libpappsomspp
Library for mass spectrometry
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#include <peptidemodificatorpipeline.h>
Public Member Functions | |
PeptideModificatorPipeline () | |
PeptideModificatorPipeline (const PeptideModificatorPipeline &other) | |
virtual | ~PeptideModificatorPipeline () |
void | addFixedModificationString (const QString &mod_str) |
void | addFixedNterModificationString (const QString &mod_str) |
void | addFixedCterModificationString (const QString &mod_str) |
void | addPotentialModificationString (const QString &mod_str) |
void | addPotentialNterModificationString (const QString &mod_str) |
void | addPotentialCterModificationString (const QString &mod_str) |
void | setSink (PeptideModificatorInterface *sink) override |
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 | setPeptide (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const QString &peptide_str, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override |
function to give the products of a protein digestion by an enzyme More... | |
void | addLabeledModificationString (const QString &mod_str) |
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virtual | ~PeptideModificatorInterface () |
Private Member Functions | |
void | parseFixedModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot) |
void | privAddFixedModificationString (const QString &mod_str, bool Nter, bool Cter, bool else_prot) |
void | parsePotentialModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot) |
void | privAddPotentialModificationString (const QString &mod_str, bool Nter, bool Cter, bool else_prot) |
void | parseLabeledModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot) |
Private Attributes | |
PeptideModificatorTee * | mp_peptideModificatorTee = nullptr |
PeptideModificatorInterface * | m_sink = nullptr |
PeptideSpSinkInterface * | mp_lastPeptideSinkInterface |
PeptideModificatorInterface * | mp_firstModificator = nullptr |
std::vector< PeptideModificatorInterface * > | m_pepModificatorPtrList |
Definition at line 33 of file peptidemodificatorpipeline.h.
PeptideModificatorPipeline::PeptideModificatorPipeline | ( | ) |
Definition at line 35 of file peptidemodificatorpipeline.cpp.
PeptideModificatorPipeline::PeptideModificatorPipeline | ( | const PeptideModificatorPipeline & | other | ) |
Definition at line 39 of file peptidemodificatorpipeline.cpp.
References m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, and mp_peptideModificatorTee.
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virtual |
Definition at line 67 of file peptidemodificatorpipeline.cpp.
References m_pepModificatorPtrList, and mp_peptideModificatorTee.
void PeptideModificatorPipeline::addFixedCterModificationString | ( | const QString & | mod_str | ) |
Definition at line 108 of file peptidemodificatorpipeline.cpp.
References privAddFixedModificationString().
void PeptideModificatorPipeline::addFixedModificationString | ( | const QString & | mod_str | ) |
Definition at line 97 of file peptidemodificatorpipeline.cpp.
References privAddFixedModificationString().
void PeptideModificatorPipeline::addFixedNterModificationString | ( | const QString & | mod_str | ) |
Definition at line 102 of file peptidemodificatorpipeline.cpp.
References privAddFixedModificationString().
void PeptideModificatorPipeline::addLabeledModificationString | ( | const QString & | mod_str | ) |
Definition at line 261 of file peptidemodificatorpipeline.cpp.
References pappso::PeptideModificatorTee::addModificator(), m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, mp_peptideModificatorTee, parseLabeledModification(), and pappso::PeptideSpSinkInterface::setSink().
void PeptideModificatorPipeline::addPotentialCterModificationString | ( | const QString & | mod_str | ) |
Definition at line 181 of file peptidemodificatorpipeline.cpp.
References privAddPotentialModificationString().
void PeptideModificatorPipeline::addPotentialModificationString | ( | const QString & | mod_str | ) |
Definition at line 167 of file peptidemodificatorpipeline.cpp.
References privAddPotentialModificationString().
void PeptideModificatorPipeline::addPotentialNterModificationString | ( | const QString & | mod_str | ) |
Definition at line 174 of file peptidemodificatorpipeline.cpp.
References privAddPotentialModificationString().
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private |
Definition at line 135 of file peptidemodificatorpipeline.cpp.
