#include <peptidestrparser.h>

Static Public Member Functions
static PeptideSp	parseString (const QString &pepstr)

static NoConstPeptideSp	parseNoConstString (const QString &pepstr)

Static Private Member Functions
static void	parseStringToPeptide (const QString &pepstr, Peptide &peptide)

Static Private Attributes
static QRegularExpression	_mod_parser

static QRegularExpression	_rx_psimod

static QRegularExpression	_rx_modmass

Detailed Description

Definition at line 32 of file peptidestrparser.h.

Member Function Documentation

◆ parseNoConstString()

NoConstPeptideSp pappso::PeptideStrParser::parseNoConstString ( const QString & pepstr )

static

Definition at line 149 of file peptidestrparser.cpp.

{
 
  qDebug() << pepstr;
  QString new_pep = QString(pepstr).replace(_mod_parser, "");
  qDebug() << new_pep;
  // QMutexLocker locker(&_mutex);
  Peptide peptide(new_pep);
  qDebug();
  PeptideStrParser::parseStringToPeptide(pepstr, peptide);
 
  return (peptide.makeNoConstPeptideSp());
}

References _mod_parser, pappso::Peptide::makeNoConstPeptideSp(), and parseStringToPeptide().

◆ parseString()

PeptideSp pappso::PeptideStrParser::parseString ( const QString & pepstr )

static

Definition at line 137 of file peptidestrparser.cpp.

{
 
  qDebug();
  // QMutexLocker locker(&_mutex);
  Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
  PeptideStrParser::parseStringToPeptide(pepstr, peptide);
 
  return (peptide.makePeptideSp());
}

References _mod_parser, pappso::Peptide::makePeptideSp(), and parseStringToPeptide().

◆ parseStringToPeptide()

void pappso::PeptideStrParser::parseStringToPeptide	(	const QString &	pepstr,
		Peptide &	peptide )

staticprivate

Definition at line 38 of file peptidestrparser.cpp.

{
  // Peptide
  // peptide2("C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK");
  // CCAADDKEACFAVEGPK
  /*
  <psimod position="1"  accession="MOD:00397"/>
    <psimod position="2"  accession="MOD:00397"/>
    <psimod position="10"  accession="MOD:00397"/>
    <psimod position="1"  accession="MOD:01160"/>
    */
  int matched_length_cumul = 0;
  int pos                  = 0;
 
  QRegularExpressionMatch match_mod = _mod_parser.match(pepstr, pos);
 
  while(match_mod.hasMatch())
    {
      pos              = match_mod.capturedStart(0);
      QString captured = match_mod.captured(0);
      qDebug() << " captured=" << captured << " pos=" << pos
               << " match_mod.lastCapturedIndex()=" << match_mod.lastCapturedIndex();
      QStringList mod_list =
        captured.mid(1, captured.size() - 2).split(QRegularExpression("[+,\\,]"));
      for(QString &mod : mod_list)
        {
          qDebug() << "PeptideStrParser::parseString mod " << mod;
          QRegularExpressionMatch match_psimod = _rx_psimod.match(mod);
          if(match_psimod.hasMatch())
            {
              qDebug() << "PeptideStrParser::parseString pos-1 "
                       << (pos - 1 - matched_length_cumul);
              peptide.addAaModification(AaModification::getInstance(mod),
                                        pos - 1 - matched_length_cumul);
            }
          else if(mod.startsWith("internal:Nter_"))
            {
              peptide.setCleavageNterModification(AaModification::getInstance(mod));
            }
          else if(mod.startsWith("internal:Cter_"))
            {
              peptide.setCleavageCterModification(AaModification::getInstance(mod));
            }
          else if(mod.startsWith("C13N15:"))
            {
              qDebug() << "PeptideStrParser::parseString pos-1 "
                       << (pos - 1 - matched_length_cumul);
              peptide.addAaModification(AaModification::getInstance(mod),
                                        pos - 1 - matched_length_cumul);
            }
          else
            {
              qDebug() << "mod=" << mod;
              QRegularExpressionMatch match_modmass = _rx_modmass.match(mod);
              if(match_modmass.hasMatch())
                {
                  // number
                  qDebug() << "number mod=" << mod << " cap=" << match_modmass.captured(0);
                  if(!mod.contains("."))
                    {
                      // integer
                      qDebug() << "integer mod=" << mod;
                      mod = "MOD:0000" + mod;
                      while(mod.size() > 9)
                        {
                          mod = mod.replace(4, 1, "");
                        }
                      peptide.addAaModification(AaModification::getInstance(mod),
                                                pos - 1 - matched_length_cumul);
                    }
                  else
                    {
                      qDebug() << "double mod=" << mod;
                      peptide.addAaModification(
                        AaModification::getInstanceCustomizedMod(mod.toDouble()),
                        pos - 1 - matched_length_cumul);
                    }
                }
              else
                {
                  qDebug() << "not a number mod=" << mod;
                  FilterOboPsiModSink term_list;
                  FilterOboPsiModTermLabel filter_label(term_list, mod);
 
                  OboPsiMod psimod(filter_label);
 
                  peptide.addAaModification(AaModification::getInstance(term_list.getFirst()),
                                            pos - 1 - matched_length_cumul);
                }
            }
        }
      qDebug();
      matched_length_cumul += captured.size();
      match_mod = _mod_parser.match(pepstr, pos + 1);
      qDebug();
    }
}