libpappsomspp
Library for mass spectrometry
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#include <psmfeatures.h>
Public Member Functions | |
PsmFeatures (PrecisionPtr ms2precision, double minimumMz) | |
compute psm features More... | |
~PsmFeatures () | |
void | setPeptideSpectrumCharge (const pappso::PeptideSp peptideSp, const MassSpectrum *p_spectrum, unsigned int parent_charge) |
double | getIntensityOfMatchedIon (PeptideIon ion_type) |
get the sum of intensity of a specific ion More... | |
double | getTotalIntensity () const |
sum of all peak intensities (matched or not) More... | |
double | getTotalIntensityOfMatchedIons () const |
sum of matched peak intensities More... | |
std::size_t | getNumberOfMatchedIons () const |
number of matched ions (peaks) More... | |
std::size_t | countMatchedIonComplementPairs () const |
count the number of matched ion complement More... | |
double | getTotalIntensityOfMatchedIonComplementPairs () const |
intensity of matched ion complement More... | |
const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > & | getPeakIonPairs () const |
double | getMatchedMzDiffMean () const |
get mean deviation of matched peak mass delta More... | |
double | getMatchedMzDiffSd () const |
get standard deviation of matched peak mass delta More... | |
double | getMaxIntensityMatchedIonComplementPairPrecursorMassDelta () const |
get the precursor mass delta of the maximum intensity pair of complement ions More... | |
std::size_t | getMaxConsecutiveIon (PeptideIon ion_type) |
get the maximum consecutive fragments of one ion type More... | |
std::size_t | getAaSequenceCoverage (PeptideIon ion_type) |
number of amino acid covered by matched ions More... | |
std::size_t | getComplementPairsAaSequenceCoverage () |
number of amino acid covered by matched complement pairs of ions More... | |
double | getMaxIntensityPeakIonMatch (PeptideIon ion_type) const |
double | getIonPairPrecursorMassDelta (const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > &ion_pair) const |
Private Member Functions | |
void | findComplementIonPairs (const pappso::PeptideSp &peptideSp) |
Private Attributes | |
std::shared_ptr< FilterChargeDeconvolution > | msp_filterChargeDeconvolution |
std::shared_ptr< FilterMzExclusion > | msp_filterMzExclusion |
std::shared_ptr< FilterResampleKeepGreater > | msp_filterKeepGreater |
std::shared_ptr< PeptideIsotopeSpectrumMatch > | msp_peptideSpectrumMatch |
pappso::PeptideSp | msp_peptide |
PrecisionPtr | m_ms2precision |
std::list< PeptideIon > | m_ionList |
double | m_spectrumSumIntensity |
double | m_precursorTheoreticalMz |
double | m_precursorTheoreticalMass |
unsigned int | m_parentCharge = 1 |
std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > | m_peakIonPairs |
double | m_matchedMzDiffMean = 0 |
double | m_matchedMzDiffMedian = 0 |
double | m_matchedMzDiffSd = 0 |
Definition at line 43 of file psmfeatures.h.
PsmFeatures::PsmFeatures | ( | PrecisionPtr | ms2precision, |
double | minimumMz | ||
) |
compute psm features
ms2precision | precision of mass measurements for MS2 fragments |
minimumMz | ignore mz values under this threshold |
Definition at line 35 of file psmfeatures.cpp.
References pappso::b, pappso::PrecisionFactory::getPrecisionPtrFractionInstance(), m_ionList, m_ms2precision, msp_filterChargeDeconvolution, msp_filterKeepGreater, msp_filterMzExclusion, and pappso::y.
PsmFeatures::~PsmFeatures | ( | ) |
std::size_t pappso::PsmFeatures::countMatchedIonComplementPairs | ( | ) | const |
count the number of matched ion complement
matched ion complement are ions with a sum compatible to the precursor mass
Definition at line 166 of file psmfeatures.cpp.
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private |
Definition at line 366 of file psmfeatures.cpp.
References pappso::findComplementIonType(), and pappso::peptideIonIsNter().
Referenced by setPeptideSpectrumCharge().
std::size_t pappso::PsmFeatures::getAaSequenceCoverage | ( | pappso::PeptideIon | ion_type | ) |
std::size_t pappso::PsmFeatures::getComplementPairsAaSequenceCoverage | ( | ) |
number of amino acid covered by matched complement pairs of ions
Definition at line 285 of file psmfeatures.cpp.
double PsmFeatures::getIntensityOfMatchedIon | ( | PeptideIon | ion_type | ) |
get the sum of intensity of a specific ion
ion_type | ion species (y, b, ...) |
Definition at line 136 of file psmfeatures.cpp.
