libpappsomspp
Library for mass spectrometry
pappso::OboPsiModTerm Class Reference

#include <obopsimodterm.h>

Public Member Functions

 OboPsiModTerm ()
 
virtual ~OboPsiModTerm ()
 
 OboPsiModTerm (const OboPsiModTerm &)
 
OboPsiModTermoperator= (const OboPsiModTerm &)
 
bool isValid () const
 

Public Attributes

QString m_accession
 
QString m_name
 
QString m_definition
 
QString m_psiModLabel
 
QString m_psiMsLabel
 
QString m_diffFormula
 
QString m_origin
 
double m_diffMono = 0
 

Private Member Functions

void parseLine (const QString &line)
 
void clearTerm ()
 

Private Attributes

friend OboPsiMod
 

Static Private Attributes

static QRegularExpression m_firstParse
 
static QRegularExpression m_findExactPsiModLabel
 
static QRegularExpression m_findRelatedPsiMsLabel
 

Detailed Description

Definition at line 31 of file obopsimodterm.h.

Constructor & Destructor Documentation

◆ OboPsiModTerm() [1/2]

pappso::OboPsiModTerm::OboPsiModTerm ( )

Definition at line 51 of file obopsimodterm.cpp.

52{
53}

◆ ~OboPsiModTerm()

pappso::OboPsiModTerm::~OboPsiModTerm ( )
virtual

Definition at line 55 of file obopsimodterm.cpp.

56{
57}

◆ OboPsiModTerm() [2/2]

pappso::OboPsiModTerm::OboPsiModTerm ( const OboPsiModTerm other)

Definition at line 58 of file obopsimodterm.cpp.

59{
60 m_accession = other.m_accession;
61 m_name = other.m_name;
62 m_definition = other.m_definition;
63 m_psiModLabel = other.m_psiModLabel;
64 m_psiMsLabel = other.m_psiMsLabel;
65 m_diffFormula = other.m_diffFormula;
66 m_origin = other.m_origin;
67
68 m_diffMono = other.m_diffMono;
69}

References m_accession, m_definition, m_diffFormula, m_diffMono, m_name, m_origin, m_psiModLabel, and m_psiMsLabel.

Member Function Documentation

◆ clearTerm()

void pappso::OboPsiModTerm::clearTerm ( )
private

Definition at line 175 of file obopsimodterm.cpp.

176{
177 m_accession = "";
178 m_name = "";
179 m_definition = "";
180 m_psiModLabel = "";
181 m_diffFormula = "";
182 m_diffMono = 0;
183 m_origin = "";
184}

References m_accession, m_definition, m_diffFormula, m_diffMono, m_name, m_origin, and m_psiModLabel.

Referenced by pappso::OboPsiMod::parse().

◆ isValid()

bool pappso::OboPsiModTerm::isValid ( ) const

Definition at line 88 of file obopsimodterm.cpp.

89{
90 return (!m_accession.isEmpty());
91}

References m_accession.

Referenced by pappso::OboTermForm::displayOboTerm().

◆ operator=()

OboPsiModTerm & pappso::OboPsiModTerm::operator= ( const OboPsiModTerm other)

Definition at line 72 of file obopsimodterm.cpp.

73{
74 m_accession = other.m_accession;
75 m_name = other.m_name;
76 m_definition = other.m_definition;
77 m_psiModLabel = other.m_psiModLabel;
78 m_psiMsLabel = other.m_psiMsLabel;
79 m_diffFormula = other.m_diffFormula;
80 m_origin = other.m_origin;
81
82 m_diffMono = other.m_diffMono;
83 return *this;
84}

References m_accession, m_definition, m_diffFormula, m_diffMono, m_name, m_origin, m_psiModLabel, and m_psiMsLabel.

◆ parseLine()

void pappso::OboPsiModTerm::parseLine ( const QString &  line)
private

Definition at line 94 of file obopsimodterm.cpp.

