#include <peptidemodificatorpipeline.h>

Inheritance diagram for pappso::PeptideModificatorPipeline:

Public Member Functions
	PeptideModificatorPipeline ()

	PeptideModificatorPipeline (const PeptideModificatorPipeline &other)

virtual	~PeptideModificatorPipeline ()

void	addFixedModificationString (const QString &mod_str)

void	addFixedNterModificationString (const QString &mod_str)

void	addFixedCterModificationString (const QString &mod_str)

void	addPotentialModificationString (const QString &mod_str)

void	addPotentialNterModificationString (const QString &mod_str)

void	addPotentialCterModificationString (const QString &mod_str)

void	setSink (PeptideModificatorInterface *sink) override

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	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	addLabeledModificationString (const QString &mod_str)

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

Private Member Functions
void	parseFixedModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot)

void	privAddFixedModificationString (const QString &mod_str, bool Nter, bool Cter, bool else_prot)

void	parsePotentialModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot)

void	privAddPotentialModificationString (const QString &mod_str, bool Nter, bool Cter, bool else_prot)

void	parseLabeledModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot)

Private Attributes
PeptideModificatorTee *	mp_peptideModificatorTee = nullptr

PeptideModificatorInterface *	m_sink = nullptr

PeptideSpSinkInterface *	mp_lastPeptideSinkInterface

PeptideModificatorInterface *	mp_firstModificator = nullptr

std::vector< PeptideModificatorInterface * >	m_pepModificatorPtrList

Detailed Description

Definition at line 33 of file peptidemodificatorpipeline.h.

Constructor & Destructor Documentation

◆ PeptideModificatorPipeline() [1/2]

PeptideModificatorPipeline::PeptideModificatorPipeline ( )

Definition at line 36 of file peptidemodificatorpipeline.cpp.

37{

38}

Referenced by PeptideModificatorPipeline().

◆ PeptideModificatorPipeline() [2/2]

PeptideModificatorPipeline::PeptideModificatorPipeline ( const PeptideModificatorPipeline & other )

Definition at line 40 of file peptidemodificatorpipeline.cpp.

{
  throw PappsoException(
    QObject::tr("unable to copy PeptideModificatorPipeline object"));
  if(other.mp_peptideModificatorTee != nullptr)
    {
      // mp_peptideModificatorTee = new
      // PeptideModificatorTee(other.mp_peptideModificatorTee);
    }
 
  mp_lastPeptideSinkInterface = nullptr;
  mp_firstModificator         = nullptr;
  for(auto p_mod : other.m_pepModificatorPtrList)
    {
      delete(p_mod);
    }
 
 
  m_sink = other.m_sink;
 
  mp_lastPeptideSinkInterface = other.mp_lastPeptideSinkInterface;
 
  mp_firstModificator = other.mp_firstModificator;
 
  m_pepModificatorPtrList = other.m_pepModificatorPtrList;
}

References PeptideModificatorPipeline(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, and mp_peptideModificatorTee.

◆ ~PeptideModificatorPipeline()

PeptideModificatorPipeline::~PeptideModificatorPipeline ( )

virtual

Definition at line 68 of file peptidemodificatorpipeline.cpp.

{
 
  for(auto p_mod : m_pepModificatorPtrList)
    {
      delete(p_mod);
    }
  if(mp_peptideModificatorTee == nullptr)
    {
      delete(mp_peptideModificatorTee);
    }
}

References m_pepModificatorPtrList, and mp_peptideModificatorTee.

Member Function Documentation

◆ addFixedCterModificationString()

void PeptideModificatorPipeline::addFixedCterModificationString ( const QString & mod_str )

Definition at line 109 of file peptidemodificatorpipeline.cpp.

{
  privAddFixedModificationString(mod_str, false, true, false);
}

References privAddFixedModificationString().

◆ addFixedModificationString()

void PeptideModificatorPipeline::addFixedModificationString ( const QString & mod_str )

Definition at line 98 of file peptidemodificatorpipeline.cpp.

{
  privAddFixedModificationString(mod_str, true, true, true);
}

References privAddFixedModificationString().

◆ addFixedNterModificationString()

void PeptideModificatorPipeline::addFixedNterModificationString ( const QString & mod_str )

Definition at line 103 of file peptidemodificatorpipeline.cpp.

{
  privAddFixedModificationString(mod_str, true, false, false);
}

References privAddFixedModificationString().

◆ addLabeledModificationString()

void PeptideModificatorPipeline::addLabeledModificationString ( const QString & mod_str )

Definition at line 262 of file peptidemodificatorpipeline.cpp.

{
 
  if(m_sink == nullptr)
    {
      throw PappsoException(QObject::tr(
        "Please use setSink before addLabeledModificationString function"));
    }
  if(mp_peptideModificatorTee == nullptr)
    {
      mp_peptideModificatorTee = new PeptideModificatorTee;
    }
  if(mp_firstModificator == nullptr)
    {
      mp_firstModificator = mp_peptideModificatorTee;
    }
 
  // backup pointers
  PeptideModificatorInterface *backup_sink = m_sink;
 
  PeptideSpSinkInterface *backup_p_last_peptide_sink_interface =
    mp_lastPeptideSinkInterface;
 
  PeptideModificatorInterface *backup_p_first_modificator = mp_firstModificator;
 
 
  QStringList mod_list_str =
    mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
  for(auto i = 0; i < mod_list_str.size(); ++i)
    {
      parseLabeledModification(mod_list_str[i], true, true, true);
 
      if(i == 0)
        {
          mp_peptideModificatorTee->addModificator(mp_firstModificator);
        }
    }
 
  m_sink                      = backup_sink;
  mp_lastPeptideSinkInterface = backup_p_last_peptide_sink_interface;
  mp_firstModificator         = backup_p_first_modificator;
 
  mp_lastPeptideSinkInterface->setSink(mp_peptideModificatorTee);
}

References m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, mp_peptideModificatorTee, and parseLabeledModification().

◆ addPotentialCterModificationString()

void PeptideModificatorPipeline::addPotentialCterModificationString ( const QString & mod_str )

Definition at line 182 of file peptidemodificatorpipeline.cpp.

{
  privAddPotentialModificationString(mod_str, false, true, false);
}

References privAddPotentialModificationString().

◆ addPotentialModificationString()

void PeptideModificatorPipeline::addPotentialModificationString ( const QString & mod_str )

Definition at line 168 of file peptidemodificatorpipeline.cpp.

{
  privAddPotentialModificationString(mod_str, true, true, true);
}

References privAddPotentialModificationString().

◆ addPotentialNterModificationString()

void PeptideModificatorPipeline::addPotentialNterModificationString ( const QString & mod_str )

Definition at line 175 of file peptidemodificatorpipeline.cpp.

{
  privAddPotentialModificationString(mod_str, true, false, false);
}

References privAddPotentialModificationString().

◆ parseFixedModification()

void PeptideModificatorPipeline::parseFixedModification	(	const QString &	mod_str,
		bool	Nter,
		bool	Cter,
		bool	else_prot )

private

Definition at line 136 of file peptidemodificatorpipeline.cpp.

{
 
  QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts);
 
  pappso::AaModificationP aa_mod = AaModification::getInstance(str_split[0]);
 
  PeptideFixedModificationBuilder *mod =
    new PeptideFixedModificationBuilder(aa_mod);
  mod->setModificationPattern(str_split[1]);
  mod->setSink(m_sink);
  mod->setProtNter(Nter);
  mod->setProtCter(Cter);
  mod->setProtElse(else_prot);
 
  m_pepModificatorPtrList.push_back(mod);
 
  if(mp_firstModificator == nullptr)
    {
      mp_firstModificator = mod;
    }
  else
    {
      mp_lastPeptideSinkInterface->setSink(mod);
    }
  mp_lastPeptideSinkInterface = mod;
}

References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideFixedModificationBuilder::setProtCter(), pappso::PeptideFixedModificationBuilder::setProtElse(), pappso::PeptideFixedModificationBuilder::setProtNter(), and pappso::PeptideFixedModificationBuilder::setSink().