References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideFixedModificationBuilder::setProtCter(), pappso::PeptideFixedModificationBuilder::setProtElse(), pappso::PeptideFixedModificationBuilder::setProtNter(), pappso::PeptideFixedModificationBuilder::setSink(), and pappso::PeptideSpSinkInterface::setSink().
Referenced by privAddFixedModificationString().
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private |
Definition at line 308 of file peptidemodificatorpipeline.cpp.
References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideFixedModificationBuilder::setProtCter(), pappso::PeptideFixedModificationBuilder::setProtNter(), pappso::PeptideFixedModificationBuilder::setSink(), and pappso::PeptideSpSinkInterface::setSink().
Referenced by addLabeledModificationString().
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private |
Definition at line 209 of file peptidemodificatorpipeline.cpp.
References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideVariableModificationBuilder::setMaxNumberMod(), pappso::PeptideVariableModificationBuilder::setMinNumberMod(), pappso::PeptideVariableModificationBuilder::setModificationCounter(), pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideVariableModificationBuilder::setProtCter(), pappso::PeptideVariableModificationBuilder::setProtElse(), pappso::PeptideVariableModificationBuilder::setProtNter(), pappso::PeptideVariableModificationBuilder::setSink(), and pappso::PeptideSpSinkInterface::setSink().
Referenced by privAddPotentialModificationString().
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private |
Definition at line 115 of file peptidemodificatorpipeline.cpp.
References pappso::Cter, mp_peptideModificatorTee, pappso::Nter, and parseFixedModification().
Referenced by addFixedCterModificationString(), addFixedModificationString(), and addFixedNterModificationString().
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private |
Definition at line 188 of file peptidemodificatorpipeline.cpp.
References pappso::Cter, mp_peptideModificatorTee, pappso::Nter, and parsePotentialModification().
Referenced by addPotentialCterModificationString(), addPotentialModificationString(), and addPotentialNterModificationString().
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overridevirtual |
function to give the products of a protein digestion by an enzyme
sequence_database_id | integer that references the sequence fatabase (file, stream, url...) |
protein_sp | shared pointer on the protein that was digested |
is_decoy | tell if the current protein is a decoy (true) or normal (false) protein |
peptide | amino acid sequence of the peptide (string) produced by the digestion |
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::EnzymeProductInterface.
Definition at line 369 of file peptidemodificatorpipeline.cpp.
References pappso::Peptide::makePeptideSp(), and 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 |
Implements pappso::PeptideModificatorInterface.
Definition at line 334 of file peptidemodificatorpipeline.cpp.
References m_sink, mp_firstModificator, and pappso::PeptideModificatorInterface::setPeptideSp().
Referenced by setPeptide().
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overridevirtual |
Implements pappso::PeptideSpSinkInterface.
Definition at line 81 of file peptidemodificatorpipeline.cpp.
References m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, mp_peptideModificatorTee, and pappso::PeptideSpSinkInterface::setSink().
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Definition at line 86 of file peptidemodificatorpipeline.h.
Referenced by PeptideModificatorPipeline(), ~PeptideModificatorPipeline(), parseFixedModification(), parseLabeledModification(), and parsePotentialModification().
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Definition at line 80 of file peptidemodificatorpipeline.h.
Referenced by PeptideModificatorPipeline(), addLabeledModificationString(), parseFixedModification(), parseLabeledModification(), parsePotentialModification(), setPeptideSp(), and setSink().
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Definition at line 84 of file peptidemodificatorpipeline.h.
Referenced by PeptideModificatorPipeline(), addLabeledModificationString(), parseFixedModification(), parseLabeledModification(), parsePotentialModification(), setPeptideSp(), and setSink().
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Definition at line 82 of file peptidemodificatorpipeline.h.
Referenced by PeptideModificatorPipeline(), addLabeledModificationString(), parseFixedModification(), parseLabeledModification(), parsePotentialModification(), and setSink().
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private |
Definition at line 78 of file peptidemodificatorpipeline.h.
Referenced by PeptideModificatorPipeline(), ~PeptideModificatorPipeline(), addLabeledModificationString(), privAddFixedModificationString(), privAddPotentialModificationString(), and setSink().