libpappsomspp
Library for mass spectrometry
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#include <peptide.h>
Public Member Functions | |
Peptide (const QString &pepstr) | |
virtual | ~Peptide () |
Peptide (const Peptide &peptide) | |
Peptide (Peptide &&toCopy) | |
PeptideSp | makePeptideSp () const |
NoConstPeptideSp | makeNoConstPeptideSp () const |
void | addAaModification (AaModificationP aaModification, unsigned int position) |
adds a modification to amino acid sequence More... | |
std::vector< Aa >::iterator | begin () |
std::vector< Aa >::iterator | end () |
std::vector< Aa >::const_iterator | begin () const |
std::vector< Aa >::const_iterator | end () const |
std::vector< Aa >::const_reverse_iterator | rbegin () const |
std::vector< Aa >::const_reverse_iterator | rend () const |
Aa & | getAa (unsigned int position) |
const Aa & | getConstAa (unsigned int position) const |
pappso_double | getMass () |
pappso_double | getMass () const override |
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... | |
const QString | getSequence () const override |
print amino acid sequence without modifications More... | |
unsigned int | size () const override |
unsigned int | getNumberOfModification (AaModificationP mod) const |
count modification occurence More... | |
unsigned int | countModificationOnAa (AaModificationP mod, const std::vector< char > &aa_list) const |
count modification occurence More... | |
void | replaceAaModification (AaModificationP oldmod, AaModificationP newmod) |
replaces all occurences of a modification by a new one More... | |
void | removeAaModification (AaModificationP mod) |
removes all occurences of a modification More... | |
std::vector< unsigned int > | getModificationPositionList (AaModificationP mod) const |
get modification positions More... | |
std::vector< unsigned int > | getModificationPositionList (AaModificationP mod, const std::vector< char > &aa_list) const |
get modification positions More... | |
std::vector< unsigned int > | getAaPositionList (char aa) const |
get positions of one amino acid in peptide More... | |
std::vector< unsigned int > | getAaPositionList (std::list< char > list_aa) const |
const QString | toString () const |
print modification except internal modifications More... | |
const QString | toAbsoluteString () const |
print all modifications More... | |
const QString | getLiAbsoluteString () const |
get all sequence string with modifications and converting Leucine to Isoleucine More... | |
AaModificationP | getInternalNterModification () const |
AaModificationP | getInternalCterModification () const |
void | removeInternalNterModification () |
void | removeInternalCterModification () |
void | setInternalNterModification (AaModificationP mod) |
void | setInternalCterModification (AaModificationP mod) |
void | rotate () |
void | reverse () |
virtual bool | isPalindrome () const override |
tells if the peptide sequence is a palindrome More... | |
void | replaceLeucineIsoleucine () |
void | removeNterAminoAcid () |
void | removeCterAminoAcid () |
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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 |
Protected Attributes | |
std::vector< Aa > | m_aaVec |
pappso_double | m_proxyMass = -1 |
Friends | |
bool | operator< (const Peptide &l, const Peptide &r) |
bool | operator== (const Peptide &l, const Peptide &r) |
pappso::Peptide::Peptide | ( | const QString & | pepstr | ) |
Definition at line 84 of file peptide.cpp.
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virtual |
Definition at line 113 of file peptide.cpp.
pappso::Peptide::Peptide | ( | const Peptide & | peptide | ) |
Definition at line 117 of file peptide.cpp.
pappso::Peptide::Peptide | ( | Peptide && | toCopy | ) |
Definition at line 123 of file peptide.cpp.
References m_proxyMass, and size().
void pappso::Peptide::addAaModification | ( | AaModificationP | aaModification, |
unsigned int | position | ||
) |
adds a modification to amino acid sequence
aaModification | pointer on modification to add |
position | position in the amino acid sequence (starts at 0) |
Definition at line 142 of file peptide.cpp.
Referenced by pappso::PeptideFixedModificationBuilder::setPeptideSp().
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inline |
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inline |
unsigned int pappso::Peptide::countModificationOnAa | ( | AaModificationP | mod, |
const std::vector< char > & | aa_list | ||
) | const |
count modification occurence
mod | modification to look for |
aa_list | amino acid list targets (one letter code) |
Definition at line 271 of file peptide.cpp.
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inline |
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inline |
Aa & pappso::Peptide::getAa | ( | unsigned int | position | ) |
std::vector< unsigned int > pappso::Peptide::getAaPositionList | ( | char | aa | ) | const |
get positions of one amino acid in peptide
aa | the one letter code of the amino acid |
Definition at line 365 of file peptide.cpp.
std::vector< unsigned int > pappso::Peptide::getAaPositionList | ( | std::list< char > | list_aa | ) | const |
const Aa & pappso::Peptide::getConstAa | ( | unsigned int | position | ) | const |
Definition at line 550 of file peptide.cpp.
