectrumWidget::_p_ms2_precision = PrecisionFactory::getDaltonInstance(0.5)

private

Definition at line 101 of file massspectrumwidget.h.

Referenced by highlightPrecursorPeaks(), peptideAnnotate(), and setMs2Precision().

_peak_ion_isotope_match_list

std::list<PeakIonIsotopeMatch> pappso::MassSpectrumWidget::_peak_ion_isotope_match_list

private

Definition at line 107 of file massspectrumwidget.h.

Referenced by getJsonPsmIsotope(), peakChangeEvent(), peptideAnnotate(), and plot().

_peptide_charge

unsigned int pappso::MassSpectrumWidget::_peptide_charge = 3

private

Definition at line 102 of file massspectrumwidget.h.

Referenced by computeIsotopeMassList(), highlightPrecursorPeaks(), peptideAnnotate(), and setPeptideCharge().

_peptide_sp

PeptideSp pappso::MassSpectrumWidget::_peptide_sp

private

Definition at line 104 of file massspectrumwidget.h.

Referenced by computeIsotopeMassList(), getJsonPsmIsotope(), highlightPrecursorPeaks(), peptideAnnotate(), and setPeptideSp().

_spectrum_sp

MassSpectrumCstSPtr pappso::MassSpectrumWidget::_spectrum_sp

private

Definition at line 99 of file massspectrumwidget.h.

Referenced by clearData(), getJsonPsmIsotope(), peptideAnnotate(), plot(), and setMassSpectrumCstSPtr().

_tag_nmost_intense

unsigned int pappso::MassSpectrumWidget::_tag_nmost_intense = 10

private

Definition at line 96 of file massspectrumwidget.h.

Referenced by plot().

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The documentation for this class was generated from the following files:

• pappsomspp/gui/massspectrumwidget/massspectrumwidget.h
• pappsomspp/gui/massspectrumwidget/massspectrumwidget.cpp