builds a peptide shared pointer from peptide string and adds fixed modifications More...

#include <peptidebuilder.h>

Inheritance diagram for pappso::PeptideBuilder:

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

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

Detailed Description

builds a peptide shared pointer from peptide string and adds fixed modifications

Definition at line 35 of file peptidebuilder.h.

Constructor & Destructor Documentation

◆ PeptideBuilder()

pappso::PeptideBuilder::PeptideBuilder ( )

Definition at line 29 of file peptidebuilder.cpp.

30{

31}

◆ ~PeptideBuilder()

pappso::PeptideBuilder::~PeptideBuilder ( )

virtual

Definition at line 33 of file peptidebuilder.cpp.

34{

35}

Member Function Documentation

◆ addFixedAaModification()

void pappso::PeptideBuilder::addFixedAaModification	(	char	aa,
		AaModificationP	modification )

Definition at line 37 of file peptidebuilder.cpp.

{
 
  m_fixedModificationList.push_back(
    std::pair<char, AaModificationP>(aa, modification));
}

References m_fixedModificationList.

◆ setPeptide()

void pappso::PeptideBuilder::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_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.

{
 
  qDebug() << "PeptideBuilder::setPeptide begin";
 
  Peptide peptide(peptide_str);
 
  for(auto &&aamod_pair : m_fixedModificationList)
    {
      std::vector<unsigned int> position_list =
        peptide.getAaPositionList(aamod_pair.first);
      for(auto &&position : position_list)
        {
          peptide.addAaModification(aamod_pair.second, position);
        }
    }
 
  PeptideSp peptide_sp = peptide.makePeptideSp();
  // set fixed modifications
 
  qDebug() << "PeptideBuilder::setPeptide m_sink->setPeptideSp";
  m_sink->setPeptideSp(sequence_database_id,
                       protein_sp,
                       is_decoy,
                       peptide_sp,
                       start,
                       is_nter,
                       missed_cleavage_number,
                       semi_enzyme);
  qDebug() << "PeptideBuilder::setPeptide end";
}

References pappso::Peptide::addAaModification(), pappso::Peptide::getAaPositionList(), m_fixedModificationList, m_sink, and pappso::Peptide::makePeptideSp().

◆ setSink()

void pappso::PeptideBuilder::setSink ( PeptideModificatorInterface * sink )

inlineoverridevirtual

Implements pappso::PeptideSpSinkInterface.

Definition at line 54 of file peptidebuilder.h.

  {
    m_sink = sink;
  };

References m_sink.

Member Data Documentation

◆ m_fixedModificationList

std::list<std::pair<char, AaModificationP> > pappso::PeptideBuilder::m_fixedModificationList

private

Definition at line 62 of file peptidebuilder.h.

Referenced by addFixedAaModification(), and setPeptide().

◆ m_sink

PeptideModificatorInterface* pappso::PeptideBuilder::m_sink = nullptr