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: