libpappsomspp
Library for mass spectrometry
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#include <peptideisotopespectrummatch.h>
Public Types | |
typedef std::list< PeakIonIsotopeMatch >::const_iterator | const_iterator |
Public Member Functions | |
PeptideIsotopeSpectrumMatch (const MassSpectrum &spectrum, const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, const std::list< PeptideIon > &ion_type_list, unsigned int max_isotope_number, unsigned int max_isotope_rank) | |
annotate spectrum with peptide ions and isotopes More... | |
PeptideIsotopeSpectrumMatch (const MassSpectrum &spectrum, std::vector< PeptideNaturalIsotopeAverageSp > v_peptideIsotopeList, std::vector< PeptideFragmentIonSp > v_peptideIonList, PrecisionPtr precision) | |
PeptideIsotopeSpectrumMatch (const PeptideIsotopeSpectrumMatch &other) | |
virtual | ~PeptideIsotopeSpectrumMatch () |
const std::list< PeakIonIsotopeMatch > & | getPeakIonIsotopeMatchList () const |
std::size_t | size () const |
const_iterator | begin () const |
const_iterator | end () const |
void | dropPeaksLackingMonoisotope () |
Private Member Functions | |
virtual std::vector< DataPoint >::iterator | getBestPeakIterator (std::vector< DataPoint > &peak_list, const PeptideNaturalIsotopeAverage &ion) const |
Private Attributes | |
PrecisionPtr | _precision |
std::list< PeakIonIsotopeMatch > | _peak_ion_match_list |
Definition at line 39 of file peptideisotopespectrummatch.h.
typedef std::list<PeakIonIsotopeMatch>::const_iterator pappso::PeptideIsotopeSpectrumMatch::const_iterator |
Definition at line 71 of file peptideisotopespectrummatch.h.
pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch | ( | const MassSpectrum & | spectrum, |
const PeptideSp & | peptide_sp, | ||
unsigned int | parent_charge, | ||
PrecisionPtr | precision, | ||
const std::list< PeptideIon > & | ion_type_list, | ||
unsigned int | max_isotope_number, | ||
unsigned int | max_isotope_rank | ||
) |
annotate spectrum with peptide ions and isotopes
spectrum | the spectrum to annotate |
peptide_sp | peptide to fragment |
parent_charge | charge of the ion parent |
precision | MS2 mass measurement precision |
ion_list | ion types to compute fragments |
max_isotope_number | maximum isotope number to compute (0 means only monoisotope is computed) |
max_isotope_rank | maximum rank inside isotope level to compute |
pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch | ( | const MassSpectrum & | spectrum, |
std::vector< PeptideNaturalIsotopeAverageSp > | v_peptideIsotopeList, | ||
std::vector< PeptideFragmentIonSp > | v_peptideIonList, | ||
PrecisionPtr | precision | ||
) |
Definition at line 112 of file peptideisotopespectrummatch.cpp.
References _peak_ion_match_list, and getBestPeakIterator().
pappso::PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch | ( | const PeptideIsotopeSpectrumMatch & | other | ) |
Definition at line 150 of file peptideisotopespectrummatch.cpp.
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virtual |
Definition at line 158 of file peptideisotopespectrummatch.cpp.
PeptideIsotopeSpectrumMatch::const_iterator pappso::PeptideIsotopeSpectrumMatch::begin | ( | ) | const |
Definition at line 203 of file peptideisotopespectrummatch.cpp.
References _peak_ion_match_list.
void pappso::PeptideIsotopeSpectrumMatch::dropPeaksLackingMonoisotope | ( | ) |
Definition at line 214 of file peptideisotopespectrummatch.cpp.
References _peak_ion_match_list, pappso::a, and pappso::b.
PeptideIsotopeSpectrumMatch::const_iterator pappso::PeptideIsotopeSpectrumMatch::end | ( | ) | const |
Definition at line 208 of file peptideisotopespectrummatch.cpp.
References _peak_ion_match_list.
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privatevirtual |
Definition at line 164 of file peptideisotopespectrummatch.cpp.
References pappso::PeptideNaturalIsotopeAverage::matchPeak().
Referenced by PeptideIsotopeSpectrumMatch().
const std::list< PeakIonIsotopeMatch > & pappso::PeptideIsotopeSpectrumMatch::getPeakIonIsotopeMatchList | ( | ) | const |
Definition at line 192 of file peptideisotopespectrummatch.cpp.
References _peak_ion_match_list.
Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), and pappso::MassSpectrumWidget::peptideAnnotate().
std::size_t pappso::PeptideIsotopeSpectrumMatch::size | ( | ) | const |
Definition at line 198 of file peptideisotopespectrummatch.cpp.
References _peak_ion_match_list.
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private |
Definition at line 85 of file peptideisotopespectrummatch.h.
Referenced by PeptideIsotopeSpectrumMatch(), begin(), dropPeaksLackingMonoisotope(), end(), getPeakIonIsotopeMatchList(), and size().
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private |
Definition at line 84 of file peptideisotopespectrummatch.h.