libpappsomspp
Library for mass spectrometry
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#include <peptidemodel.h>
Public Member Functions | |
PeptideModel (const pappso::QualifiedMassSpectrum &qmass_spectrum, const pappso::Peptide &peptide) | |
PeptideModel () | |
PeptideModel (const PeptideModel &other) | |
virtual | ~PeptideModel () |
QString | toString () const |
double | getMass () const |
double | getMassDelta () const |
mass delta between experimental and theoretical mass | |
std::size_t | modifCount () const |
void | setBeginMassDelta (double) |
void | matchExperimentalPeaks (pappso::PrecisionPtr precision) |
std::vector< double > | getTheoreticalIonMassList () const |
std::size_t | getCountSharedPeaks () const |
double | getIntensitySharedPeaks () const |
double | getIntensityExperimentalPeaks () const |
void | assignResidualMass2Cter () |
bool | eliminateComplementaryDelta (pappso::PrecisionPtr precision) |
bool | checkForMutations (const std::vector< AminoAcidChar > &aa_list, pappso::PrecisionPtr precision) |
try to replace mass differences with corresponding mutations mass delta | |
bool | checkForMutation (const pappso::Aa &amino_acid_candidate, pappso::PrecisionPtr precision) |
try to replace mass differences with corresponding mutation mass delta | |
bool | checkForAaModification (const pappso::Aa &aa_modified, pappso::PrecisionPtr precision) |
try to replace mass differences with the given modifications on a specific amino acid | |
bool | checkForAaModificationP (pappso::AaModificationP modification, pappso::PrecisionPtr precision) |
try to replace mass differences with the given modification | |
PeptideModel & | operator= (const PeptideModel &other) |
PeptideModel & | copyDeep (const PeptideModel &other) |
bool | eliminateNegativeOffset (pappso::PrecisionPtr precision) |
bool | removeBracketsForAlignedAA () |
const std::vector< TheoreticalPeakDataPoint > & | getTheoreticalPeakDataPointList () const |
QString | getTheoreticalPeakDataPointListToString () const |
QString | toProForma () const |
get the peptide model in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md | |
Private Member Functions | |
void | generateTheoreticalPeaks (pappso::PrecisionPtr precision) |
Private Attributes | |
std::vector< TheoreticalPeakDataPoint > | m_theoreticalPeakList |
double | m_experimentalPrecursorMass |
double | m_beginMassDelta = 0 |
pappso::MassSpectrumCstSPtr | mcsp_peakList = nullptr |
pappso::AaModificationP | m_nterModification |
pappso::AaModificationP | m_cterModification |
std::size_t | m_countSharedPeaks = 0 |
double | m_intensitySharedPeaks = 0 |
double | m_intensityExperimentalPeaks = 0 |
Definition at line 72 of file peptidemodel.h.
pappso::specglob::PeptideModel::PeptideModel | ( | const pappso::QualifiedMassSpectrum & | qmass_spectrum, |
const pappso::Peptide & | peptide | ||
) |
Default constructor
Definition at line 53 of file peptidemodel.cpp.
References pappso::Peptide::getInternalCterModification(), pappso::Peptide::getInternalNterModification(), pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getPrecursorMass(), m_cterModification, m_experimentalPrecursorMass, m_nterModification, mcsp_peakList, and pappso::specglob::nonAlign.
pappso::specglob::PeptideModel::PeptideModel | ( | ) |
Definition at line 48 of file peptidemodel.cpp.
pappso::specglob::PeptideModel::PeptideModel | ( | const PeptideModel & | other | ) |
Copy constructor
other | TODO |
Definition at line 75 of file peptidemodel.cpp.
References m_beginMassDelta, m_countSharedPeaks, m_cterModification, m_experimentalPrecursorMass, m_intensityExperimentalPeaks, m_intensitySharedPeaks, m_nterModification, and mcsp_peakList.
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void pappso::specglob::PeptideModel::assignResidualMass2Cter | ( | ) |
Definition at line 426 of file peptidemodel.cpp.
References getMassDelta().
Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel().
bool pappso::specglob::PeptideModel::checkForAaModification | ( | const pappso::Aa & | aa_modified, |
pappso::PrecisionPtr | precision | ||
) |
try to replace mass differences with the given modifications on a specific amino acid
aa_modified | the modified amino acid |
precision | The mass spectrometer precision |
Definition at line 751 of file peptidemodel.cpp.
References pappso::AaBase::getLetter(), pappso::Aa::getModificationList(), pappso::PrecisionBase::getNominal(), pappso::Aa::getTotalModificationMass(), and m_beginMassDelta.
bool pappso::specglob::PeptideModel::checkForAaModificationP | ( | pappso::AaModificationP | modification, |
pappso::PrecisionPtr | precision | ||
) |
try to replace mass differences with the given modification
modification | : The proposed modification pointer |
precision | : The mass spectrometer precision |
Definition at line 723 of file peptidemodel.cpp.