Referenced by privAddFixedModificationString().

◆ parseLabeledModification()

void PeptideModificatorPipeline::parseLabeledModification	(	const QString &	mod_str,
		bool	Nter,
		bool	Cter,
		bool	else_prot )

private

Definition at line 309 of file peptidemodificatorpipeline.cpp.

{
 
  QStringList str_split          = mod_str.split("@", Qt::SkipEmptyParts);
  pappso::AaModificationP aa_mod = AaModification::getInstance(str_split[0]);
 
  PeptideFixedModificationBuilder *mod =
    new PeptideFixedModificationBuilder(aa_mod);
  mod->setModificationPattern(str_split[1]);
  mod->setSink(m_sink);
  mod->setProtNter(Nter);
  mod->setProtCter(Cter);
  mod->setProtCter(else_prot);
 
  m_pepModificatorPtrList.push_back(mod);
 
  mp_lastPeptideSinkInterface->setSink(mod);
  mp_lastPeptideSinkInterface = mod;
  mp_firstModificator         = mod;
}

References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideFixedModificationBuilder::setProtCter(), pappso::PeptideFixedModificationBuilder::setProtNter(), and pappso::PeptideFixedModificationBuilder::setSink().

Referenced by addLabeledModificationString().

◆ parsePotentialModification()

void PeptideModificatorPipeline::parsePotentialModification	(	const QString &	mod_str,
		bool	Nter,
		bool	Cter,
		bool	else_prot )

private

Definition at line 210 of file peptidemodificatorpipeline.cpp.

{
 
  QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts);
 
  QString mod_acc_str       = str_split[0];
  QStringList str_acc_split = mod_acc_str.split("(", Qt::SkipEmptyParts);
  pappso::AaModificationP aa_mod =
    AaModification::getInstance(str_acc_split[0]);
 
  PeptideVariableModificationBuilder *mod =
    new PeptideVariableModificationBuilder(aa_mod);
 
  // qDebug() << "PeptideModificatorPipeline::parsePotentialModification " << ;
  if(str_acc_split.length() == 2)
    {
      QStringList max_num_str_list =
        str_acc_split[1].replace(")", "").split("-", Qt::SkipEmptyParts);
      if(max_num_str_list.length() == 1)
        {
          mod->setModificationCounter(max_num_str_list[0].toUInt());
        }
      else if(max_num_str_list.length() == 2)
        {
          mod->setMinNumberMod(max_num_str_list[0].toUInt());
          mod->setMaxNumberMod(max_num_str_list[1].toUInt());
        }
    }
  mod->setModificationPattern(str_split[1]);
  mod->setSink(m_sink);
  mod->setProtNter(Nter);
  mod->setProtCter(Cter);
  mod->setProtElse(else_prot);
 
  m_pepModificatorPtrList.push_back(mod);
 
  if(mp_firstModificator == nullptr)
    {
      mp_firstModificator = mod;
    }
  else
    {
      mp_lastPeptideSinkInterface->setSink(mod);
    }
  mp_lastPeptideSinkInterface = mod;
}

References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideVariableModificationBuilder::setMaxNumberMod(), pappso::PeptideVariableModificationBuilder::setMinNumberMod(), pappso::PeptideVariableModificationBuilder::setModificationCounter(), pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideVariableModificationBuilder::setProtCter(), pappso::PeptideVariableModificationBuilder::setProtElse(), pappso::PeptideVariableModificationBuilder::setProtNter(), and pappso::PeptideVariableModificationBuilder::setSink().

Referenced by privAddPotentialModificationString().

