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 QRegExp _mod_parser
 
static QRegExp _rx_psimod
 
static QRegExp _rx_modmass
 

Detailed Description

Definition at line 52 of file peptidestrparser.h.

Member Function Documentation

◆ parseNoConstString()

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

Definition at line 150 of file peptidestrparser.cpp.

◆ parseString()

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

Definition at line 139 of file peptidestrparser.cpp.

◆ parseStringToPeptide()

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

Definition at line 60 of file peptidestrparser.cpp.

60  {
61  qDebug() << "PeptideStrParser::parseString mod " << mod;
62  if(rx_psimod.exactMatch(mod))
63  {
64  qDebug() << "PeptideStrParser::parseString pos-1 "
65  << (pos - 1 - matched_length_cumul);
66  peptide.addAaModification(AaModification::getInstance(mod),
67  pos - 1 - matched_length_cumul);
68  }
69  else if(mod.startsWith("internal:Nter_"))
70  {
71  peptide.setInternalNterModification(
73  }
74  else if(mod.startsWith("internal:Cter_"))
75  {
76  peptide.setInternalCterModification(
78  }
79  else if(rx_modmass.exactMatch(mod))
80  {
81  // number
82  if(!mod.contains("."))
83  {
84  // integer
85  mod = "MOD:0000" + mod;
86  while(mod.size() > 9)
87  {
88  mod = mod.replace(4, 1, "");
89  }
90  peptide.addAaModification(AaModification::getInstance(mod),
91  pos - 1 - matched_length_cumul);
92  }
93  else
94  {
95  peptide.addAaModification(
97  pos - 1 - matched_length_cumul);
98  }
99  }
100  else
101  {
102  FilterOboPsiModSink term_list;
103  FilterOboPsiModTermLabel filter_label(term_list, mod);
104 
105  OboPsiMod psimod(filter_label);
106 
107  peptide.addAaModification(
108  AaModification::getInstance(term_list.getFirst()),
109  pos - 1 - matched_length_cumul);
110  }
111  }
112  matched_length_cumul += mod_parser.matchedLength();
113  pos += mod_parser.matchedLength();
114  }
115 }
116 
117 PeptideSp
118 PeptideStrParser::parseString(const QString &pepstr)
119 {
120 
121  // QMutexLocker locker(&_mutex);
122  Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
124 
125  return (peptide.makePeptideSp());
126 }
127 
129 PeptideStrParser::parseNoConstString(const QString &pepstr)
130 {
131 
132  // QMutexLocker locker(&_mutex);
133  Peptide peptide(QString(pepstr).replace(_mod_parser, ""));
135 
136  return (peptide.makeNoConstPeptideSp());

References pappso::FilterOboPsiModSink::getFirst(), pappso::AaModification::getInstance(), and pappso::AaModification::getInstanceCustomizedMod().

Member Data Documentation

◆ _mod_parser

QRegExp pappso::PeptideStrParser::_mod_parser
staticprivate

Definition at line 83 of file peptidestrparser.h.

◆ _rx_modmass

QRegExp pappso::PeptideStrParser::_rx_modmass
staticprivate

Definition at line 85 of file peptidestrparser.h.

◆ _rx_psimod

QRegExp pappso::PeptideStrParser::_rx_psimod
staticprivate

Definition at line 84 of file peptidestrparser.h.


The documentation for this class was generated from the following files:
pappso::PeptideStrParser::parseNoConstString
static NoConstPeptideSp parseNoConstString(const QString &pepstr)
Definition: peptidestrparser.cpp:150
pappso::PeptideStrParser::parseString
static PeptideSp parseString(const QString &pepstr)
Definition: peptidestrparser.cpp:139
pappso::AaModification::getInstance
static AaModificationP getInstance(const QString &accession)
Definition: aamodification.cpp:388
pappso::AaModification::getInstanceCustomizedMod
static AaModificationP getInstanceCustomizedMod(pappso_double modificationMass)
Definition: aamodification.cpp:368
pappso::PeptideStrParser::_mod_parser
static QRegExp _mod_parser
Definition: peptidestrparser.h:83
pappso::PeptideStrParser::parseStringToPeptide
static void parseStringToPeptide(const QString &pepstr, Peptide &peptide)
Definition: peptidestrparser.cpp:60
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:68
pappso::NoConstPeptideSp
std::shared_ptr< Peptide > NoConstPeptideSp
Definition: peptide.h:111