libpappsomspp
Library for mass spectrometry
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Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | Friends | List of all members
pappso::GrpProtein Class Reference

#include <grpprotein.h>

Public Types

typedef std::vector< GrpPeptide * >::const_iterator const_iterator
 

Public Member Functions

 GrpProtein (const GrpProtein &other)
 
 ~GrpProtein ()
 
void push_back (GrpPeptide *p_grpPeptide)
 
bool operator== (const GrpProtein &other) const
 
const QString & getAccession () const
 
const QString & getDescription () const
 
const QString getGroupingId () const
 
const_iterator begin () const
 
const_iterator end () const
 
void setRank (unsigned int i)
 
void setGroupNumber (unsigned int i)
 
void setSubGroupNumber (unsigned int i)
 
unsigned int getGroupNumber () const
 
unsigned int getSubGroupNumber () const
 
unsigned int getRank () const
 
unsigned int getCount () const
 

Protected Member Functions

 GrpProtein (const QString &accession, const QString &description)
 
void countPlus ()
 
void strip ()
 ensure that each peptide in peptide list is unique and sorted by pointer adress
 

Protected Attributes

std::vector< GrpPeptide * > m_grpPeptidePtrList
 

Private Attributes

const QString m_accession
 
const QString m_description
 
unsigned int m_groupNumber = 0
 
unsigned int m_subGroupNumber = 0
 
unsigned int m_rank = 0
 
unsigned int m_count = 0
 

Friends

class GrpExperiment
 

Detailed Description

Definition at line 39 of file grpprotein.h.

Member Typedef Documentation

◆ const_iterator

typedef std::vector<GrpPeptide*>::const_iterator pappso::GrpProtein::const_iterator

Definition at line 54 of file grpprotein.h.

Constructor & Destructor Documentation

◆ GrpProtein() [1/2]

GrpProtein::GrpProtein ( const GrpProtein & other)

Definition at line 39 of file grpprotein.cpp.

40 : m_grpPeptidePtrList(other.m_grpPeptidePtrList),
41 m_accession(other.m_accession),
42 m_description(other.m_description)
43
44{
45
46 m_groupNumber = other.m_groupNumber;
47 m_subGroupNumber = other.m_subGroupNumber;
48 m_rank = other.m_rank;
49 m_count = other.m_count;
50}
pappso::GrpProtein::m_accession
const QString m_accession
Definition grpprotein.h:80
pappso::GrpProtein::m_description
const QString m_description
Definition grpprotein.h:81
pappso::GrpProtein::m_rank
unsigned int m_rank
Definition grpprotein.h:84
pappso::GrpProtein::m_grpPeptidePtrList
std::vector< GrpPeptide * > m_grpPeptidePtrList
Definition grpprotein.h:77
pappso::GrpProtein::m_groupNumber
unsigned int m_groupNumber
Definition grpprotein.h:82
pappso::GrpProtein::m_subGroupNumber
unsigned int m_subGroupNumber
Definition grpprotein.h:83
pappso::GrpProtein::m_count
unsigned int m_count
Definition grpprotein.h:85

References GrpProtein(), m_accession, m_count, m_description, m_groupNumber, m_grpPeptidePtrList, m_rank, and m_subGroupNumber.

Referenced by GrpProtein(), GrpExperiment, and operator==().

◆ ~GrpProtein()

GrpProtein::~GrpProtein ( )

Definition at line 52 of file grpprotein.cpp.

53{
54}

◆ GrpProtein() [2/2]

GrpProtein::GrpProtein ( const QString & accession,
const QString & description )
protected

Definition at line 33 of file grpprotein.cpp.

34 : m_accession(accession.simplified()), m_description(description.simplified())
35{
36}

References m_accession, and m_description.

Member Function Documentation

◆ begin()

GrpProtein::const_iterator GrpProtein::begin ( ) const

Definition at line 57 of file grpprotein.cpp.

58{
59 return m_grpPeptidePtrList.begin();
60}

References m_grpPeptidePtrList.

Referenced by pappso::GrpPeptideSet::GrpPeptideSet().

◆ countPlus()

void GrpProtein::countPlus ( )
protected

Definition at line 73 of file grpprotein.cpp.

74{
75 m_count++;
76}

References m_count.

Referenced by pappso::GrpExperiment::setGrpPeptide().

◆ end()

GrpProtein::const_iterator GrpProtein::end ( ) const

Definition at line 62 of file grpprotein.cpp.

63{
64 return m_grpPeptidePtrList.end();
65}

References m_grpPeptidePtrList.

Referenced by pappso::GrpPeptideSet::GrpPeptideSet().

◆ getAccession()

const QString & GrpProtein::getAccession ( ) const

Definition at line 119 of file grpprotein.cpp.

120{
121 return m_accession;
122}

References m_accession.

Referenced by GrpExperiment.

◆ getCount()

unsigned int GrpProtein::getCount ( ) const

Definition at line 68 of file grpprotein.cpp.

69{
70 return m_count;
71}

References m_count.

◆ getDescription()

const QString & GrpProtein::getDescription ( ) const

Definition at line 124 of file grpprotein.cpp.

125{
126 return m_description;
127}

References m_description.

Referenced by GrpExperiment.

◆ getGroupingId()

const QString GrpProtein::getGroupingId ( ) const

Definition at line 100 of file grpprotein.cpp.

