libpappsomspp
Library for mass spectrometry
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#include <massspectrumwidget.h>
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< 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 () |
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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< PeptideIon > | _ion_list |
std::list< PeakIonIsotopeMatch > | _peak_ion_isotope_match_list |
std::vector< pappso::PeptideNaturalIsotopeAverageSp > | _isotope_mass_list |
list of isotope precursors More... | |
QCPSpectrum * | _custom_plot = nullptr |
bool | _is_visible_mass_delta |
const DataPoint * | _p_mouse_peak = nullptr |
Friends | |
class | QCPSpectrum |
Definition at line 47 of file massspectrumwidget.h.
MassSpectrumWidget::MassSpectrumWidget | ( | QWidget * | parent = 0 | ) |
Definition at line 40 of file massspectrumwidget.cpp.
References _custom_plot, _ion_list, _ms_level, pappso::PeptideFragmentIonListBase::getCIDionList(), and setVisibleMassDelta().
MassSpectrumWidget::~MassSpectrumWidget | ( | ) |
Definition at line 55 of file massspectrumwidget.cpp.
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private |
Definition at line 119 of file massspectrumwidget.cpp.
References _custom_plot, _spectrum_sp, pappso::QCPSpectrum::clearData(), and pappso::QCPSpectrum::setSpectrumP().
Referenced by peptideAnnotate(), and setMassSpectrumCstSPtr().
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Definition at line 411 of file massspectrumwidget.cpp.
References _isotope_mass_list, _p_ms1_precision, _peptide_charge, _peptide_sp, pappso::PeptideNaturalIsotopeAverage::getIntensityRatio(), pappso::PeptideNaturalIsotopeList::getIntensityRatioPerIsotopeNumber(), pappso::PeptideNaturalIsotopeAverage::getIsotopeRank(), pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp(), and pappso::PrecisionBase::toString().
Referenced by peptideAnnotate().
void pappso::MassSpectrumWidget::highlightPrecursorPeaks | ( | ) |
Definition at line 454 of file massspectrumwidget.cpp.
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signal |
Referenced by peakChangeEvent().
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signal |
Referenced by mzChangeEvent().
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Definition at line 365 of file massspectrumwidget.cpp.
References pappso::mz, and mzChanged().
Referenced by pappso::QCPSpectrum::mouseMoveEvent().
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signal |
Referenced by peakChangeEvent().
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Definition at line 371 of file massspectrumwidget.cpp.
References _p_mouse_peak, _peak_ion_isotope_match_list, ionChanged(), pappso::DataPoint::makeDataPointCstSPtr(), peakChanged(), and pappso::DataPoint::x.
Referenced by pappso::QCPSpectrum::getMostIntensePeakBetween(), and pappso::QCPSpectrum::getNearestPeakBetween().
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Definition at line 185 of file massspectrumwidget.cpp.
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().
void MassSpectrumWidget::plot | ( | ) |
Definition at line 264 of file massspectrumwidget.cpp.
References _custom_plot, _isotope_mass_list, _ms_level, _p_ms1_precision, _peak_ion_isotope_match_list, _spectrum_sp, _tag_nmost_intense, pappso::a, pappso::QCPSpectrum::addMassDelta(), pappso::QCPSpectrum::addMs1IsotopePattern(), pappso::QCPSpectrum::addPeakIonIsotopeMatch(), pappso::b, pappso::MzRange::contains(), pappso::PeptideFragmentIon::getPeptideIonColor(), peptideAnnotate(), pappso::y, and pappso::DataPoint::y.
void MassSpectrumWidget::rescale | ( | ) |
Definition at line 236 of file massspectrumwidget.cpp.
References _custom_plot, and pappso::QCPSpectrum::rescale().
bool MassSpectrumWidget::savePdf | ( | const QString & | fileName, |
int | width = 0 , |
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int | height = 0 |
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void MassSpectrumWidget::setIonList | ( | const std::list< PeptideIon > & | ion_list | ) |
Definition at line 135 of file massspectrumwidget.cpp.
References _ion_list.
void MassSpectrumWidget::setMassSpectrumCstSPtr | ( | const MassSpectrumCstSPtr & | spectrum | ) |
Definition at line 226 of file massspectrumwidget.cpp.
References _spectrum_sp, and clearData().
