libpappsomspp
Library for mass spectrometry
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#include <peptidespectrummatch.h>
Public Types | |
typedef std::list< PeakIonMatch >::const_iterator | const_iterator |
Public Member Functions | |
PeptideSpectrumMatch (const MassSpectrum &spectrum, const pappso::PeptideSp &peptideSp, unsigned int parent_charge, PrecisionPtr precision, const std::list< PeptideIon > &ion_type_list) | |
PeptideSpectrumMatch (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &peptide_fragment_ion_list, unsigned int parent_charge, PrecisionPtr precision, const std::list< PeptideIon > &ion_type_list) | |
PeptideSpectrumMatch (const MassSpectrum &spectrum, std::vector< PeptideFragmentIonSp > &v_peptide_fragment_ion, std::vector< unsigned int > &v_peptide_fragment_ion_charge, PrecisionPtr precision) | |
PeptideSpectrumMatch (const PeptideSpectrumMatch &other) | |
virtual | ~PeptideSpectrumMatch () |
bool | contains (const PeptideFragmentIon *peptideFragmentIonSp, unsigned int z) const |
unsigned int | size () const |
const_iterator | begin () const |
const_iterator | end () const |
unsigned int | countTotalMatchedIons () const |
const std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > & | getIonTypeCountArray () const |
Private Member Functions | |
void | privMatchIonList (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &fragmentIonList, unsigned int max_charge, const std::list< PeptideIon > &ion_type_list) |
virtual std::list< DataPoint >::iterator | getBestPeakIterator (std::list< DataPoint > &peak_list, const PeptideFragmentIonSp &ion, unsigned int charge) const |
Private Attributes | |
PrecisionPtr | _precision |
std::list< PeakIonMatch > | _peak_ion_match_list |
std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > | _ion_type_count = {{0}} |
Definition at line 43 of file peptidespectrummatch.h.
typedef std::list<PeakIonMatch>::const_iterator pappso::PeptideSpectrumMatch::const_iterator |
Definition at line 69 of file peptidespectrummatch.h.
pappso::PeptideSpectrumMatch::PeptideSpectrumMatch | ( | const MassSpectrum & | spectrum, |
const pappso::PeptideSp & | peptideSp, | ||
unsigned int | parent_charge, | ||
PrecisionPtr | precision, | ||
const std::list< PeptideIon > & | ion_type_list | ||
) |
Definition at line 146 of file peptidespectrummatch.cpp.
References _ion_type_count, privMatchIonList(), and pappso::y.
pappso::PeptideSpectrumMatch::PeptideSpectrumMatch | ( | const MassSpectrum & | spectrum, |
const PeptideFragmentIonListBase & | peptide_fragment_ion_list, | ||
unsigned int | parent_charge, | ||
PrecisionPtr | precision, | ||
const std::list< PeptideIon > & | ion_type_list | ||
) |
Definition at line 132 of file peptidespectrummatch.cpp.
References _ion_type_count, privMatchIonList(), and pappso::y.
pappso::PeptideSpectrumMatch::PeptideSpectrumMatch | ( | const MassSpectrum & | spectrum, |
std::vector< PeptideFragmentIonSp > & | v_peptide_fragment_ion, | ||
std::vector< unsigned int > & | v_peptide_fragment_ion_charge, | ||
PrecisionPtr | precision | ||
) |
Definition at line 86 of file peptidespectrummatch.cpp.
References _ion_type_count, _peak_ion_match_list, getBestPeakIterator(), and pappso::y.
pappso::PeptideSpectrumMatch::PeptideSpectrumMatch | ( | const PeptideSpectrumMatch & | other | ) |
Definition at line 162 of file peptidespectrummatch.cpp.
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virtual |
Definition at line 202 of file peptidespectrummatch.cpp.
PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::begin | ( | ) | const |
Definition at line 214 of file peptidespectrummatch.cpp.
References _peak_ion_match_list.
bool pappso::PeptideSpectrumMatch::contains | ( | const PeptideFragmentIon * | peptideFragmentIonSp, |
unsigned int | z | ||
) | const |
Definition at line 237 of file peptidespectrummatch.cpp.
References _peak_ion_match_list, pappso::PeakIonMatch::getCharge(), pappso::PeakIonMatch::getPeptideFragmentIonSp(), and pappso::z.
unsigned int pappso::PeptideSpectrumMatch::countTotalMatchedIons | ( | ) | const |
Definition at line 225 of file peptidespectrummatch.cpp.
References _ion_type_count.
PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::end | ( | ) | const |
Definition at line 219 of file peptidespectrummatch.cpp.
References _peak_ion_match_list.
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privatevirtual |
Definition at line 169 of file peptidespectrummatch.cpp.
References _precision.
Referenced by PeptideSpectrumMatch(), and privMatchIonList().
const std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > & pappso::PeptideSpectrumMatch::getIonTypeCountArray | ( | ) | const |
Definition at line 231 of file peptidespectrummatch.cpp.
References _ion_type_count.
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private |
Definition at line 45 of file peptidespectrummatch.cpp.
References _ion_type_count, _peak_ion_match_list, getBestPeakIterator(), and pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp().
Referenced by PeptideSpectrumMatch().
unsigned int pappso::PeptideSpectrumMatch::size | ( | ) | const |
Definition at line 208 of file peptidespectrummatch.cpp.
References _peak_ion_match_list.
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private |
Definition at line 96 of file peptidespectrummatch.h.
Referenced by PeptideSpectrumMatch(), countTotalMatchedIons(), getIonTypeCountArray(), and privMatchIonList().
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private |
Definition at line 94 of file peptidespectrummatch.h.
Referenced by PeptideSpectrumMatch(), begin(), contains(), end(), privMatchIonList(), and size().
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private |
Definition at line 92 of file peptidespectrummatch.h.
Referenced by getBestPeakIterator().