References pappso::AaModification::getMass(), pappso::PrecisionBase::getNominal(), and m_beginMassDelta.
bool pappso::specglob::PeptideModel::checkForMutation | ( | const pappso::Aa & | amino_acid_candidate, |
pappso::PrecisionPtr | precision | ||
) |
try to replace mass differences with corresponding mutation mass delta
amino acid candidate tested could bear some modifications
amino_acid_candidate | : The amino acid candidate to check |
precision | : The mass spectrometer precision |
Definition at line 617 of file peptidemodel.cpp.
References pappso::AaModification::getInstanceInsertionAccessionByAaLetter(), pappso::AaModification::getInstanceRemovalAccessionByAaLetter(), pappso::AaBase::getLetter(), pappso::AaModification::getMass(), pappso::Aa::getMass(), pappso::Aa::getModificationList(), pappso::PrecisionBase::getNominal(), and m_beginMassDelta.
bool pappso::specglob::PeptideModel::checkForMutations | ( | const std::vector< AminoAcidChar > & | aa_list, |
pappso::PrecisionPtr | precision | ||
) |
try to replace mass differences with corresponding mutations mass delta
amino acid list is tested as raw (no modification)
aa_list | amno acid list to test (beware of cysteine + carbamidomethyl) |
precision | : The mass spectrometer precision |
Definition at line 663 of file peptidemodel.cpp.
References pappso::AaModification::getInstanceInsertionAccessionByAaLetter(), pappso::AaModification::getInstanceRemovalAccessionByAaLetter(), pappso::AaModification::getMass(), pappso::PrecisionBase::getNominal(), and m_beginMassDelta.
PeptideModel & pappso::specglob::PeptideModel::copyDeep | ( | const PeptideModel & | other | ) |
Definition at line 112 of file peptidemodel.cpp.
References m_theoreticalPeakList, and operator=().
Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), pappso::specglob::PostTreatment::tryToCumulateOffSets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().
bool pappso::specglob::PeptideModel::eliminateComplementaryDelta | ( | pappso::PrecisionPtr | precision | ) |
Use to delete offset when there is two opposite mass in the hit modified example : [150.2]SDS[-150.2]KR --> SDSKR
precision | : The mass spectrometer precision |
Definition at line 432 of file peptidemodel.cpp.
References pappso::PrecisionBase::getNominal(), m_beginMassDelta, pappso::specglob::AminoAcidModel::mass_difference, and toString().
Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel().
bool pappso::specglob::PeptideModel::eliminateNegativeOffset | ( | pappso::PrecisionPtr | precision | ) |
Use to try to explain negative offset with deletion of amino acids
precision | : The mass spectrometer precision |
Definition at line 513 of file peptidemodel.cpp.
References pappso::PrecisionBase::getNominal().
Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel().
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private |
Definition at line 352 of file peptidemodel.cpp.
References pappso::a, pappso::b, pappso::PeptideRawFragmentMasses::getDeltaMass(), pappso::AaModification::getMass(), m_beginMassDelta, m_nterModification, m_theoreticalPeakList, mcsp_peakList, pappso::MHPLUS(), pappso::MPROTIUM(), and pappso::y.
Referenced by matchExperimentalPeaks().
std::size_t pappso::specglob::PeptideModel::getCountSharedPeaks | ( | ) | const |
Definition at line 408 of file peptidemodel.cpp.
References m_countSharedPeaks.
Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), pappso::specglob::PostTreatment::tryToCumulateOffSets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().
double pappso::specglob::PeptideModel::getIntensityExperimentalPeaks | ( | ) | const |
Definition at line 420 of file peptidemodel.cpp.
References m_intensityExperimentalPeaks.
double pappso::specglob::PeptideModel::getIntensitySharedPeaks | ( | ) | const |
Definition at line 414 of file peptidemodel.cpp.
References m_intensitySharedPeaks.
double pappso::specglob::PeptideModel::getMass | ( | ) | const |
Definition at line 232 of file peptidemodel.cpp.
References pappso::AaModification::getMass(), m_beginMassDelta, m_cterModification, and m_nterModification.
Referenced by getMassDelta().
double pappso::specglob::PeptideModel::getMassDelta | ( | ) | const |
mass delta between experimental and theoretical mass
Definition at line 248 of file peptidemodel.cpp.
References getMass(), and m_experimentalPrecursorMass.
Referenced by assignResidualMass2Cter(), pappso::specglob::PostTreatment::findBetterPeptideModel(), toString(), and pappso::specglob::PostTreatment::tryToCumulateOffSets().
std::vector< double > pappso::specglob::PeptideModel::getTheoreticalIonMassList | ( | ) | const |
Definition at line 397 of file peptidemodel.cpp.
References m_theoreticalPeakList.
const std::vector< TheoreticalPeakDataPoint > & pappso::specglob::PeptideModel::getTheoreticalPeakDataPointList | ( | ) | const |
Definition at line 589 of file peptidemodel.cpp.
