libpappsomspp
Library for mass spectrometry
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#include <peptidefragmentionlistbase.h>
Public Member Functions | |
PeptideFragmentIonListBase (const PeptideSp &peptide, const IonList &ions) | |
PeptideFragmentIonListBase (const PeptideFragmentIonListBase &other) | |
virtual | ~PeptideFragmentIonListBase () |
PeptideFragmentIonListBaseSp | makePeptideFragmentIonListBaseSp () const |
const std::list< PeptideIon > & | getIonList () const |
unsigned int | getPhosphorylationNumber () const |
virtual const PeptideSp & | getPeptideSp () const |
const std::list< PeptideFragmentIonSp > | getPeptideFragmentIonSp (PeptideIon ion_type) const |
const PeptideFragmentIonSp & | getPeptideFragmentIonSp (PeptideIon ion_type, unsigned int size) const |
const PeptideFragmentIonSp & | getPeptideFragmentIonSp (PeptideIon ion_type, unsigned int size, unsigned int number_of_neutral_phospho_loss) const |
std::list< PeptideFragmentIonSp >::const_iterator | begin () const |
std::list< PeptideFragmentIonSp >::const_iterator | end () const |
const std::list< PeptideFragmentIonSp > & | getPeptideFragmentIonList () const |
unsigned int | size () const |
Static Public Member Functions | |
static std::list< PeptideIon > | getCIDionList () |
static std::list< PeptideIon > | getETDionList () |
Static Protected Member Functions | |
static const std::list< PeptideFragmentSp > | getPeptideFragmentList (const PeptideSp &peptide) |
Protected Attributes | |
const PeptideSp | msp_peptide |
std::list< PeptideFragmentIonSp > | msp_peptide_fragment_ion_list |
IonList | m_ionList |
unsigned int | m_phosphorylationNumber |
Private Types | |
using | IonList = std::list< PeptideIon > |
Definition at line 45 of file peptidefragmentionlistbase.h.
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private |
Definition at line 47 of file peptidefragmentionlistbase.h.
pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase | ( | const PeptideSp & | peptide, |
const IonList & | ions | ||
) |
Definition at line 78 of file peptidefragmentionlistbase.cpp.
References pappso::a, pappso::b, pappso::bo, pappso::bp, pappso::bstar, pappso::c, pappso::Cter, pappso::AaModification::getInstance(), getPeptideFragmentList(), m_ionList, m_phosphorylationNumber, msp_peptide, msp_peptide_fragment_ion_list, pappso::PappsoException::qwhat(), pappso::y, pappso::yo, pappso::yp, pappso::ystar, and pappso::z.
pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase | ( | const PeptideFragmentIonListBase & | other | ) |
Definition at line 195 of file peptidefragmentionlistbase.cpp.
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virtual |
Definition at line 212 of file peptidefragmentionlistbase.cpp.
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inline |
Definition at line 88 of file peptidefragmentionlistbase.h.
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inline |
Definition at line 94 of file peptidefragmentionlistbase.h.
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static |
Definition at line 41 of file peptidefragmentionlistbase.cpp.
References pappso::a, pappso::b, pappso::bo, pappso::bp, pappso::bstar, pappso::y, pappso::yo, pappso::yp, and pappso::ystar.
Referenced by pappso::MassSpectrumWidget::MassSpectrumWidget().
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static |
Definition at line 59 of file peptidefragmentionlistbase.cpp.
References pappso::c, pappso::y, pappso::yo, pappso::ystar, and pappso::z.
const std::list< PeptideIon > & pappso::PeptideFragmentIonListBase::getIonList | ( | ) | const |
Definition at line 73 of file peptidefragmentionlistbase.cpp.
References m_ionList.
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inline |
Definition at line 101 of file peptidefragmentionlistbase.h.
const std::list< PeptideFragmentIonSp > pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp | ( | PeptideIon | ion_type | ) | const |
Definition at line 234 of file peptidefragmentionlistbase.cpp.
References msp_peptide_fragment_ion_list.
Referenced by getPeptideFragmentIonSp(), and pappso::PeptideSpectrumMatch::privMatchIonList().
const PeptideFragmentIonSp & pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp | ( | PeptideIon | ion_type, |
unsigned int | size | ||
) | const |
Definition at line 248 of file peptidefragmentionlistbase.cpp.
References getPeptideFragmentIonSp(), and size().
const PeptideFragmentIonSp & pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp | ( | PeptideIon | ion_type, |
unsigned int | size, | ||
unsigned int | number_of_neutral_phospho_loss | ||
) | const |
Definition at line 256 of file peptidefragmentionlistbase.cpp.
References pappso::PeptideFragmentIon::getPeptideIonName(), msp_peptide_fragment_ion_list, and size().
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staticprotected |
Definition at line 217 of file peptidefragmentionlistbase.cpp.
References pappso::Cter, pappso::max, and pappso::Nter.
Referenced by PeptideFragmentIonListBase().
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inlinevirtual |
Definition at line 72 of file peptidefragmentionlistbase.h.
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inline |
Definition at line 66 of file peptidefragmentionlistbase.h.
PeptideFragmentIonListBaseSp pappso::PeptideFragmentIonListBase::makePeptideFragmentIonListBaseSp | ( | ) | const |
Definition at line 206 of file peptidefragmentionlistbase.cpp.
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inline |
Definition at line 111 of file peptidefragmentionlistbase.h.
Referenced by getPeptideFragmentIonSp().
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protected |
Definition at line 52 of file peptidefragmentionlistbase.h.
Referenced by PeptideFragmentIonListBase(), and getIonList().
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protected |
Definition at line 53 of file peptidefragmentionlistbase.h.
Referenced by PeptideFragmentIonListBase().
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protected |
Definition at line 50 of file peptidefragmentionlistbase.h.
Referenced by PeptideFragmentIonListBase().
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protected |
Definition at line 51 of file peptidefragmentionlistbase.h.
Referenced by PeptideFragmentIonListBase(), and getPeptideFragmentIonSp().