AaModificationP pappso::Peptide::getInternalCterModification | ( | ) | const |
Definition at line 416 of file peptide.cpp.
References m_aaVec, and m_proxyMass.
Referenced by removeNterAminoAcid().
AaModificationP pappso::Peptide::getInternalNterModification | ( | ) | const |
const QString pappso::Peptide::getLiAbsoluteString | ( | ) | const |
get all sequence string with modifications and converting Leucine to Isoleucine
Definition at line 185 of file peptide.cpp.
pappso_double pappso::Peptide::getMass | ( | ) |
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inlineoverridevirtual |
Implements pappso::Ion.
std::vector< unsigned int > pappso::Peptide::getModificationPositionList | ( | AaModificationP | mod | ) | const |
get modification positions
mod | modification to look for |
Definition at line 318 of file peptide.cpp.
References m_aaVec.
std::vector< unsigned int > pappso::Peptide::getModificationPositionList | ( | AaModificationP | mod, |
const std::vector< char > & | aa_list | ||
) | const |
get modification positions
mod | modification to look for |
aa_list | amino acid list targets (one letter code) |
Definition at line 339 of file peptide.cpp.
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overridevirtual |
get the number of atom C, O, N, H in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 228 of file peptide.cpp.
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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 242 of file peptide.cpp.
unsigned int pappso::Peptide::getNumberOfModification | ( | AaModificationP | mod | ) | const |
count modification occurence
mod | modification to look for |
Definition at line 257 of file peptide.cpp.
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overridevirtual |
print amino acid sequence without modifications
Implements pappso::PeptideInterface.
Definition at line 160 of file peptide.cpp.
Referenced by pappso::XtandemHyperscoreBis::computeXtandemHyperscore().
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overridevirtual |
tells if the peptide sequence is a palindrome
Implements pappso::PeptideInterface.
Definition at line 525 of file peptide.cpp.
NoConstPeptideSp pappso::Peptide::makeNoConstPeptideSp | ( | ) | const |
Definition at line 136 of file peptide.cpp.
PeptideSp pappso::Peptide::makePeptideSp | ( | ) | const |
Definition at line 130 of file peptide.cpp.
Referenced by pappso::PeptideModificatorPipeline::setPeptide(), and pappso::PeptideFixedModificationBuilder::setPeptideSp().
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inline |
void pappso::Peptide::removeAaModification | ( | AaModificationP | mod | ) |
removes all occurences of a modification
mod | modification to remove |
Definition at line 304 of file peptide.cpp.
void pappso::Peptide::removeCterAminoAcid | ( | ) |
Definition at line 598 of file peptide.cpp.
void pappso::Peptide::removeInternalCterModification | ( | ) |
Definition at line 438 of file peptide.cpp.
void pappso::Peptide::removeInternalNterModification | ( | ) |
Definition at line 427 of file peptide.cpp.
void pappso::Peptide::removeNterAminoAcid | ( | ) |
Definition at line 575 of file peptide.cpp.
References pappso::AaModificationP, getInternalCterModification(), getMass(), m_aaVec, and m_proxyMass.
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inline |
void pappso::Peptide::replaceAaModification | ( | AaModificationP | oldmod, |
AaModificationP | newmod | ||
) |
replaces all occurences of a modification by a new one
oldmod | modification to change |
newmod | new modification |
Definition at line 290 of file peptide.cpp.
void pappso::Peptide::replaceLeucineIsoleucine | ( | ) |
void pappso::Peptide::reverse | ( | ) |
Definition at line 512 of file peptide.cpp.
void pappso::Peptide::rotate | ( | ) |
void pappso::Peptide::setInternalCterModification | ( | AaModificationP | mod | ) |
Definition at line 475 of file peptide.cpp.
void pappso::Peptide::setInternalNterModification | ( | AaModificationP | mod | ) |
Definition at line 452 of file peptide.cpp.
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inlineoverridevirtual |
Implements pappso::PeptideInterface.
Definition at line 199 of file peptide.h.
Referenced by Peptide(), and pappso::PeptideFixedModificationBuilder::setPeptideSp().
const QString pappso::Peptide::toAbsoluteString | ( | ) | const |
print all modifications
Definition at line 172 of file peptide.cpp.
const QString pappso::Peptide::toString | ( | ) | const |
print modification except internal modifications
Definition at line 199 of file peptide.cpp.
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protected |
Definition at line 116 of file peptide.h.
Referenced by getAa(), getAaPositionList(), getInternalCterModification(), getInternalNterModification(), getModificationPositionList(), pappso::getPeptideIonDirection(), removeNterAminoAcid(), and replaceLeucineIsoleucine().
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protected |
Definition at line 117 of file peptide.h.
Referenced by getInternalCterModification(), getInternalNterModification(), Peptide(), and removeNterAminoAcid().