libpappsomspp
Library for mass spectrometry
pappso::PeptideStrParser Class Reference

#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 146 of file peptidestrparser.cpp.

147 {
148 
149  // QMutexLocker locker(&_mutex);
150  Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
152 
153  return (peptide.makeNoConstPeptideSp());
154 }
static void parseStringToPeptide(const QString &pepstr, Peptide &peptide)
static QRegularExpression _mod_parser

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

◆ parseString()

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

Definition at line 135 of file peptidestrparser.cpp.

136 {
137 
138  // QMutexLocker locker(&_mutex);
139  Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
141 
142  return (peptide.makePeptideSp());
143 }

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.

39 {
40  // Peptide
41  // peptide2("C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK");
42  // CCAADDKEACFAVEGPK
43  /*
44  <psimod position="1" accession="MOD:00397"/>
45  <psimod position="2" accession="MOD:00397"/>
46  <psimod position="10" accession="MOD:00397"/>
47  <psimod position="1" accession="MOD:01160"/>
48  */
49  int matched_length_cumul = 0;
50  int pos = 0;
51 
52  QRegularExpressionMatch match_mod = _mod_parser.match(pepstr, pos);
53 
54  while(match_mod.hasMatch())
55  {
56  pos = match_mod.capturedStart(0);
57  QString captured = match_mod.captured(0);
58  qDebug() << " captured=" << captured << " pos=" << pos
59  << " match_mod.lastCapturedIndex()="
60  << match_mod.lastCapturedIndex();
61  QStringList mod_list = captured.mid(1, captured.size() - 2)
62  .split(QRegularExpression("[+,\\,]"));
63  for(QString &mod : mod_list)
64  {
65  qDebug() << "PeptideStrParser::parseString mod " << mod;
66  QRegularExpressionMatch match_psimod = _rx_psimod.match(mod);
67  if(match_psimod.hasMatch())
68  {
69  qDebug() << "PeptideStrParser::parseString pos-1 "
70  << (pos - 1 - matched_length_cumul);
71  peptide.addAaModification(AaModification::getInstance(mod),
72  pos - 1 - matched_length_cumul);
73  }
74  else if(mod.startsWith("internal:Nter_"))
75  {
76  peptide.setInternalNterModification(
78  }
79  else if(mod.startsWith("internal:Cter_"))
80  {
81  peptide.setInternalCterModification(
83  }
84  else
85  {
86  qDebug() << "mod=" << mod;
87  QRegularExpressionMatch match_modmass = _rx_modmass.match(mod);
88  if(match_modmass.hasMatch())
89  {
90  // number
91  qDebug() << "number mod=" << mod
92  << " cap=" << match_modmass.captured(0);
93  if(!mod.contains("."))
94  {
95  // integer
96  qDebug() << "integer mod=" << mod;
97  mod = "MOD:0000" + mod;
98  while(mod.size() > 9)
99  {
100  mod = mod.replace(4, 1, "");
101  }
102  peptide.addAaModification(
104  pos - 1 - matched_length_cumul);
105  }
106  else
107  {
108  qDebug() << "double mod=" << mod;
109  peptide.addAaModification(
111  mod.toDouble()),
112  pos - 1 - matched_length_cumul);
113  }
114  }
115  else
116  {
117  qDebug() << "not a number mod=" << mod;
118  FilterOboPsiModSink term_list;
119  FilterOboPsiModTermLabel filter_label(term_list, mod);
120 
121  OboPsiMod psimod(filter_label);
122 
123  peptide.addAaModification(
124  AaModification::getInstance(term_list.getFirst()),
125  pos - 1 - matched_length_cumul);
126  }
127  }
128  }
129  matched_length_cumul += captured.size();
130  match_mod = _mod_parser.match(pepstr, pos + 1);
131  }
132 }
static AaModificationP getInstance(const QString &accession)
static AaModificationP getInstanceCustomizedMod(pappso_double modificationMass)
static QRegularExpression _rx_psimod
static QRegularExpression _rx_modmass

References _mod_parser, _rx_modmass, _rx_psimod, pappso::Peptide::addAaModification(), pappso::FilterOboPsiModSink::getFirst(), pappso::AaModification::getInstance(), pappso::AaModification::getInstanceCustomizedMod(), pappso::Peptide::setInternalCterModification(), and pappso::Peptide::setInternalNterModification().

Referenced by parseNoConstString(), and parseString().

Member Data Documentation

◆ _mod_parser

QRegularExpression pappso::PeptideStrParser::_mod_parser
staticprivate

Definition at line 42 of file peptidestrparser.h.

Referenced by parseNoConstString(), parseString(), and parseStringToPeptide().

◆ _rx_modmass

QRegularExpression pappso::PeptideStrParser::_rx_modmass
staticprivate

Definition at line 44 of file peptidestrparser.h.

Referenced by parseStringToPeptide().

◆ _rx_psimod

QRegularExpression pappso::PeptideStrParser::_rx_psimod
staticprivate

Definition at line 43 of file peptidestrparser.h.

Referenced by parseStringToPeptide().


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