libpappsomspp
Library for mass spectrometry
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#include <peptidefragmention.h>
Public Member Functions | |
PeptideFragmentIon (const PeptideFragmentSp &sp_fragment, PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss) | |
PeptideFragmentIon (const PeptideFragmentSp &sp_fragment, PeptideIon ion_type) | |
PeptideFragmentIon (const PeptideFragmentIon &other) | |
PeptideFragmentIon (PeptideFragmentIon &&toCopy) | |
virtual | ~PeptideFragmentIon () |
PeptideFragmentIonSp | makePeptideFragmentIonSp () const |
virtual unsigned int | size () const override |
virtual const QString | getSequence () const override |
amino acid sequence without modification More... | |
virtual const PeptideFragmentSp & | getPeptideFragmentSp () const |
virtual int | getNumberOfAtom (AtomIsotopeSurvey atom) const override |
get the number of atom C, O, N, H in the molecule More... | |
virtual int | getNumberOfIsotope (Isotope isotope) const override |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More... | |
virtual const QString | getName () const override |
pappso_double | getMass () const override |
const QString | getPeptideIonName () const |
const QString | getCompletePeptideIonName (unsigned int charge) const |
get a complete ion name string More... | |
PeptideIon | getPeptideIonType () const |
PeptideDirection | getPeptideIonDirection () const |
unsigned int | getNumberOfNeutralPhosphoLoss () const |
virtual bool | isPalindrome () const override |
tells if the peptide sequence is a palindrome More... | |
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virtual const QString | getSequenceLi () const |
amino acid sequence without modification where L are replaced by I More... | |
virtual const QString | getFormula (unsigned int charge) const final |
virtual bool | matchPeak (PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final |
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Ion () | |
~Ion () | |
virtual pappso_double | getMz (unsigned int charge) const final |
Static Public Member Functions | |
static PeptideDirection | getPeptideIonDirection (PeptideIon ion_type) |
static const QString | getPeptideIonName (PeptideIon ion_type) |
static const QColor | getPeptideIonColor (PeptideIon ion_type) |
Private Attributes | |
const PeptideFragmentSp | msp_fragment |
const PeptideIon | m_ionType |
pappso_double | m_mass = 0 |
unsigned int | m_neutralPhosphoLossNumber = 0 |
Definition at line 49 of file peptidefragmention.h.
pappso::PeptideFragmentIon::PeptideFragmentIon | ( | const PeptideFragmentSp & | sp_fragment, |
PeptideIon | ion_type, | ||
unsigned int | number_of_neutral_phospho_loss | ||
) |
Definition at line 45 of file peptidefragmention.cpp.
References pappso::b, pappso::bp, pappso::PeptideRawFragmentMasses::getDeltaMass(), pappso::getPeptideIonDirection(), pappso::PeptideFragment::getPeptideIonDirectionName(), getPeptideIonName(), m_ionType, m_mass, m_neutralPhosphoLossNumber, pappso::MASSH2O(), pappso::MASSPHOSPHORYLATEDR(), msp_fragment, pappso::y, and pappso::yp.
pappso::PeptideFragmentIon::PeptideFragmentIon | ( | const PeptideFragmentSp & | sp_fragment, |
PeptideIon | ion_type | ||
) |
Definition at line 39 of file peptidefragmention.cpp.
pappso::PeptideFragmentIon::PeptideFragmentIon | ( | const PeptideFragmentIon & | other | ) |
pappso::PeptideFragmentIon::PeptideFragmentIon | ( | PeptideFragmentIon && | toCopy | ) |
Definition at line 89 of file peptidefragmention.cpp.
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virtual |
Definition at line 97 of file peptidefragmention.cpp.
const QString pappso::PeptideFragmentIon::getCompletePeptideIonName | ( | unsigned int | charge | ) | const |
get a complete ion name string
charge |
Definition at line 110 of file peptidefragmention.cpp.
References pappso::bp, getPeptideIonName(), m_ionType, m_neutralPhosphoLossNumber, msp_fragment, size(), and pappso::yp.
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overridevirtual |
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overridevirtual |
Reimplemented from pappso::PeptideInterface.
Definition at line 575 of file peptidefragmention.cpp.
References getPeptideIonName(), m_ionType, and size().
