libpappsomspp
Library for mass spectrometry
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#include <peptidefragment.h>
Public Member Functions | |
PeptideFragment (const PeptideSp &sp_peptide, PeptideDirection direction, unsigned int size) | |
PeptideFragment (const PeptideFragment &other) | |
PeptideFragment (PeptideFragment &&toCopy) | |
virtual | ~PeptideFragment () |
virtual const PeptideSp & | getPeptideSp () const |
virtual unsigned int | size () const override |
virtual const QString | getSequence () const override |
amino acid sequence without modification More... | |
virtual pappso_double | getMass () const override |
PeptideDirection | getPeptideIonDirection () 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 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 | getName () const |
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 const QString | getPeptideIonDirectionName (PeptideDirection direction) |
Private Attributes | |
const PeptideSp | msp_peptide |
const PeptideDirection | m_direction |
const unsigned int | m_size = 0 |
AaModificationP | m_nterCterCleavage |
pappso_double | m_mass = 0 |
Definition at line 47 of file peptidefragment.h.
pappso::PeptideFragment::PeptideFragment | ( | const PeptideSp & | sp_peptide, |
PeptideDirection | direction, | ||
unsigned int | size | ||
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Definition at line 38 of file peptidefragment.cpp.
References pappso::AaModification::getInstance(), pappso::AaModification::getMass(), m_direction, m_mass, m_nterCterCleavage, m_size, msp_peptide, and pappso::Nter.
pappso::PeptideFragment::PeptideFragment | ( | const PeptideFragment & | other | ) |
pappso::PeptideFragment::PeptideFragment | ( | PeptideFragment && | toCopy | ) |
Definition at line 84 of file peptidefragment.cpp.
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virtual |
Definition at line 93 of file peptidefragment.cpp.
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overridevirtual |
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overridevirtual |
get the number of atom C, O, N, H in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 132 of file peptidefragment.cpp.
References pappso::AaModification::getNumberOfAtom(), m_direction, m_nterCterCleavage, m_size, msp_peptide, and pappso::Nter.
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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 165 of file peptidefragment.cpp.
References m_direction, m_size, msp_peptide, and pappso::Nter.
PeptideDirection pappso::PeptideFragment::getPeptideIonDirection | ( | ) | const |
Definition at line 216 of file peptidefragment.cpp.
References m_direction.
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static |
Definition at line 98 of file peptidefragment.cpp.
References pappso::Cter, and pappso::Nter.
Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon(), and pappso::XtandemHyperscore::getXtandemPredictedIonIntensityFactor().
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virtual |
Definition at line 199 of file peptidefragment.cpp.
References msp_peptide.
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overridevirtual |
amino acid sequence without modification
Implements pappso::PeptideInterface.
Definition at line 115 of file peptidefragment.cpp.
References m_direction, m_size, msp_peptide, and pappso::Nter.
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overridevirtual |
tells if the peptide sequence is a palindrome
Implements pappso::PeptideInterface.
Definition at line 222 of file peptidefragment.cpp.
References msp_peptide.
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overridevirtual |
Implements pappso::PeptideInterface.
Definition at line 204 of file peptidefragment.cpp.
References m_size.
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private |
Definition at line 75 of file peptidefragment.h.
Referenced by PeptideFragment(), getNumberOfAtom(), getNumberOfIsotope(), getPeptideIonDirection(), and getSequence().
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private |
Definition at line 81 of file peptidefragment.h.
Referenced by PeptideFragment(), and getMass().
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private |
Definition at line 79 of file peptidefragment.h.
Referenced by PeptideFragment(), and getNumberOfAtom().
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private |
Definition at line 76 of file peptidefragment.h.
Referenced by PeptideFragment(), getNumberOfAtom(), getNumberOfIsotope(), getSequence(), and size().
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private |
Definition at line 74 of file peptidefragment.h.
Referenced by PeptideFragment(), getNumberOfAtom(), getNumberOfIsotope(), getPeptideSp(), getSequence(), and isPalindrome().