libpappsomspp
Library for mass spectrometry
pappso::PeptideModificatorInterface Class Referenceabstract

#include <enzymeproductinterface.h>

Inheritance diagram for pappso::PeptideModificatorInterface:
pappso::PeptideModificatorBase pappso::PeptideModificatorPipeline pappso::PeptideModificatorTee pappso::PeptideFixedModificationBuilder pappso::PeptideVariableModificationBuilder pappso::PeptideVariableModificationReplacement

Public Member Functions

virtual ~PeptideModificatorInterface ()
 
virtual void setPeptideSp (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
 function to give the products of modifications for a digested peptide More...
 

Detailed Description

Definition at line 64 of file enzymeproductinterface.h.

Constructor & Destructor Documentation

◆ ~PeptideModificatorInterface()

virtual pappso::PeptideModificatorInterface::~PeptideModificatorInterface ( )
inlinevirtual

Definition at line 67 of file enzymeproductinterface.h.

67 {};

Member Function Documentation

◆ setPeptideSp()

virtual void pappso::PeptideModificatorInterface::setPeptideSp ( std::int8_t  sequence_database_id,
const ProteinSp protein_sp,
bool  is_decoy,
const PeptideSp peptide_sp,
unsigned int  start,
bool  is_nter,
unsigned int  missed_cleavage_number,
bool  semi_enzyme 
)
pure virtual

function to give the products of modifications for a digested peptide

Parameters
sequence_database_idinteger that references the sequence fatabase (file, stream, url...)
protein_spshared pointer on the protein that was initialy digested
is_decoytell if the current protein is a decoy (true) or normal (false) protein
peptidePeptide object containing sequence and possible modifications
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::PeptideVariableModificationReplacement, pappso::PeptideVariableModificationBuilder, pappso::PeptideModificatorTee, pappso::PeptideModificatorPipeline, and pappso::PeptideFixedModificationBuilder.

Referenced by pappso::PeptideBuilder::setPeptide(), pappso::PeptideFixedModificationBuilder::setPeptideSp(), pappso::PeptideModificatorPipeline::setPeptideSp(), pappso::PeptideVariableModificationBuilder::setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().


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