libpappsomspp
Library for mass spectrometry
pappso::EnzymeProductInterface Class Referenceabstract

#include <enzymeproductinterface.h>

Inheritance diagram for pappso::EnzymeProductInterface:
pappso::PeptideBuilder pappso::PeptideMethioninRemove pappso::PeptideModificatorPipeline pappso::PeptideSemiEnzyme pappso::PeptideSizeFilter

Public Member Functions

virtual void setPeptide (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideStr &peptide, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
 function to give the products of a protein digestion by an enzyme More...
 

Detailed Description

Definition at line 33 of file enzymeproductinterface.h.

Member Function Documentation

◆ setPeptide()

virtual void pappso::EnzymeProductInterface::setPeptide ( std::int8_t  sequence_database_id,
const ProteinSp protein_sp,
bool  is_decoy,
const PeptideStr peptide,
unsigned int  start,
bool  is_nter,
unsigned int  missed_cleavage_number,
bool  semi_enzyme 
)
pure virtual

function to give the products of a protein digestion by an enzyme

Parameters
sequence_database_idinteger that references the sequence fatabase (file, stream, url...)
protein_spshared pointer on the protein that was digested
is_decoytell if the current protein is a decoy (true) or normal (false) protein
peptideamino acid sequence of the peptide (string) produced by the digestion
startthe 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_nterboolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal)
missed_cleavage_numbernumber of missed cleavage sites (that the enzyme has not cut) fot the product
semi_enzymeboolean that tells if this peptide is the produce of a semi enzymatic lysis

Implemented in pappso::PeptideModificatorPipeline, pappso::PeptideBuilder, pappso::PeptideSizeFilter, pappso::PeptideSemiEnzyme, and pappso::PeptideMethioninRemove.

Referenced by pappso::Enzyme::sanityCheck(), pappso::PeptideMethioninRemove::setPeptide(), pappso::PeptideSemiEnzyme::setPeptide(), and pappso::PeptideSizeFilter::setPeptide().


The documentation for this class was generated from the following file: