#include <peptidefixedmodificationbuilder.h>

Inheritance diagram for pappso::PeptideFixedModificationBuilder:

Public Member Functions
	PeptideFixedModificationBuilder (AaModificationP p_mod)

virtual	~PeptideFixedModificationBuilder ()

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

void	addAa (char aa)

void	setSink (PeptideModificatorInterface *sink) override

void	setProtNter (bool arg1)
	this modification concerns the Nter peptide

void	setProtCter (bool arg1)
	this modification concerns the Cter peptide

void	setProtElse (bool arg1)
	this modification concerns all peptides between Nter and Cter

Public Member Functions inherited from pappso::PeptideModificatorBase
	PeptideModificatorBase ()

virtual	~PeptideModificatorBase ()

virtual void	setModificationPattern (QString &pattern) final
	set the pattern on which the modification will be applied (usually the list of concerned AA)

Public Member Functions inherited from pappso::PeptideModificatorInterface
virtual	~PeptideModificatorInterface ()

Private Attributes
PeptideModificatorInterface *	m_sink = nullptr

const AaModificationP	mp_mod

bool	m_isProtNterMod = true

bool	m_isProtCterMod = true

bool	m_isProtElseMod = true

QString	m_aaModificationList

Additional Inherited Members
Protected Member Functions inherited from pappso::PeptideModificatorBase
virtual void	getModificationPositionList (std::vector< unsigned int > &position_list, const QString &peptide_str) final

virtual void	getModificationPositionList (std::vector< unsigned int > &position_list, const Peptide *p_peptide, AaModificationP mod, unsigned int modification_counter)

Protected Attributes inherited from pappso::PeptideModificatorBase
QRegularExpression	m_pattern

Detailed Description

Definition at line 33 of file peptidefixedmodificationbuilder.h.

Constructor & Destructor Documentation

◆ PeptideFixedModificationBuilder()

PeptideFixedModificationBuilder::PeptideFixedModificationBuilder ( AaModificationP p_mod )

Definition at line 29 of file peptidefixedmodificationbuilder.cpp.

  : mp_mod(p_mod)
{
}

References mp_mod.

◆ ~PeptideFixedModificationBuilder()

PeptideFixedModificationBuilder::~PeptideFixedModificationBuilder ( )

virtual

Definition at line 35 of file peptidefixedmodificationbuilder.cpp.

36{

37}

Member Function Documentation

◆ addAa()

void PeptideFixedModificationBuilder::addAa ( char aa )

Definition at line 40 of file peptidefixedmodificationbuilder.cpp.

{
 
  m_aaModificationList.append(aa);
 
  m_pattern.setPattern(QString("[%1]").arg(m_aaModificationList));
}

References m_aaModificationList, and pappso::PeptideModificatorBase::m_pattern.

◆ setPeptideSp()

void PeptideFixedModificationBuilder::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_id	integer that references the sequence fatabase (file, stream, url...)
protein_sp	shared pointer on the protein that was initialy digested
is_decoy	tell if the current protein is a decoy (true) or normal (false) protein
peptide	Peptide object containing sequence and possible modifications
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::PeptideModificatorInterface.

Definition at line 51 of file peptidefixedmodificationbuilder.cpp.

{
 
  qDebug() << "PeptideFixedModificationBuilder::setPeptide begin";
 
  std::vector<unsigned int> position_list;
  getModificationPositionList(position_list,
                              peptide_sp_original.get()->getSequence());
 
  Peptide peptide(*peptide_sp_original.get());
  unsigned int size = peptide.size();
 
  for(unsigned int pos : position_list)
    {
      if((m_isProtNterMod) && (is_nter))
        {
          peptide.addAaModification(mp_mod, pos);
        }
      else if((m_isProtCterMod) && (protein_sp.get()->size() == (start + size)))
        {
          peptide.addAaModification(mp_mod, pos);
        }
      else if(m_isProtElseMod)
        {
          peptide.addAaModification(mp_mod, pos);
        }
    }
 
  PeptideSp peptide_sp = peptide.makePeptideSp();
  // set fixed modifications
  m_sink->setPeptideSp(sequence_database_id,
                       protein_sp,
                       is_decoy,
                       peptide_sp,
                       start,
                       is_nter,
                       missed_cleavage_number,
                       semi_enzyme);
  qDebug() << "PeptideFixedModificationBuilder::setPeptide end";
}