#include <peptidemodificatorbase.h>

Inheritance diagram for pappso::PeptideModificatorBase:

Public Member Functions
	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 ()

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

Public Member Functions inherited from pappso::PeptideSpSinkInterface
virtual void	setSink (PeptideModificatorInterface *sink)=0

Protected Member Functions
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
QRegularExpression	m_pattern

Detailed Description

Definition at line 40 of file peptidemodificatorbase.h.

Constructor & Destructor Documentation

◆ PeptideModificatorBase()

pappso::PeptideModificatorBase::PeptideModificatorBase ( )

Definition at line 35 of file peptidemodificatorbase.cpp.

36{

37}

◆ ~PeptideModificatorBase()

pappso::PeptideModificatorBase::~PeptideModificatorBase ( )

virtual

Definition at line 39 of file peptidemodificatorbase.cpp.

40{

41}

Member Function Documentation

◆ getModificationPositionList() [1/2]

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

protectedvirtual

Definition at line 86 of file peptidemodificatorbase.cpp.

{
 
  int pos                               = 0;
  const QString peptide_str             = p_peptide->getSequence();
  QRegularExpressionMatch match_pattern = m_pattern.match(peptide_str, pos);
 
  while(match_pattern.hasMatch())
    {
      pos = match_pattern.capturedStart(0);
      if(match_pattern.lastCapturedIndex() == 0)
        {
          // no motif, just push position
          if(p_peptide->getConstAa(pos).getNumberOfModification(mod) ==
             modification_counter)
            {
              position_list.push_back(pos);
            }
          pos++;
        }
      else
        {
          // there is a motif : target this position
          pos = match_pattern.capturedStart(1);
          if((position_list.size() > 0) &&
             (position_list.back() == (unsigned int)pos))
            {
              pos = match_pattern.capturedStart(0) + 1;
            }
          else
            {
              if(p_peptide->getConstAa(pos).getNumberOfModification(mod) ==
                 modification_counter)
                {
                  position_list.push_back(pos);
                }
              pos = match_pattern.capturedStart(0) + 1;
            }
        }
      match_pattern = m_pattern.match(peptide_str, pos);
    }
}

References pappso::Peptide::getConstAa(), pappso::Aa::getNumberOfModification(), pappso::Peptide::getSequence(), and m_pattern.

◆ getModificationPositionList() [2/2]

void pappso::PeptideModificatorBase::getModificationPositionList	(	std::vector< unsigned int > &	position_list,
		const QString &	peptide_str )

finalprotectedvirtual

Definition at line 50 of file peptidemodificatorbase.cpp.

{
 
  int pos                               = 0;
  QRegularExpressionMatch match_pattern = m_pattern.match(peptide_str, pos);
 
  while(match_pattern.hasMatch())
    {
      pos = match_pattern.capturedStart(0);
      if(match_pattern.lastCapturedIndex() == 0)
        {
          // no motif, just push position
          position_list.push_back(pos);
          pos++;
        }
      else
        {
          // there is a motif : target this position
          pos = match_pattern.capturedStart(1);
          if((position_list.size() > 0) &&
             (position_list.back() == (unsigned int)pos))
            {
              pos = match_pattern.capturedStart(0) + 1;
            }
          else
            {
              position_list.push_back(pos);
              pos = match_pattern.capturedStart(0) + 1;
            }
        }
      match_pattern = m_pattern.match(peptide_str, pos);
    }
}

References m_pattern.

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

◆ setModificationPattern()

void pappso::PeptideModificatorBase::setModificationPattern ( QString & pattern )

finalvirtual

set the pattern on which the modification will be applied (usually the list of concerned AA)

the pattern is a standard regular expression : it describes the target site to modify. This standard regular expression is used to make a replacement of all motifs describes by an underscore ("_") The underscore is taken as a landmark to apply the modification.

Parameters

pattern the regular expression pattern ( [YST] to replace Y, S and T with _ and modify it ). The pattern can also contain the / separator to eventually specify the replacement motif. This can be used to described very complex modification patterns

Definition at line 44 of file peptidemodificatorbase.cpp.

{
  m_pattern.setPattern(pattern);
}

References m_pattern.

Referenced by pappso::PeptideModificatorPipeline::parseFixedModification(), pappso::PeptideModificatorPipeline::parseLabeledModification(), and pappso::PeptideModificatorPipeline::parsePotentialModification().

Member Data Documentation

◆ m_pattern

QRegularExpression pappso::PeptideModificatorBase::m_pattern

protected

Definition at line 66 of file peptidemodificatorbase.h.

Referenced by pappso::PeptideFixedModificationBuilder::addAa(), pappso::PeptideVariableModificationBuilder::addAa(), getModificationPositionList(), getModificationPositionList(), and setModificationPattern().

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

pappsomspp/core/protein/peptidemodificatorbase.h
pappsomspp/core/protein/peptidemodificatorbase.cpp

Public Member Functions

Protected Member Functions

Protected Attributes