References msp_peptideSpectrumMatch, and pappso::sum.
double pappso::PsmFeatures::getIonPairPrecursorMassDelta | ( | const std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > & | ion_pair | ) | const |
Definition at line 346 of file psmfeatures.cpp.
References pappso::MHPLUS().
double pappso::PsmFeatures::getMatchedMzDiffMean | ( | ) | const |
double pappso::PsmFeatures::getMatchedMzDiffSd | ( | ) | const |
std::size_t pappso::PsmFeatures::getMaxConsecutiveIon | ( | pappso::PeptideIon | ion_type | ) |
get the maximum consecutive fragments of one ion type
ion_type | ion species (y, b, ...) |
Definition at line 211 of file psmfeatures.cpp.
References pappso::a, pappso::b, and pappso::max.
double pappso::PsmFeatures::getMaxIntensityMatchedIonComplementPairPrecursorMassDelta | ( | ) | const |
get the precursor mass delta of the maximum intensity pair of complement ions
Definition at line 325 of file psmfeatures.cpp.
double pappso::PsmFeatures::getMaxIntensityPeakIonMatch | ( | pappso::PeptideIon | ion_type | ) | const |
Definition at line 303 of file psmfeatures.cpp.
std::size_t pappso::PsmFeatures::getNumberOfMatchedIons | ( | ) | const |
number of matched ions (peaks)
Definition at line 205 of file psmfeatures.cpp.
const std::vector< std::pair< pappso::PeakIonIsotopeMatch, pappso::PeakIonIsotopeMatch > > & pappso::PsmFeatures::getPeakIonPairs | ( | ) | const |
Definition at line 173 of file psmfeatures.cpp.
double PsmFeatures::getTotalIntensity | ( | ) | const |
sum of all peak intensities (matched or not)
Definition at line 160 of file psmfeatures.cpp.
References m_spectrumSumIntensity.
double pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs | ( | ) | const |
intensity of matched ion complement
Definition at line 179 of file psmfeatures.cpp.
References pappso::sum.
double PsmFeatures::getTotalIntensityOfMatchedIons | ( | ) | const |
sum of matched peak intensities
Definition at line 149 of file psmfeatures.cpp.
References msp_peptideSpectrumMatch, and pappso::sum.
void PsmFeatures::setPeptideSpectrumCharge | ( | const pappso::PeptideSp | peptideSp, |
const MassSpectrum * | p_spectrum, | ||
unsigned int | parent_charge | ||
) |
Definition at line 58 of file psmfeatures.cpp.
References findComplementIonPairs(), m_ionList, m_matchedMzDiffMean, m_matchedMzDiffMedian, m_matchedMzDiffSd, m_ms2precision, m_parentCharge, m_peakIonPairs, m_precursorTheoreticalMass, m_precursorTheoreticalMz, m_spectrumSumIntensity, msp_filterKeepGreater, msp_peptide, msp_peptideSpectrumMatch, pappso::sum, and pappso::Trace::sumY().
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Definition at line 145 of file psmfeatures.h.
Referenced by PsmFeatures(), and setPeptideSpectrumCharge().
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Definition at line 157 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 158 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 159 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 144 of file psmfeatures.h.
Referenced by PsmFeatures(), and setPeptideSpectrumCharge().
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Definition at line 151 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 155 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 150 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 149 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 147 of file psmfeatures.h.
Referenced by getTotalIntensity(), and setPeptideSpectrumCharge().
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Definition at line 137 of file psmfeatures.h.
Referenced by PsmFeatures().
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Definition at line 139 of file psmfeatures.h.
Referenced by PsmFeatures(), and setPeptideSpectrumCharge().
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Definition at line 138 of file psmfeatures.h.
Referenced by PsmFeatures().
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Definition at line 142 of file psmfeatures.h.
Referenced by setPeptideSpectrumCharge().
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Definition at line 141 of file psmfeatures.h.
Referenced by getIntensityOfMatchedIon(), getTotalIntensityOfMatchedIons(), and setPeptideSpectrumCharge().