101{
102 if(m_groupNumber == 0)
103 {
104 return "";
105 }
106 return QString("%1.%2.%3")
107 .arg(Utils::getLexicalOrderedString(m_groupNumber))
108 .arg(Utils::getLexicalOrderedString(m_subGroupNumber))
109 .arg(Utils::getLexicalOrderedString(m_rank));
110}
pappso::Utils::getLexicalOrderedString
static const QString getLexicalOrderedString(unsigned int num)
Definition utils.cpp:72

References pappso::Utils::getLexicalOrderedString(), m_groupNumber, m_rank, and m_subGroupNumber.

Referenced by GrpExperiment.

◆ getGroupNumber()

unsigned int GrpProtein::getGroupNumber ( ) const

Definition at line 84 of file grpprotein.cpp.

85{
86 return m_groupNumber;
87}

References m_groupNumber.

◆ getRank()

unsigned int GrpProtein::getRank ( ) const

Definition at line 95 of file grpprotein.cpp.

96{
97 return m_rank;
98}

References m_rank.

◆ getSubGroupNumber()

unsigned int GrpProtein::getSubGroupNumber ( ) const

Definition at line 90 of file grpprotein.cpp.

91{
92 return m_subGroupNumber;
93}

References m_subGroupNumber.

◆ operator==()

bool GrpProtein::operator== ( const GrpProtein & other) const

Definition at line 112 of file grpprotein.cpp.

113{
114 return (m_accession == other.m_accession);
115}

References GrpProtein(), and m_accession.

Referenced by GrpExperiment.

◆ push_back()

void GrpProtein::push_back ( GrpPeptide * p_grpPeptide)

Definition at line 129 of file grpprotein.cpp.

130{
131 // p_grpPeptide->push_back(this);
132 m_grpPeptidePtrList.push_back(p_grpPeptide);
133}

References m_grpPeptidePtrList.

Referenced by GrpExperiment, and pappso::GrpExperiment::setGrpPeptide().

◆ setGroupNumber()

void GrpProtein::setGroupNumber ( unsigned int i)

Definition at line 154 of file grpprotein.cpp.

155{
156 m_groupNumber = i;
157}

References m_groupNumber.

◆ setRank()

void GrpProtein::setRank ( unsigned int i)

Definition at line 149 of file grpprotein.cpp.

150{
151 m_rank = i;
152}

References m_rank.

◆ setSubGroupNumber()

void GrpProtein::setSubGroupNumber ( unsigned int i)

Definition at line 78 of file grpprotein.cpp.

79{
80 m_subGroupNumber = i;
81}

References m_subGroupNumber.

◆ strip()

void GrpProtein::strip ( )
protected

ensure that each peptide in peptide list is unique and sorted by pointer adress

Definition at line 136 of file grpprotein.cpp.

137{
138 qDebug() << "GrpProtein::strip begin " << this->m_accession;
139 // m_grpPeptidePtrList.sort();
140 std::sort(m_grpPeptidePtrList.begin(), m_grpPeptidePtrList.end());
141 // m_grpPeptidePtrList.unique();
142 m_grpPeptidePtrList.erase(
143 std::unique(m_grpPeptidePtrList.begin(), m_grpPeptidePtrList.end()),
144 m_grpPeptidePtrList.end());
145 qDebug() << "GrpProtein::strip end";
146}

References m_accession, and m_grpPeptidePtrList.

Friends And Related Symbol Documentation

◆ GrpExperiment

friend class GrpExperiment
friend

Definition at line 41 of file grpprotein.h.

References GrpProtein(), getAccession(), getDescription(), getGroupingId(), GrpExperiment, operator==(), and push_back().

Referenced by GrpExperiment.

Member Data Documentation

◆ m_accession

const QString pappso::GrpProtein::m_accession
private

Definition at line 80 of file grpprotein.h.

Referenced by GrpProtein(), GrpProtein(), getAccession(), operator==(), and strip().

◆ m_count

unsigned int pappso::GrpProtein::m_count = 0
private

Definition at line 85 of file grpprotein.h.

Referenced by GrpProtein(), countPlus(), and getCount().

◆ m_description

const QString pappso::GrpProtein::m_description
private

Definition at line 81 of file grpprotein.h.

Referenced by GrpProtein(), GrpProtein(), and getDescription().

◆ m_groupNumber

unsigned int pappso::GrpProtein::m_groupNumber = 0
private

Definition at line 82 of file grpprotein.h.

Referenced by GrpProtein(), getGroupingId(), getGroupNumber(), and setGroupNumber().

◆ m_grpPeptidePtrList

std::vector<GrpPeptide *> pappso::GrpProtein::m_grpPeptidePtrList
protected

Definition at line 77 of file grpprotein.h.

Referenced by GrpProtein(), begin(), end(), push_back(), and strip().

◆ m_rank

unsigned int pappso::GrpProtein::m_rank = 0
private

Definition at line 84 of file grpprotein.h.

Referenced by GrpProtein(), getGroupingId(), getRank(), and setRank().

◆ m_subGroupNumber

unsigned int pappso::GrpProtein::m_subGroupNumber = 0
private

Definition at line 83 of file grpprotein.h.

Referenced by GrpProtein(), getGroupingId(), getSubGroupNumber(), and setSubGroupNumber().

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