libpappsomspp
Library for mass spectrometry
pappso::PeptideModificatorTee Class Reference

#include <peptidemodificatortee.h>

Inheritance diagram for pappso::PeptideModificatorTee:
pappso::PeptideModificatorInterface

Public Member Functions

 PeptideModificatorTee ()
 
 PeptideModificatorTee (const PeptideModificatorTee &other)
 
virtual ~PeptideModificatorTee ()
 
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 addModificator (PeptideModificatorInterface *p_peptide_mod)
 
- Public Member Functions inherited from pappso::PeptideModificatorInterface
virtual ~PeptideModificatorInterface ()
 

Private Attributes

std::list< PeptideModificatorInterface * > m_peptideModPtrList
 

Detailed Description

Definition at line 34 of file peptidemodificatortee.h.

Constructor & Destructor Documentation

◆ PeptideModificatorTee() [1/2]

PeptideModificatorTee::PeptideModificatorTee ( )

Definition at line 28 of file peptidemodificatortee.cpp.

29 {
30 }

◆ PeptideModificatorTee() [2/2]

PeptideModificatorTee::PeptideModificatorTee ( const PeptideModificatorTee other)

Definition at line 32 of file peptidemodificatortee.cpp.

33 {
34  throw PappsoException(
35  QObject::tr("unable to copy PeptideModificatorTee object"));
37 }
std::list< PeptideModificatorInterface * > m_peptideModPtrList

References m_peptideModPtrList.

◆ ~PeptideModificatorTee()

PeptideModificatorTee::~PeptideModificatorTee ( )
virtual

Definition at line 38 of file peptidemodificatortee.cpp.

39 {
40 }

Member Function Documentation

◆ addModificator()

void PeptideModificatorTee::addModificator ( PeptideModificatorInterface p_peptide_mod)

Definition at line 43 of file peptidemodificatortee.cpp.

45 {
46  m_peptideModPtrList.push_back(p_peptide_mod);
47 }

References m_peptideModPtrList.

Referenced by pappso::PeptideModificatorPipeline::addLabeledModificationString().

◆ setPeptideSp()

void PeptideModificatorTee::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 
)
overridevirtual

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

Implements pappso::PeptideModificatorInterface.

Definition at line 51 of file peptidemodificatortee.cpp.

59 {
60 
61  qDebug() << "PeptideModificatorTee::setPeptide begin";
62 
63  for(auto p_peptide_mod : m_peptideModPtrList)
64  {
65  p_peptide_mod->setPeptideSp(sequence_database_id,
66  protein_sp,
67  is_decoy,
68  peptide_sp_original,
69  start,
70  is_nter,
71  missed_cleavage_number,
72  semi_enzyme);
73  }
74 
75  qDebug() << "PeptideModificatorTee::setPeptide end";
76 }

References m_peptideModPtrList.

Member Data Documentation

◆ m_peptideModPtrList

std::list<PeptideModificatorInterface *> pappso::PeptideModificatorTee::m_peptideModPtrList
private

Definition at line 54 of file peptidemodificatortee.h.

Referenced by PeptideModificatorTee(), addModificator(), and setPeptideSp().


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