libpappsomspp
Library for mass spectrometry
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#include <peptidefixedmodificationbuilder.h>
Public Member Functions | |
PeptideFixedModificationBuilder (AaModificationP p_mod) | |
virtual | ~PeptideFixedModificationBuilder () |
void | setPeptideSp (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp_original, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override |
function to give the products of modifications for a digested peptide More... | |
void | addAa (char aa) |
void | setSink (PeptideModificatorInterface *sink) override |
void | setProtNter (bool arg1) |
this modification concerns the Nter peptide More... | |
void | setProtCter (bool arg1) |
this modification concerns the Cter peptide More... | |
void | setProtElse (bool arg1) |
this modification concerns all peptides between Nter and Cter More... | |
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PeptideModificatorBase () | |
virtual | ~PeptideModificatorBase () |
virtual void | setModificationPattern (QString &pattern) final |
set the pattern on which the modification will be applied (usually the list of concerned AA) More... | |
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virtual | ~PeptideModificatorInterface () |
Private Attributes | |
PeptideModificatorInterface * | m_sink = nullptr |
const AaModificationP | mp_mod |
bool | m_isProtNterMod = true |
bool | m_isProtCterMod = true |
bool | m_isProtElseMod = true |
QString | m_aaModificationList |
Additional Inherited Members | |
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virtual void | getModificationPositionList (std::vector< unsigned int > &position_list, const QString &peptide_str) final |
virtual void | getModificationPositionList (std::vector< unsigned int > &position_list, const Peptide *p_peptide, AaModificationP mod, unsigned int modification_counter) |
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QRegularExpression | m_pattern |
Definition at line 33 of file peptidefixedmodificationbuilder.h.
PeptideFixedModificationBuilder::PeptideFixedModificationBuilder | ( | AaModificationP | p_mod | ) |
Definition at line 29 of file peptidefixedmodificationbuilder.cpp.
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virtual |
Definition at line 35 of file peptidefixedmodificationbuilder.cpp.
void PeptideFixedModificationBuilder::addAa | ( | char | aa | ) |
Definition at line 40 of file peptidefixedmodificationbuilder.cpp.
References m_aaModificationList, and pappso::PeptideModificatorBase::m_pattern.
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overridevirtual |
function to give the products of modifications for a digested peptide
sequence_database_id | integer that references the sequence fatabase (file, stream, url...) |
protein_sp | shared pointer on the protein that was initialy digested |
is_decoy | tell if the current protein is a decoy (true) or normal (false) protein |
peptide | Peptide object containing sequence and possible modifications |
start | the position of the first amino acid of the peptide in the original protein sequence. the first amino acid of the protein is at position 1. |
is_nter | boolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal) |
missed_cleavage_number | number of missed cleavage sites (that the enzyme has not cut) fot the product |
semi_enzyme | boolean that tells if this peptide is the produce of a semi enzymatic lysis |
Implements pappso::PeptideModificatorInterface.
Definition at line 51 of file peptidefixedmodificationbuilder.cpp.
References pappso::Peptide::addAaModification(), pappso::PeptideModificatorBase::getModificationPositionList(), m_isProtCterMod, m_isProtElseMod, m_isProtNterMod, m_sink, pappso::Peptide::makePeptideSp(), mp_mod, pappso::PeptideModificatorInterface::setPeptideSp(), and pappso::Peptide::size().
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inline |
this modification concerns the Cter peptide
Definition at line 65 of file peptidefixedmodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parseFixedModification(), and pappso::PeptideModificatorPipeline::parseLabeledModification().
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inline |
this modification concerns all peptides between Nter and Cter
Definition at line 72 of file peptidefixedmodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parseFixedModification().
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inline |
this modification concerns the Nter peptide
Definition at line 58 of file peptidefixedmodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parseFixedModification(), and pappso::PeptideModificatorPipeline::parseLabeledModification().
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inlineoverridevirtual |
Implements pappso::PeptideSpSinkInterface.
Definition at line 51 of file peptidefixedmodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parseFixedModification(), and pappso::PeptideModificatorPipeline::parseLabeledModification().
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private |
Definition at line 89 of file peptidefixedmodificationbuilder.h.
Referenced by addAa().
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private |
Definition at line 85 of file peptidefixedmodificationbuilder.h.
Referenced by setPeptideSp().
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private |
Definition at line 87 of file peptidefixedmodificationbuilder.h.
Referenced by setPeptideSp().
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private |
Definition at line 83 of file peptidefixedmodificationbuilder.h.
Referenced by setPeptideSp().
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private |
Definition at line 78 of file peptidefixedmodificationbuilder.h.
Referenced by setPeptideSp().
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private |
Definition at line 80 of file peptidefixedmodificationbuilder.h.
Referenced by setPeptideSp().