libpappsomspp
Library for mass spectrometry
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pappso::PeptideProFormaParser Class Reference

#include <peptideproformaparser.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 _rx_psimod
 
static QRegularExpression _rx_modmass
 

Detailed Description

Todo:
write docs

Definition at line 38 of file peptideproformaparser.h.

Member Function Documentation

◆ parseNoConstString()

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

Definition at line 121 of file peptideproformaparser.cpp.

122{
123
124 // QMutexLocker locker(&_mutex);
125 Peptide peptide("");
127
128 return (peptide.makeNoConstPeptideSp());
129}
static void parseStringToPeptide(const QString &pepstr, Peptide &peptide)

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

◆ parseString()

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

Definition at line 110 of file peptideproformaparser.cpp.

111{
112
113 // QMutexLocker locker(&_mutex);
114 Peptide peptide("");
116 // qDebug() << peptide.toProForma();
117 return (peptide.makePeptideSp());
118}

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

◆ parseStringToPeptide()

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

Definition at line 41 of file peptideproformaparser.cpp.

43{
44 // Peptide
45 // peptide2("C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAVEGPK");
46 // CCAADDKEACFAVEGPK
47 /*
48 <psimod position="1" accession="MOD:00397"/>
49 <psimod position="2" accession="MOD:00397"/>
50 <psimod position="10" accession="MOD:00397"/>
51 <psimod position="1" accession="MOD:01160"/>
52 */
53
54 std::size_t i = 0;
55 std::size_t end = pepstr.size();
56 while(i < end)
57 {
58 QChar aa_char = pepstr[i];
59 if(aa_char == '[')
60 {
61 QString mod;
62 i++;
63 aa_char = pepstr[i];
64 while((i < end) && (aa_char != ']'))
65 {
66 mod.append(aa_char);
67 i++;
68 aa_char = pepstr[i];
69 }
70 // we have a mod
71 // is it a double ?
72 bool is_double = false;
73 double mass_modif = mod.toDouble(&is_double);
74 if(is_double)
75 {
76 peptide.m_aaVec.back().addAaModification(
78 }
79 else
80 {
81 peptide.m_aaVec.back().addAaModification(
83 }
84 }
85 else
86 {
87 if(aa_char.isLetter())
88 {
89 Aa pappso_aa(aa_char.toLatin1());
90 if(peptide.size() == 0)
91 {
92 pappso_aa.addAaModification(AaModification::getInstance(
93 "internal:Nter_hydrolytic_cleavage_H"));
94 }
95 peptide.m_aaVec.push_back(pappso_aa);
96 }
97 }
98 i++;
99 }
100
101 peptide.m_aaVec.back().addAaModification(
102 AaModification::getInstance("internal:Cter_hydrolytic_cleavage_HO"));
103
104 // qDebug() << peptide.toProForma();
105 peptide.m_proxyMass = -1;
106 peptide.getMass();
107}
static AaModificationP getInstance(const QString &accession)
static AaModificationP getInstanceCustomizedMod(pappso_double modificationMass)

References pappso::Aa::addAaModification(), pappso::AaModification::getInstance(), pappso::AaModification::getInstanceCustomizedMod(), pappso::Peptide::getMass(), pappso::Peptide::m_aaVec, pappso::Peptide::m_proxyMass, and pappso::Peptide::size().

Referenced by parseNoConstString(), and parseString().

Member Data Documentation

◆ _rx_modmass

QRegularExpression pappso::PeptideProFormaParser::_rx_modmass
staticprivate

Definition at line 52 of file peptideproformaparser.h.

◆ _rx_psimod

QRegularExpression pappso::PeptideProFormaParser::_rx_psimod
staticprivate

Definition at line 51 of file peptideproformaparser.h.


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