libpappsomspp
Library for mass spectrometry
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builds a peptide shared pointer from peptide string and adds fixed modifications More...
#include <peptidebuilder.h>
Public Member Functions | |
PeptideBuilder () | |
virtual | ~PeptideBuilder () |
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 | addFixedAaModification (char aa, AaModificationP modification) |
void | setSink (PeptideModificatorInterface *sink) override |
Private Attributes | |
PeptideModificatorInterface * | m_sink = nullptr |
std::list< std::pair< char, AaModificationP > > | m_fixedModificationList |
Additional Inherited Members |
builds a peptide shared pointer from peptide string and adds fixed modifications
Definition at line 35 of file peptidebuilder.h.
pappso::PeptideBuilder::PeptideBuilder | ( | ) |
Definition at line 29 of file peptidebuilder.cpp.
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virtual |
Definition at line 33 of file peptidebuilder.cpp.
void pappso::PeptideBuilder::addFixedAaModification | ( | char | aa, |
AaModificationP | modification | ||
) |
Definition at line 37 of file peptidebuilder.cpp.
References m_fixedModificationList.
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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 45 of file peptidebuilder.cpp.
References pappso::Peptide::addAaModification(), pappso::Peptide::getAaPositionList(), m_fixedModificationList, m_sink, pappso::Peptide::makePeptideSp(), and pappso::PeptideModificatorInterface::setPeptideSp().
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inlineoverridevirtual |
Implements pappso::PeptideSpSinkInterface.
Definition at line 54 of file peptidebuilder.h.
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private |
Definition at line 62 of file peptidebuilder.h.
Referenced by addFixedAaModification(), and setPeptide().
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private |
Definition at line 60 of file peptidebuilder.h.
Referenced by setPeptide().