References m_theoreticalPeakList.
QString pappso::specglob::PeptideModel::getTheoreticalPeakDataPointListToString | ( | ) | const |
Definition at line 595 of file peptidemodel.cpp.
References m_theoreticalPeakList, and mcsp_peakList.
void pappso::specglob::PeptideModel::matchExperimentalPeaks | ( | pappso::PrecisionPtr | precision | ) |
Definition at line 274 of file peptidemodel.cpp.
References generateTheoreticalPeaks(), m_countSharedPeaks, m_intensityExperimentalPeaks, m_intensitySharedPeaks, m_theoreticalPeakList, and mcsp_peakList.
Referenced by pappso::specglob::PostTreatment::PostTreatment(), pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), pappso::specglob::PostTreatment::tryToCumulateOffSets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().
std::size_t pappso::specglob::PeptideModel::modifCount | ( | ) | const |
Definition at line 254 of file peptidemodel.cpp.
References m_beginMassDelta.
PeptideModel & pappso::specglob::PeptideModel::operator= | ( | const PeptideModel & | other | ) |
Definition at line 92 of file peptidemodel.cpp.
References m_beginMassDelta, m_countSharedPeaks, m_cterModification, m_experimentalPrecursorMass, m_intensityExperimentalPeaks, m_intensitySharedPeaks, m_nterModification, m_theoreticalPeakList, and mcsp_peakList.
Referenced by copyDeep().
bool pappso::specglob::PeptideModel::removeBracketsForAlignedAA | ( | ) |
Use to remove brackets around not found Amino acids when the B or Y peak corresponding to the amino acid in the sequence is in the experimental peak list
betterModified | : The better sequence of hit Modified |
experimentalMassList | : The list of mass that are in the experimental spectrum |
precision | : The precision of the mass spectrometer |
Definition at line 566 of file peptidemodel.cpp.
References m_theoreticalPeakList, and mcsp_peakList.
Referenced by pappso::specglob::PostTreatment::findBetterPeptideModel().
void pappso::specglob::PeptideModel::setBeginMassDelta | ( | double | delta | ) |
Definition at line 268 of file peptidemodel.cpp.
References m_beginMassDelta.
Referenced by pappso::specglob::SpectralAlignment::buildPeptideModel().
QString pappso::specglob::PeptideModel::toProForma | ( | ) | const |
get the peptide model in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md
Definition at line 175 of file peptidemodel.cpp.
References pappso::AaModification::getAccession(), pappso::AaModification::getInstanceRemovalAccessionByAaLetter(), m_beginMassDelta, and pappso::Utils::toString().
QString pappso::specglob::PeptideModel::toString | ( | ) | const |
Definition at line 125 of file peptidemodel.cpp.
References getMassDelta(), m_beginMassDelta, and pappso::Utils::toString().
Referenced by eliminateComplementaryDelta(), pappso::specglob::PostTreatment::findBetterPeptideModel(), pappso::specglob::PostTreatment::tryBetterPositionOffsets(), and pappso::specglob::PostTreatment::tryToRemoveOffsets().
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Definition at line 219 of file peptidemodel.h.
Referenced by PeptideModel(), checkForAaModification(), checkForAaModificationP(), checkForMutation(), checkForMutations(), eliminateComplementaryDelta(), generateTheoreticalPeaks(), getMass(), modifCount(), operator=(), setBeginMassDelta(), toProForma(), and toString().
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Definition at line 225 of file peptidemodel.h.
Referenced by PeptideModel(), getCountSharedPeaks(), matchExperimentalPeaks(), and operator=().
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Definition at line 223 of file peptidemodel.h.
Referenced by PeptideModel(), PeptideModel(), getMass(), and operator=().
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Definition at line 218 of file peptidemodel.h.
Referenced by PeptideModel(), PeptideModel(), getMassDelta(), and operator=().
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Definition at line 227 of file peptidemodel.h.
Referenced by PeptideModel(), getIntensityExperimentalPeaks(), matchExperimentalPeaks(), and operator=().
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Definition at line 226 of file peptidemodel.h.
Referenced by PeptideModel(), getIntensitySharedPeaks(), matchExperimentalPeaks(), and operator=().
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Definition at line 222 of file peptidemodel.h.
Referenced by PeptideModel(), PeptideModel(), generateTheoreticalPeaks(), getMass(), and operator=().
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Definition at line 216 of file peptidemodel.h.
Referenced by copyDeep(), generateTheoreticalPeaks(), getTheoreticalIonMassList(), getTheoreticalPeakDataPointList(), getTheoreticalPeakDataPointListToString(), matchExperimentalPeaks(), operator=(), and removeBracketsForAlignedAA().
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Definition at line 220 of file peptidemodel.h.
Referenced by PeptideModel(), PeptideModel(), generateTheoreticalPeaks(), getTheoreticalPeakDataPointListToString(), matchExperimentalPeaks(), operator=(), and removeBracketsForAlignedAA().