libpappsomspp
Library for mass spectrometry
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#include <experimentalspectrum.h>
Public Member Functions | |
ExperimentalSpectrum (const pappso::QualifiedMassSpectrum &qmass_spectrum, pappso::PrecisionPtr precision_ptr) | |
ExperimentalSpectrum (const ExperimentalSpectrum &other) | |
virtual | ~ExperimentalSpectrum () |
std::vector< double > | getMassList () const |
double | getSymetricMz (double mz) const |
compute the symetric mass for debuggin purpose | |
double | getTargetMzSum () const |
double | getPrecursorMass () const |
std::vector< double > | getMassList (ExperimentalSpectrumDataPointType type) const |
QString | toString () const |
const pappso::QualifiedMassSpectrum & | getQualifiedMassSpectrum () const |
std::vector< ExperimentalSpectrumDataPoint >::const_reverse_iterator | reverseFindDiffMz (std::size_t start_position, const pappso::MzRange &targeted_mass_range) const |
find the peak for wich mass difference from rbegin corresponds to aaTheoMass Find if a peak back in the peak list has a mass difference that corresponds to the targeted mass | |
Private Member Functions | |
void | createSymetricPeakList () |
add symetric peaks to the spectrum Create a SymetricPeakList that contain symmetric peaks and the information if a peak is the initial peak, the symmetric peak, or both if already exist. assuming fragment ion charge is 1 | |
std::vector< pappso::DataPoint >::const_iterator | findMz (double mz) |
find the correspondin mz in the mass spectrum (given the precision) | |
Private Attributes | |
pappso::QualifiedMassSpectrum | m_qualifiedMassSpectrum |
double | m_targetMzSum |
double | m_precursorMass |
pappso::PrecisionPtr | m_precisionPtr |
Definition at line 63 of file experimentalspectrum.h.
pappso::specglob::ExperimentalSpectrum::ExperimentalSpectrum | ( | const pappso::QualifiedMassSpectrum & | qmass_spectrum, |
pappso::PrecisionPtr | precision_ptr | ||
) |
Default constructor
Definition at line 45 of file experimentalspectrum.cpp.
References createSymetricPeakList(), m_precisionPtr, and m_qualifiedMassSpectrum.
pappso::specglob::ExperimentalSpectrum::ExperimentalSpectrum | ( | const ExperimentalSpectrum & | other | ) |
Copy constructor
other | TODO |
Definition at line 55 of file experimentalspectrum.cpp.
References m_precisionPtr, m_qualifiedMassSpectrum, and m_targetMzSum.
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add symetric peaks to the spectrum Create a SymetricPeakList that contain symmetric peaks and the information if a peak is the initial peak, the symmetric peak, or both if already exist. assuming fragment ion charge is 1
Definition at line 68 of file experimentalspectrum.cpp.
References pappso::a, pappso::b, pappso::specglob::both, findMz(), pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getNativeId(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), pappso::QualifiedMassSpectrum::getPrecursorMz(), getSymetricMz(), m_precursorMass, m_qualifiedMassSpectrum, m_targetMzSum, pappso::MASSH2O(), pappso::MHPLUS(), pappso::MPROTIUM(), pappso::specglob::native, pappso::specglob::symetric, and pappso::specglob::synthetic.
Referenced by ExperimentalSpectrum().
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find the correspondin mz in the mass spectrum (given the precision)
Definition at line 160 of file experimentalspectrum.cpp.
References pappso::findFirstEqualOrGreaterX(), pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::MzRange::lower(), m_precisionPtr, m_qualifiedMassSpectrum, pappso::mz, and pappso::MzRange::upper().
Referenced by createSymetricPeakList().
std::vector< double > pappso::specglob::ExperimentalSpectrum::getMassList | ( | ) | const |
Definition at line 186 of file experimentalspectrum.cpp.
std::vector< double > pappso::specglob::ExperimentalSpectrum::getMassList | ( | ExperimentalSpectrumDataPointType | type | ) | const |
Definition at line 204 of file experimentalspectrum.cpp.
double pappso::specglob::ExperimentalSpectrum::getPrecursorMass | ( | ) | const |
Definition at line 229 of file experimentalspectrum.cpp.
References m_precursorMass.
const pappso::QualifiedMassSpectrum & pappso::specglob::ExperimentalSpectrum::getQualifiedMassSpectrum | ( | ) | const |
Definition at line 278 of file experimentalspectrum.cpp.
References m_qualifiedMassSpectrum.
double pappso::specglob::ExperimentalSpectrum::getSymetricMz | ( | double | mz | ) | const |
compute the symetric mass for debuggin purpose
Definition at line 198 of file experimentalspectrum.cpp.
References m_targetMzSum, and pappso::mz.
Referenced by createSymetricPeakList().
double pappso::specglob::ExperimentalSpectrum::getTargetMzSum | ( | ) | const |
Definition at line 180 of file experimentalspectrum.cpp.
References m_targetMzSum.
std::vector< ExperimentalSpectrumDataPoint >::const_reverse_iterator pappso::specglob::ExperimentalSpectrum::reverseFindDiffMz | ( | std::size_t | start_position, |
const pappso::MzRange & | targeted_mass_range | ||
) | const |
find the peak for wich mass difference from rbegin corresponds to aaTheoMass Find if a peak back in the peak list has a mass difference that corresponds to the targeted mass
start_position | reverse iterator on the reference peak to look for mass difference from |
targeted_mass_range | the mass difference to look forconst pappso::PeptideSp peptide_sp |
Definition at line 235 of file experimentalspectrum.cpp.
References pappso::MzRange::getMz(), pappso::MzRange::lower(), and pappso::MzRange::upper().
Referenced by pappso::specglob::SpectralAlignment::fillMatricesWithScores().
QString pappso::specglob::ExperimentalSpectrum::toString | ( | ) | const |
Definition at line 217 of file experimentalspectrum.cpp.
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Definition at line 133 of file experimentalspectrum.h.
Referenced by ExperimentalSpectrum(), ExperimentalSpectrum(), and findMz().
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Definition at line 132 of file experimentalspectrum.h.
Referenced by createSymetricPeakList(), and getPrecursorMass().
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Definition at line 130 of file experimentalspectrum.h.
Referenced by ExperimentalSpectrum(), ExperimentalSpectrum(), createSymetricPeakList(), findMz(), and getQualifiedMassSpectrum().
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Definition at line 131 of file experimentalspectrum.h.
Referenced by ExperimentalSpectrum(), createSymetricPeakList(), getSymetricMz(), and getTargetMzSum().