Referenced by setQualifiedMassSpectrum().
void MassSpectrumWidget::setMaximumIsotopeNumber | ( | unsigned int | max_isotope_number | ) |
Definition at line 174 of file massspectrumwidget.cpp.
References _max_isotope_number.
void MassSpectrumWidget::setMaximumIsotopeRank | ( | unsigned int | max_isotope_rank | ) |
Definition at line 180 of file massspectrumwidget.cpp.
References _max_isotope_rank.
void MassSpectrumWidget::setMs1Precision | ( | PrecisionPtr | precision | ) |
Definition at line 159 of file massspectrumwidget.cpp.
References _p_ms1_precision, and pappso::PrecisionBase::toString().
void MassSpectrumWidget::setMs2Precision | ( | PrecisionPtr | precision | ) |
Definition at line 166 of file massspectrumwidget.cpp.
References _p_ms2_precision, and pappso::PrecisionBase::toString().
void MassSpectrumWidget::setMsLevel | ( | unsigned int | ms_level | ) |
Definition at line 141 of file massspectrumwidget.cpp.
References _ms_level, and setVisibleMassDelta().
Referenced by setQualifiedMassSpectrum().
void MassSpectrumWidget::setPeptideCharge | ( | unsigned int | parent_ion_charge | ) |
Definition at line 130 of file massspectrumwidget.cpp.
References _peptide_charge.
void MassSpectrumWidget::setPeptideSp | ( | const PeptideSp & | peptide_sp | ) |
Definition at line 216 of file massspectrumwidget.cpp.
References _peptide_sp.
void MassSpectrumWidget::setQualifiedMassSpectrum | ( | const QualifiedMassSpectrum & | spectrum | ) |
Definition at line 252 of file massspectrumwidget.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getMsLevel(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), setMassSpectrumCstSPtr(), and setMsLevel().
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Definition at line 87 of file massspectrumwidget.cpp.
References _custom_plot, _is_visible_mass_delta, and QCPSpectrum.
Referenced by MassSpectrumWidget(), and setMsLevel().
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Implements GraphicDeviceWidget.
Definition at line 75 of file massspectrumwidget.cpp.
References _custom_plot.
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Definition at line 82 of file massspectrumwidget.h.
Referenced by setVisibleMassDelta().
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Definition at line 110 of file massspectrumwidget.h.
Referenced by MassSpectrumWidget(), clearData(), plot(), rescale(), savePdf(), setVisibleMassDelta(), and toQPaintDevice().
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Definition at line 102 of file massspectrumwidget.h.
Referenced by MassSpectrumWidget(), peptideAnnotate(), and setIonList().
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Definition at line 111 of file massspectrumwidget.h.
Referenced by setVisibleMassDelta().
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list of isotope precursors
Definition at line 108 of file massspectrumwidget.h.
Referenced by computeIsotopeMassList(), and plot().
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Definition at line 94 of file massspectrumwidget.h.
Referenced by peptideAnnotate(), and setMaximumIsotopeNumber().
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Definition at line 95 of file massspectrumwidget.h.
Referenced by peptideAnnotate(), and setMaximumIsotopeRank().
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Definition at line 100 of file massspectrumwidget.h.
Referenced by MassSpectrumWidget(), peptideAnnotate(), plot(), and setMsLevel().
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Definition at line 113 of file massspectrumwidget.h.
Referenced by peakChangeEvent().
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Definition at line 97 of file massspectrumwidget.h.
Referenced by computeIsotopeMassList(), plot(), and setMs1Precision().
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Definition at line 98 of file massspectrumwidget.h.
Referenced by peptideAnnotate(), and setMs2Precision().
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Definition at line 104 of file massspectrumwidget.h.
Referenced by peakChangeEvent(), peptideAnnotate(), and plot().
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Definition at line 99 of file massspectrumwidget.h.
Referenced by computeIsotopeMassList(), peptideAnnotate(), and setPeptideCharge().
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Definition at line 101 of file massspectrumwidget.h.
Referenced by computeIsotopeMassList(), peptideAnnotate(), and setPeptideSp().
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Definition at line 96 of file massspectrumwidget.h.
Referenced by clearData(), peptideAnnotate(), plot(), and setMassSpectrumCstSPtr().
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Definition at line 93 of file massspectrumwidget.h.
Referenced by plot().