95{
96 // qDebug() << "OboPsiModTerm::parseLine begin " << line;
97 // id: MOD:00007
98 QRegularExpressionMatch match_line = m_firstParse.match(line);
99 if(match_line.hasMatch())
100 {
101 QStringList pline = match_line.capturedTexts();
102 // qDebug() << "OboPsiModTerm::parseLine match " << pline[0] << pline[1];
103 if(pline[1] == "id")
104 {
105 m_accession = pline[2].trimmed();
106 // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession;
107 }
108 else if(pline[1] == "name")
109 {
110 m_name = pline[2].trimmed();
111 // qDebug() << "OboPsiModTerm::parseLine accession = " << m_accession;
112 }
113 else if(pline[1] == "xref")
114 {
115 // xref: DiffMono: "1.007276"
116 QRegularExpressionMatch match_subline = m_firstParse.match(pline[2]);
117 if(match_subline.hasMatch())
118 {
119 QStringList psecond = match_subline.capturedTexts();
120 if(psecond[1] == "DiffMono")
121 {
122 m_diffMono = psecond[2].replace("\"", "").toDouble();
123 // qDebug() << "OboPsiModTerm::parseLine m_diffMono = " <<
124 // m_diffMono;
125 }
126 else if(psecond[1] == "DiffFormula")
127 {
128 m_diffFormula = psecond[2].trimmed().replace("\"", "");
129 // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
130 // m_diffFormula<<"|";
131 }
132 else if(psecond[1] == "Origin")
133 {
134 m_origin =
135 psecond[2].trimmed().replace("\"", "").replace(",", "");
136 // qDebug() << "OboPsiModTerm::parseLine m_diffFormula = |" <<
137 // m_diffFormula<<"|";
138 }
139 }
140 }
141 else if(pline[1] == "synonym")
142 {
143 // synonym: "Se(S)Res" EXACT PSI-MOD-label []
144 QRegularExpressionMatch match_exact_psimod =
145 m_findExactPsiModLabel.match(pline[2]);
146 if(match_exact_psimod.hasMatch())
147 {
149 match_exact_psimod.captured(1).trimmed().replace("\"", "");
150 // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" <<
151 // m_psiModLabel<<"|";
152 }
153 else
154 {
155 QRegularExpressionMatch match_related_psims =
156 m_findRelatedPsiMsLabel.match(pline[2]);
157 if(match_related_psims.hasMatch())
158 {
160 match_related_psims.captured(1).trimmed().replace("\"", "");
161 // qDebug() << "OboPsiModTerm::parseLine m_psiModLabel = |" <<
162 // m_psiModLabel<<"|";
163 }
164 }
165 }
166 else if(pline[1] == "def")
167 {
168 // def: "A protein modification that modifies an L-asparagine
169 // residue." [PubMed:18688235]
170 m_definition = pline[2];
171 }
172 }
173}
static QRegularExpression m_firstParse
Definition: obopsimodterm.h:58
static QRegularExpression m_findRelatedPsiMsLabel
Definition: obopsimodterm.h:60
static QRegularExpression m_findExactPsiModLabel
Definition: obopsimodterm.h:59

References m_accession, m_definition, m_diffFormula, m_diffMono, m_findExactPsiModLabel, m_findRelatedPsiMsLabel, m_firstParse, m_name, m_origin, m_psiModLabel, and m_psiMsLabel.

Referenced by pappso::OboPsiMod::parse().

Member Data Documentation

◆ m_accession

◆ m_definition

QString pappso::OboPsiModTerm::m_definition

◆ m_diffFormula

QString pappso::OboPsiModTerm::m_diffFormula

◆ m_diffMono

◆ m_findExactPsiModLabel

QRegularExpression pappso::OboPsiModTerm::m_findExactPsiModLabel
staticprivate

Definition at line 59 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_findRelatedPsiMsLabel

QRegularExpression pappso::OboPsiModTerm::m_findRelatedPsiMsLabel
staticprivate

Definition at line 60 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_firstParse

QRegularExpression pappso::OboPsiModTerm::m_firstParse
staticprivate

Definition at line 58 of file obopsimodterm.h.

Referenced by parseLine().

◆ m_name

◆ m_origin

QString pappso::OboPsiModTerm::m_origin

◆ m_psiModLabel

QString pappso::OboPsiModTerm::m_psiModLabel

◆ m_psiMsLabel

QString pappso::OboPsiModTerm::m_psiMsLabel

◆ OboPsiMod

friend pappso::OboPsiModTerm::OboPsiMod
private

Definition at line 33 of file obopsimodterm.h.


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