#include <peptidevariablemodificationreplacement.h>

Inheritance diagram for pappso::PeptideVariableModificationReplacement:

Public Member Functions
	PeptideVariableModificationReplacement (AaModificationP mod_before, AaModificationP mod_after)

virtual	~PeptideVariableModificationReplacement ()

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

Public Member Functions inherited from pappso::PeptideVariableModificationBuilder
	PeptideVariableModificationBuilder (AaModificationP mod)

virtual	~PeptideVariableModificationBuilder ()

void	addAa (char aa)

void	setMaxNumberMod (unsigned int max_num)

void	setMinNumberMod (unsigned int min_num)

void	setModificationCounter (unsigned int counter)

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 Member Functions
void	replaceModificationsAtPosition (Peptide &new_peptide, unsigned int position)

Private Attributes
AaModificationP	mp_modAfter

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)

Static Protected Member Functions inherited from pappso::PeptideVariableModificationBuilder
static bool	next_combination (const std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator k, const std::vector< unsigned int >::iterator last)

Protected Attributes inherited from pappso::PeptideVariableModificationBuilder
PeptideModificatorInterface *	m_sink = nullptr

AaModificationP	mp_mod

unsigned int	m_minNumberMod = 0

unsigned int	m_maxNumberMod = 30000

unsigned int	m_modificationCount = 0

bool	m_isProtNterMod = true

bool	m_isProtCterMod = true

bool	m_isProtElseMod = true

Protected Attributes inherited from pappso::PeptideModificatorBase
QRegularExpression	m_pattern

Detailed Description

Definition at line 39 of file peptidevariablemodificationreplacement.h.

Constructor & Destructor Documentation

◆ PeptideVariableModificationReplacement()

pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement	(	AaModificationP	mod_before,
		AaModificationP	mod_after )

this forces to check that the targetted modified sites really has the mod_before

Definition at line 35 of file peptidevariablemodificationreplacement.cpp.

  : PeptideVariableModificationBuilder(mod_before)
{
  mp_modAfter = mod_after;
  /** this forces to check that the targetted modified sites really has the
   * mod_before */
  m_modificationCount = 1;
}

References pappso::PeptideVariableModificationBuilder::PeptideVariableModificationBuilder(), pappso::PeptideVariableModificationBuilder::m_modificationCount, and mp_modAfter.

◆ ~PeptideVariableModificationReplacement()

pappso::PeptideVariableModificationReplacement::~PeptideVariableModificationReplacement ( )

virtual

Definition at line 45 of file peptidevariablemodificationreplacement.cpp.

47{

48}

Member Function Documentation

◆ replaceModificationsAtPosition()

void pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition	(	Peptide &	new_peptide,
		unsigned int	position )

private

Definition at line 52 of file peptidevariablemodificationreplacement.cpp.

{
  // replace all mod_before by mod_after :
  Aa &aa = new_peptide.getAa(position);
  aa.removeAaModification(mp_mod);
  unsigned int i = 0;
  while(i < m_modificationCount)
    {
      aa.addAaModification(mp_modAfter);
      i++;
    }
}

References pappso::Peptide::getAa(), pappso::PeptideVariableModificationBuilder::m_modificationCount, pappso::PeptideVariableModificationBuilder::mp_mod, and mp_modAfter.

Referenced by setPeptideSp().

◆ setPeptideSp()

void pappso::PeptideVariableModificationReplacement::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

Reimplemented from pappso::PeptideVariableModificationBuilder.

Definition at line 68 of file peptidevariablemodificationreplacement.cpp.

{
  // QString s = "Banana";
  // s.replace(QRegExp("a[mn]"), "ox");
 
 
  bool modify_this_peptide = true;
  if(m_isProtNterMod || m_isProtCterMod)
    {
      modify_this_peptide = false;
      if((m_isProtNterMod) && (is_nter))
        {
          // this an Nter peptide
          modify_this_peptide = true;
        }
      else if((m_isProtCterMod) &&
              (protein_sp.get()->size() ==
               (start + peptide_sp_original.get()->size())))
        {
          // this is a Cter peptide
          modify_this_peptide = true;
        }
      else if(m_isProtElseMod)
        {
          modify_this_peptide = true;
        }
    }
 
  if(modify_this_peptide)
    {
      std::vector<unsigned int> position_list;
      getModificationPositionList(
        position_list, peptide_sp_original.get(), mp_mod, m_modificationCount);
 
      // std::vector< unsigned int > position_list =
      // peptide_sp_original.get()->getAaPositionList(_aamp_modification_list);
      // std::string s = "12345";
      // no AA modification :
      if(m_minNumberMod == 0)
        {
          m_sink->setPeptideSp(sequence_database_id,
                               protein_sp,
                               is_decoy,
                               peptide_sp_original,
                               start,
                               is_nter,
                               missed_cleavage_number,
                               semi_enzyme);
        }
 
      unsigned int nb_pos = position_list.size();
      if(nb_pos > 0)
        {
          // loop to find 1 to n-1 AA modification combinations
          unsigned int comb_size = 1;
          while((comb_size < nb_pos) && (comb_size <= m_maxNumberMod))
            {
              do
                {
                  // std::cout << std::string(being,begin + comb_size) <<
                  // std::endl;
                  Peptide new_peptide(*(peptide_sp_original.get()));
                  for(unsigned int i = 0; i < comb_size; i++)
                    {
                      // new_peptide.addAaModification(mp_mod,position_list[i]);
                      this->replaceModificationsAtPosition(new_peptide,
                                                           position_list[i]);
                    }
                  PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
                  m_sink->setPeptideSp(sequence_database_id,
                                       protein_sp,
                                       is_decoy,
                                       new_peptide_sp,
                                       start,
                                       is_nter,
                                       missed_cleavage_number,
                                       semi_enzyme);
                }
              while(next_combination(position_list.begin(),
                                     position_list.begin() + comb_size,
                                     position_list.end()));
              comb_size++;
            }
 
          if(nb_pos <= m_maxNumberMod)
            {
              // the last combination : all aa are modified :
              Peptide new_peptide(*(peptide_sp_original.get()));
              for(unsigned int i = 0; i < nb_pos; i++)
                {
                  // new_peptide.addAaModification(mp_mod,position_list[i]);
 
                  this->replaceModificationsAtPosition(new_peptide,
                                                       position_list[i]);
                }
              PeptideSp new_peptide_sp = new_peptide.makePeptideSp();
              m_sink->setPeptideSp(sequence_database_id,
                                   protein_sp,
                                   is_decoy,
                                   new_peptide_sp,
                                   start,
                                   is_nter,
                                   missed_cleavage_number,
                                   semi_enzyme);
            }
        }
    }
  else
    {
      // no modification
      m_sink->setPeptideSp(sequence_database_id,
                           protein_sp,
                           is_decoy,
                           peptide_sp_original,
                           start,
                           is_nter,
                           missed_cleavage_number,
                           semi_enzyme);
    }
}

Member Data Documentation

◆ mp_modAfter

AaModificationP pappso::PeptideVariableModificationReplacement::mp_modAfter

private

Definition at line 61 of file peptidevariablemodificationreplacement.h.

Referenced by PeptideVariableModificationReplacement(), and replaceModificationsAtPosition().

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

pappsomspp/core/protein/peptidevariablemodificationreplacement.h
pappsomspp/core/protein/peptidevariablemodificationreplacement.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members