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overridevirtual |
get the number of atom C, O, N, H in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 259 of file peptidefragmention.cpp.
References pappso::a, pappso::ao, pappso::astar, pappso::b, pappso::bo, pappso::bp, pappso::bstar, pappso::C, pappso::c, pappso::H, m_ionType, m_neutralPhosphoLossNumber, msp_fragment, pappso::N, pappso::O, pappso::S, pappso::x, pappso::y, pappso::yo, pappso::yp, pappso::ystar, and pappso::z.
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overridevirtual |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 543 of file peptidefragmention.cpp.
References msp_fragment.
unsigned int pappso::PeptideFragmentIon::getNumberOfNeutralPhosphoLoss | ( | ) | const |
Definition at line 597 of file peptidefragmention.cpp.
References m_neutralPhosphoLossNumber.
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virtual |
Definition at line 569 of file peptidefragmention.cpp.
References msp_fragment.
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static |
Definition at line 204 of file peptidefragmention.cpp.
References pappso::a, pappso::ao, pappso::astar, pappso::b, pappso::bo, pappso::bp, pappso::bstar, pappso::c, getPeptideIonName(), m_ionType, pappso::x, pappso::y, pappso::yo, pappso::yp, pappso::ystar, and pappso::z.
Referenced by pappso::QCPSpectrum::QCPSpectrum(), and pappso::MassSpectrumWidget::plot().
PeptideDirection pappso::PeptideFragmentIon::getPeptideIonDirection | ( | ) | const |
Definition at line 592 of file peptidefragmention.cpp.
References msp_fragment.
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static |
Definition at line 103 of file peptidefragmention.cpp.
References pappso::getPeptideIonDirection().
const QString pappso::PeptideFragmentIon::getPeptideIonName | ( | ) | const |
Definition at line 138 of file peptidefragmention.cpp.
References pappso::bp, m_ionType, m_neutralPhosphoLossNumber, and pappso::yp.
Referenced by PeptideFragmentIon(), getCompletePeptideIonName(), getName(), pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp(), and getPeptideIonColor().
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static |
Definition at line 150 of file peptidefragmention.cpp.
References pappso::a, pappso::ao, pappso::astar, pappso::b, pappso::bo, pappso::bp, pappso::bstar, pappso::c, m_ionType, pappso::x, pappso::y, pappso::yo, pappso::yp, pappso::ystar, and pappso::z.
PeptideIon pappso::PeptideFragmentIon::getPeptideIonType | ( | ) | const |
Definition at line 587 of file peptidefragmention.cpp.
References m_ionType.
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overridevirtual |
amino acid sequence without modification
Implements pappso::PeptideInterface.
Definition at line 563 of file peptidefragmention.cpp.
References msp_fragment.
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overridevirtual |
tells if the peptide sequence is a palindrome
Implements pappso::PeptideInterface.
Definition at line 603 of file peptidefragmention.cpp.
References msp_fragment.
PeptideFragmentIonSp pappso::PeptideFragmentIon::makePeptideFragmentIonSp | ( | ) | const |
Definition at line 550 of file peptidefragmention.cpp.
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overridevirtual |
Implements pappso::PeptideInterface.
Definition at line 557 of file peptidefragmention.cpp.
References msp_fragment.
Referenced by getCompletePeptideIonName(), and getName().
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private |
Definition at line 96 of file peptidefragmention.h.
Referenced by PeptideFragmentIon(), getCompletePeptideIonName(), getName(), getNumberOfAtom(), getPeptideIonColor(), getPeptideIonName(), and getPeptideIonType().
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private |
Definition at line 98 of file peptidefragmention.h.
Referenced by PeptideFragmentIon(), and getMass().
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private |
Definition at line 102 of file peptidefragmention.h.
Referenced by PeptideFragmentIon(), getCompletePeptideIonName(), getNumberOfAtom(), getNumberOfNeutralPhosphoLoss(), and getPeptideIonName().
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private |
Definition at line 95 of file peptidefragmention.h.
Referenced by PeptideFragmentIon(), getCompletePeptideIonName(), getNumberOfAtom(), getNumberOfIsotope(), getPeptideFragmentSp(), getPeptideIonDirection(), getSequence(), isPalindrome(), and size().