Modify a peptide shared pointer with a variable modification on one AA. More...

#include <peptidevariablemodificationbuilder.h>

Inheritance diagram for pappso::PeptideVariableModificationBuilder:

Public Member Functions
	PeptideVariableModificationBuilder (AaModificationP mod)

virtual	~PeptideVariableModificationBuilder ()

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	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 ()

Static Protected Member Functions
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
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

Private Attributes
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)

Detailed Description

Modify a peptide shared pointer with a variable modification on one AA.

Definition at line 36 of file peptidevariablemodificationbuilder.h.

Constructor & Destructor Documentation

◆ PeptideVariableModificationBuilder()

pappso::PeptideVariableModificationBuilder::PeptideVariableModificationBuilder ( AaModificationP mod )

Definition at line 72 of file peptidevariablemodificationbuilder.cpp.

  : mp_mod(mod)
{
}

References mp_mod.

Referenced by pappso::PeptideVariableModificationReplacement::PeptideVariableModificationReplacement().

◆ ~PeptideVariableModificationBuilder()

pappso::PeptideVariableModificationBuilder::~PeptideVariableModificationBuilder ( )

virtual

Definition at line 78 of file peptidevariablemodificationbuilder.cpp.

79{

80}

Member Function Documentation

◆ addAa()

void pappso::PeptideVariableModificationBuilder::addAa ( char aa )

Definition at line 83 of file peptidevariablemodificationbuilder.cpp.

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

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

◆ next_combination()

bool pappso::PeptideVariableModificationBuilder::next_combination	(	const std::vector< unsigned int >::iterator	first,
		std::vector< unsigned int >::iterator	k,
		const std::vector< unsigned int >::iterator	last )

staticprotected

Definition at line 30 of file peptidevariablemodificationbuilder.cpp.

{
  /* Credits: Mark Nelson http://marknelson.us */
  if((first == last) || (first == k) || (last == k))
    return false;
  std::vector<unsigned int>::iterator i1 = first;
  std::vector<unsigned int>::iterator i2 = last;
  ++i1;
  if(last == i1)
    return false;
  i1 = last;
  --i1;
  i1 = k;
  --i2;
  while(first != i1)
    {
      if(*--i1 < *i2)
        {
          std::vector<unsigned int>::iterator j = k;
          while(!(*i1 < *j))
            ++j;
          std::iter_swap(i1, j);
          ++i1;
          ++j;
          i2 = k;
          std::rotate(i1, j, last);
          while(last != j)
            {
              ++j;
              ++i2;
            }
          std::rotate(k, i2, last);
          return true;
        }
    }
  std::rotate(first, k, last);
  return false;
}

References pappso::last.

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

◆ setMaxNumberMod()

void pappso::PeptideVariableModificationBuilder::setMaxNumberMod ( unsigned int max_num )

inline

Definition at line 54 of file peptidevariablemodificationbuilder.h.

  {
    m_maxNumberMod = max_num;
  };

References m_maxNumberMod.

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

◆ setMinNumberMod()

void pappso::PeptideVariableModificationBuilder::setMinNumberMod ( unsigned int min_num )

inline

Definition at line 59 of file peptidevariablemodificationbuilder.h.

  {
    m_minNumberMod = min_num;
  };

References m_minNumberMod.

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

◆ setModificationCounter()

void pappso::PeptideVariableModificationBuilder::setModificationCounter ( unsigned int counter )

inline

Definition at line 64 of file peptidevariablemodificationbuilder.h.

  {
    m_modificationCount = counter;
  };

References m_modificationCount.

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

◆ setPeptideSp()

void pappso::PeptideVariableModificationBuilder::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.

Reimplemented in pappso::PeptideVariableModificationReplacement.

Definition at line 92 of file peptidevariablemodificationbuilder.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(m_aaModificationList);
      // 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]);
                    }
                  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]);
                }
              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);
    }
}