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 130 of file peptideproformaparser.cpp.

131{
132
133 // QMutexLocker locker(&_mutex);
134 Peptide peptide("");
136
137 return (peptide.makeNoConstPeptideSp());
138}
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 119 of file peptideproformaparser.cpp.

120{
121
122 // QMutexLocker locker(&_mutex);
123 Peptide peptide("");
125 // qDebug() << peptide.toProForma();
126 return (peptide.makePeptideSp());
127}

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

◆ parseStringToPeptide()

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

Definition at line 42 of file peptideproformaparser.cpp.

44{
45 // Peptide
46 // peptide2("C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAVEGPK");
47 // CCAADDKEACFAVEGPK
48 /*
49 <psimod position="1" accession="MOD:00397"/>
50 <psimod position="2" accession="MOD:00397"/>
51 <psimod position="10" accession="MOD:00397"/>
52 <psimod position="1" accession="MOD:01160"/>
53 */
54
55 std::size_t i = 0;
56 std::size_t end = pepstr.size();
57 while(i < end)
58 {
59 QChar aa_char = pepstr[i];
60 if(aa_char == '[')
61 {
62 QString mod;
63 i++;
64 aa_char = pepstr[i];
65 while((i < end) && (aa_char != ']'))
66 {
67 mod.append(aa_char);
68 i++;
69 if(i < end)
70 aa_char = pepstr[i];
71 }
72
73 qDebug() << aa_char;
74 if(aa_char != ']')
75 {
77 QObject::tr("modification string is malformed %1").arg(mod));
78 }
79 // we have a mod
80 // is it a double ?
81 bool is_double = false;
82 double mass_modif = mod.toDouble(&is_double);
83 if(is_double)
84 {
85 peptide.m_aaVec.back().addAaModification(
87 }
88 else
89 {
90 peptide.m_aaVec.back().addAaModification(
92 }
93 }
94 else
95 {
96 if(aa_char.isLetter())
97 {
98 Aa pappso_aa(aa_char.toLatin1());
99 if(peptide.size() == 0)
100 {
101 pappso_aa.addAaModification(AaModification::getInstance(
102 "internal:Nter_hydrolytic_cleavage_H"));
103 }
104 peptide.m_aaVec.push_back(pappso_aa);
105 }
106 }
107 i++;
108 }
109
110 peptide.m_aaVec.back().addAaModification(
111 AaModification::getInstance("internal:Cter_hydrolytic_cleavage_HO"));
112
113 // qDebug() << peptide.toProForma();
114 peptide.m_proxyMass = -1;
115 peptide.getMass();
116}
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: