libpappsomspp
Library for mass spectrometry
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Modify a peptide shared pointer with a variable modification on one AA. More...
#include <peptidevariablemodificationbuilder.h>
Public Member Functions | |
PeptideVariableModificationBuilder (AaModificationP mod) | |
virtual | ~PeptideVariableModificationBuilder () |
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 | setMaxNumberMod (unsigned int max_num) |
void | setMinNumberMod (unsigned int min_num) |
void | setModificationCounter (unsigned int counter) |
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 () |
Static Protected Member Functions | |
static bool | next_combination (const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last) |
Protected Attributes | |
PeptideModificatorInterface * | m_sink = nullptr |
AaModificationP | mp_mod |
unsigned int | m_minNumberMod = 0 |
unsigned int | m_maxNumberMod = 30000 |
unsigned int | m_modificationCount = 0 |
bool | m_isProtNterMod = true |
bool | m_isProtCterMod = true |
bool | m_isProtElseMod = true |
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QRegularExpression | m_pattern |
Private Attributes | |
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) |
Modify a peptide shared pointer with a variable modification on one AA.
Definition at line 36 of file peptidevariablemodificationbuilder.h.
pappso::PeptideVariableModificationBuilder::PeptideVariableModificationBuilder | ( | AaModificationP | mod | ) |
Definition at line 72 of file peptidevariablemodificationbuilder.cpp.
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virtual |
Definition at line 78 of file peptidevariablemodificationbuilder.cpp.
void pappso::PeptideVariableModificationBuilder::addAa | ( | char | aa | ) |
Definition at line 83 of file peptidevariablemodificationbuilder.cpp.
References m_aaModificationList, and pappso::PeptideModificatorBase::m_pattern.
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staticprotected |
Definition at line 30 of file peptidevariablemodificationbuilder.cpp.
References pappso::last.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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inline |
Definition at line 54 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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inline |
Definition at line 59 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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inline |
Definition at line 64 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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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.
Reimplemented in pappso::PeptideVariableModificationReplacement.
Definition at line 92 of file peptidevariablemodificationbuilder.cpp.
References pappso::Peptide::addAaModification(), pappso::PeptideModificatorBase::getModificationPositionList(), m_isProtCterMod, m_isProtElseMod, m_isProtNterMod, m_maxNumberMod, m_minNumberMod, m_modificationCount, m_sink, pappso::Peptide::makePeptideSp(), mp_mod, next_combination(), and pappso::PeptideModificatorInterface::setPeptideSp().
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inline |
this modification concerns the Cter peptide
Definition at line 86 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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inline |
this modification concerns all peptides between Nter and Cter
Definition at line 93 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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inline |
this modification concerns the Nter peptide
Definition at line 79 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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inlineoverridevirtual |
Implements pappso::PeptideSpSinkInterface.
Definition at line 70 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideModificatorPipeline::parsePotentialModification().
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private |
Definition at line 121 of file peptidevariablemodificationbuilder.h.
Referenced by addAa().
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Definition at line 115 of file peptidevariablemodificationbuilder.h.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 117 of file peptidevariablemodificationbuilder.h.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 113 of file peptidevariablemodificationbuilder.h.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 108 of file peptidevariablemodificationbuilder.h.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 106 of file peptidevariablemodificationbuilder.h.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 110 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement(), pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition(), setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 103 of file peptidevariablemodificationbuilder.h.
Referenced by setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().
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Definition at line 104 of file peptidevariablemodificationbuilder.h.
Referenced by pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition(), setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().