◆ privAddFixedModificationString()

void PeptideModificatorPipeline::privAddFixedModificationString	(	const QString &	mod_str,
		bool	Nter,
		bool	Cter,
		bool	else_prot )

private

Definition at line 116 of file peptidemodificatorpipeline.cpp.

{
  //"MOD:00397@C, MOD:00398@R"
  if(mp_peptideModificatorTee != nullptr)
    {
      throw PappsoException(
        QObject::tr("Unable to add fixed modification string after "
                    "addLabeledModificationString function"));
    }
  QStringList mod_list_str =
    mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
  for(auto i = 0; i < mod_list_str.size(); ++i)
    {
      parseFixedModification(mod_list_str[i], Nter, Cter, else_prot);
    }
}

References pappso::Cter, mp_peptideModificatorTee, pappso::Nter, and parseFixedModification().

Referenced by addFixedCterModificationString(), addFixedModificationString(), and addFixedNterModificationString().

◆ privAddPotentialModificationString()

void PeptideModificatorPipeline::privAddPotentialModificationString	(	const QString &	mod_str,
		bool	Nter,
		bool	Cter,
		bool	else_prot )

private

Definition at line 189 of file peptidemodificatorpipeline.cpp.

{
  //"MOD:00397@C, MOD:00398@R"
  if(mp_peptideModificatorTee != nullptr)
    {
      throw PappsoException(
        QObject::tr("Unable to add potential modification string after "
                    "addLabeledModificationString function"));
    }
 
  QStringList mod_list_str =
    mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
  for(auto i = 0; i < mod_list_str.size(); ++i)
    {
      parsePotentialModification(mod_list_str[i], Nter, Cter, else_prot);
    }
}

References pappso::Cter, mp_peptideModificatorTee, pappso::Nter, and parsePotentialModification().

Referenced by addPotentialCterModificationString(), addPotentialModificationString(), and addPotentialNterModificationString().

◆ setPeptide()

void PeptideModificatorPipeline::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 370 of file peptidemodificatorpipeline.cpp.

{
 
  qDebug() << "PeptideModificatorPipeline::setPeptide begin";
 
  Peptide peptide(peptide_str);
 
  PeptideSp peptide_sp = peptide.makePeptideSp();
 
  qDebug() << "PeptideModificatorPipeline::setPeptide m_sink->setPeptideSp";
  setPeptideSp(sequence_database_id,
               protein_sp,
               is_decoy,
               peptide_sp,
               start,
               is_nter,
               missed_cleavage_number,
               semi_enzyme);
  qDebug() << "PeptideModificatorPipeline::setPeptide end";
}

References pappso::Peptide::makePeptideSp(), and setPeptideSp().

◆ setPeptideSp()

void PeptideModificatorPipeline::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 335 of file peptidemodificatorpipeline.cpp.

{
  if(mp_firstModificator == nullptr)
    {
      m_sink->setPeptideSp(sequence_database_id,
                           protein_sp,
                           is_decoy,
                           peptide_sp_original,
                           start,
                           is_nter,
                           missed_cleavage_number,
                           semi_enzyme);
    }
  else
    {
      mp_firstModificator->setPeptideSp(sequence_database_id,
                                        protein_sp,
                                        is_decoy,
                                        peptide_sp_original,
                                        start,
                                        is_nter,
                                        missed_cleavage_number,
                                        semi_enzyme);
    }
}

References m_sink, and mp_firstModificator.

Referenced by setPeptide().

◆ setSink()

void PeptideModificatorPipeline::setSink ( PeptideModificatorInterface * sink )

overridevirtual

Implements pappso::PeptideSpSinkInterface.

Definition at line 82 of file peptidemodificatorpipeline.cpp.

{
  if(mp_peptideModificatorTee != nullptr)
    {
      throw PappsoException(QObject::tr(
        "Please use setSink before addLabeledModificationString function"));
    }
 
  m_sink = sink;
  if(mp_firstModificator != nullptr)
    {
      mp_lastPeptideSinkInterface->setSink(m_sink);
    }
};