libpappsomspp
Library for mass spectrometry
pappso::PeptideMethioninRemove Class Reference

potential remove Nter Methionin More...

#include <peptidemethioninremove.h>

Inheritance diagram for pappso::PeptideMethioninRemove:
pappso::EnzymeProductInterface pappso::PeptideSinkInterface

Public Member Functions

 PeptideMethioninRemove (bool ism_isPotential)
 
virtual ~PeptideMethioninRemove ()
 
void setPeptide (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const QString &peptide, 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 setSink (EnzymeProductInterface *sink) override
 

Private Attributes

EnzymeProductInterfacem_sink = nullptr
 
bool m_isPotential = true
 

Additional Inherited Members

Detailed Description

potential remove Nter Methionin

Definition at line 34 of file peptidemethioninremove.h.

Constructor & Destructor Documentation

◆ PeptideMethioninRemove()

pappso::PeptideMethioninRemove::PeptideMethioninRemove ( bool  ism_isPotential)

Definition at line 27 of file peptidemethioninremove.cpp.

28 {
29  m_isPotential = ism_isPotential;
30 }

References m_isPotential.

◆ ~PeptideMethioninRemove()

pappso::PeptideMethioninRemove::~PeptideMethioninRemove ( )
virtual

Definition at line 32 of file peptidemethioninremove.cpp.

33 {
34 }

Member Function Documentation

◆ setPeptide()

void pappso::PeptideMethioninRemove::setPeptide ( std::int8_t  sequence_database_id,
const ProteinSp protein_sp,
bool  is_decoy,
const QString &  peptide,
unsigned int  start,
bool  is_nter,
unsigned int  missed_cleavage_number,
bool  semi_enzyme 
)
overridevirtual

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

Implements pappso::EnzymeProductInterface.

Definition at line 37 of file peptidemethioninremove.cpp.

45 {
46  if(is_nter)
47  {
48  // Nter is often acetylated : MOD:00394
49  if(peptide[0] == 'M')
50  {
51  if(m_isPotential)
52  {
53  m_sink->setPeptide(sequence_database_id,
54  protein_sp,
55  is_decoy,
56  peptide,
57  start,
58  is_nter,
59  missed_cleavage_number,
60  semi_enzyme);
61  }
62  // peptide = peptide.right(peptide.size()-1);
63  m_sink->setPeptide(sequence_database_id,
64  protein_sp,
65  is_decoy,
66  peptide.right(peptide.size() - 1),
67  start + 1,
68  is_nter,
69  missed_cleavage_number,
70  semi_enzyme);
71  }
72  else
73  {
74  m_sink->setPeptide(sequence_database_id,
75  protein_sp,
76  is_decoy,
77  peptide,
78  start,
79  is_nter,
80  missed_cleavage_number,
81  semi_enzyme);
82  }
83  }
84  else
85  {
86 
87  m_sink->setPeptide(sequence_database_id,
88  protein_sp,
89  is_decoy,
90  peptide,
91  start,
92  is_nter,
93  missed_cleavage_number,
94  semi_enzyme);
95  }
96 }
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

References m_isPotential, m_sink, and pappso::EnzymeProductInterface::setPeptide().

◆ setSink()

void pappso::PeptideMethioninRemove::setSink ( EnzymeProductInterface sink)
inlineoverridevirtual

Implements pappso::PeptideSinkInterface.

Definition at line 57 of file peptidemethioninremove.h.

58  {
59  m_sink = sink;
60  };

Member Data Documentation

◆ m_isPotential

bool pappso::PeptideMethioninRemove::m_isPotential = true
private

Definition at line 39 of file peptidemethioninremove.h.

Referenced by PeptideMethioninRemove(), and setPeptide().

◆ m_sink

EnzymeProductInterface* pappso::PeptideMethioninRemove::m_sink = nullptr
private

Definition at line 38 of file peptidemethioninremove.h.

Referenced by setPeptide().


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