libpappsomspp
Library for mass spectrometry
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#include <peptidevariablemodificationreplacement.h>
Public Member Functions | |
PeptideVariableModificationReplacement (AaModificationP mod_before, AaModificationP mod_after) | |
virtual | ~PeptideVariableModificationReplacement () |
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... | |
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PeptideVariableModificationBuilder (AaModificationP mod) | |
virtual | ~PeptideVariableModificationBuilder () |
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 () |
Private Member Functions | |
void | replaceModificationsAtPosition (Peptide &new_peptide, unsigned int position) |
Private Attributes | |
AaModificationP | mp_modAfter |
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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static bool | next_combination (const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last) |
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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 |
Definition at line 39 of file peptidevariablemodificationreplacement.h.
pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement | ( | AaModificationP | mod_before, |
AaModificationP | mod_after | ||
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this forces to check that the targetted modified sites really has the mod_before
Definition at line 35 of file peptidevariablemodificationreplacement.cpp.
References pappso::PeptideVariableModificationBuilder::m_modificationCount, and mp_modAfter.
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virtual |
Definition at line 45 of file peptidevariablemodificationreplacement.cpp.
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private |
Definition at line 52 of file peptidevariablemodificationreplacement.cpp.
References pappso::Aa::addAaModification(), pappso::Peptide::getAa(), pappso::PeptideVariableModificationBuilder::m_modificationCount, pappso::PeptideVariableModificationBuilder::mp_mod, mp_modAfter, and pappso::Aa::removeAaModification().
Referenced by setPeptideSp().
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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 |
Reimplemented from pappso::PeptideVariableModificationBuilder.
Definition at line 68 of file peptidevariablemodificationreplacement.cpp.
References pappso::PeptideModificatorBase::getModificationPositionList(), pappso::PeptideVariableModificationBuilder::m_isProtCterMod, pappso::PeptideVariableModificationBuilder::m_isProtElseMod, pappso::PeptideVariableModificationBuilder::m_isProtNterMod, pappso::PeptideVariableModificationBuilder::m_maxNumberMod, pappso::PeptideVariableModificationBuilder::m_minNumberMod, pappso::PeptideVariableModificationBuilder::m_modificationCount, pappso::PeptideVariableModificationBuilder::m_sink, pappso::Peptide::makePeptideSp(), pappso::PeptideVariableModificationBuilder::mp_mod, pappso::PeptideVariableModificationBuilder::next_combination(), replaceModificationsAtPosition(), and pappso::PeptideModificatorInterface::setPeptideSp().
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private |
Definition at line 61 of file peptidevariablemodificationreplacement.h.
Referenced by PeptideVariableModificationReplacement(), and replaceModificationsAtPosition().