libpappsomspp
Library for mass spectrometry
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#include <aa.h>
Public Member Functions | |
Aa (char aa_letter) | |
Aa (AminoAcidChar aa_char) | |
Aa (const Aa &aa) | |
Aa (Aa &&toCopy) | |
Aa & | operator= (const Aa &toCopy) |
virtual | ~Aa () |
pappso_double | getMass () const override |
int | getNumberOfAtom (AtomIsotopeSurvey atom) const override final |
get the number of atom C, O, N, H in the molecule More... | |
int | getNumberOfIsotope (Isotope isotope) const override final |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More... | |
unsigned int | getNumberOfModification (AaModificationP mod) const |
const QString | toString () const |
const QString | toAbsoluteString () const |
void | addAaModification (AaModificationP aaModification) |
void | removeAaModification (AaModificationP aaModification) |
void | replaceAaModification (AaModificationP oldmod, AaModificationP newmod) |
replaces all occurences of a modification by a new one More... | |
AaModificationP | getInternalNterModification () const |
AaModificationP | getInternalCterModification () const |
void | removeInternalNterModification () |
void | removeInternalCterModification () |
const std::vector< AaModificationP > & | getModificationList () const |
bool | isLesser (Aa const &r) const |
bool | isAaEqual (Aa const &r) const |
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virtual const char & | getLetter () const |
virtual void | replaceLeucineIsoleucine () |
Private Attributes | |
std::vector< AaModificationP > | m_listMod |
Additional Inherited Members | |
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static const std::vector< AminoAcidChar > & | getAminoAcidCharList () |
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AaBase (char aa_letter) | |
AaBase (AminoAcidChar aa_char) | |
AaBase (const AaBase &aabase) | |
virtual | ~AaBase () |
int | getNumberOfIsotope (Isotope isotope) const override |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More... | |
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static pappso_double | getAaMass (char aa_letter) |
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char | m_aaLetter |
pappso::Aa::Aa | ( | AminoAcidChar | aa_char | ) |
pappso::Aa::Aa | ( | const Aa & | aa | ) |
pappso::Aa::Aa | ( | Aa && | toCopy | ) |
void pappso::Aa::addAaModification | ( | AaModificationP | aaModification | ) |
Definition at line 150 of file aa.cpp.
References pappso::AaModification::getAccession(), and m_listMod.
Referenced by pappso::Peptide::Peptide(), and pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition().
AaModificationP pappso::Aa::getInternalCterModification | ( | ) | const |
AaModificationP pappso::Aa::getInternalNterModification | ( | ) | const |
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overridevirtual |
Reimplemented from pappso::AaBase.
Definition at line 79 of file aa.cpp.
References pappso::AaBase::getMass(), and m_listMod.
Referenced by pappso::AaModification::createInstanceMutation().
const std::vector< AaModificationP > & pappso::Aa::getModificationList | ( | ) | const |
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finaloverridevirtual |
get the number of atom C, O, N, H in the molecule
Reimplemented from pappso::AaBase.
Definition at line 166 of file aa.cpp.
References pappso::AaBase::getNumberOfAtom(), and m_listMod.
Referenced by pappso::AaModification::createInstanceMutation().
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finaloverridevirtual |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 180 of file aa.cpp.
References m_listMod.
unsigned int pappso::Aa::getNumberOfModification | ( | AaModificationP | mod | ) | const |
Definition at line 193 of file aa.cpp.
References m_listMod.
Referenced by pappso::PeptideModificatorBase::getModificationPositionList().
bool pappso::Aa::isAaEqual | ( | Aa const & | r | ) | const |
Definition at line 272 of file aa.cpp.
References pappso::AaBase::m_aaLetter, and m_listMod.
Referenced by pappso::operator==().
bool pappso::Aa::isLesser | ( | Aa const & | r | ) | const |
Definition at line 247 of file aa.cpp.
References pappso::a, pappso::b, pappso::AaBase::m_aaLetter, and m_listMod.
Referenced by pappso::operator<().
Definition at line 65 of file aa.cpp.
References pappso::AaBase::m_aaLetter, and m_listMod.
void pappso::Aa::removeAaModification | ( | AaModificationP | aaModification | ) |
Definition at line 137 of file aa.cpp.
References m_listMod.
Referenced by pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition().
void pappso::Aa::removeInternalCterModification | ( | ) |
void pappso::Aa::removeInternalNterModification | ( | ) |
void pappso::Aa::replaceAaModification | ( | AaModificationP | oldmod, |
AaModificationP | newmod | ||
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const QString pappso::Aa::toAbsoluteString | ( | ) | const |
const QString pappso::Aa::toString | ( | ) | const |
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private |
Definition at line 89 of file aa.h.
Referenced by addAaModification(), getInternalCterModification(), getInternalNterModification(), getMass(), getModificationList(), getNumberOfAtom(), getNumberOfIsotope(), getNumberOfModification(), isAaEqual(), isLesser(), operator=(), removeAaModification(), removeInternalCterModification(), removeInternalNterModification(), replaceAaModification(), toAbsoluteString(), and toString().