libpappsomspp
Library for mass spectrometry
pappso::MsRunId Class Reference

MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL) More...

#include <msrunid.h>

Public Member Functions

 MsRunId ()
 
 MsRunId (const QString &file_name)
 
 MsRunId (const QString &file_name, const QString &run_id)
 
 MsRunId (const MsRunId &other)
 
virtual ~MsRunId ()
 
bool operator== (const MsRunId &other) const
 
MsRunIdoperator= (const MsRunId &other)
 
void setFileName (const QString &file_name)
 
const QString & getFileName () const
 
void setRunId (const QString &run_id)
 
const QString & getRunId () const
 
void setXmlId (const QString &xml_id)
 set an XML unique identifier for this MsRunId More...
 
const QString & getXmlId () const
 
void setSampleName (const QString &name)
 set a sample name for this MsRunId More...
 
const QString & getSampleName () const
 
void setMzFormat (MzFormat format)
 
MzFormat getMzFormat () const
 
QString toString () const
 
bool isValid () const
 

Private Attributes

QString m_fileName = "NOT_SET"
 
QString m_runId
 
QString m_xmlId
 
QString m_sampleName
 
MzFormat m_mzFormat = MzFormat::mzXML
 

Detailed Description

MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL)

Definition at line 52 of file msrunid.h.

Constructor & Destructor Documentation

◆ MsRunId() [1/4]

pappso::MsRunId::MsRunId ( )

Definition at line 39 of file msrunid.cpp.

40 {
41 }

◆ MsRunId() [2/4]

pappso::MsRunId::MsRunId ( const QString &  file_name)

Definition at line 44 of file msrunid.cpp.

44  : m_fileName(file_name)
45 {
46  // by default, the sample name is given by the file name
47  QFileInfo fileinfo(m_fileName);
48  if(fileinfo.fileName() == "analysis.tdf")
49  {
50  m_fileName = fileinfo.absoluteDir().absolutePath();
51  }
52  m_sampleName = QFileInfo(m_fileName).baseName();
53 }
QString m_sampleName
Definition: msrunid.h:92
QString m_fileName
Definition: msrunid.h:89

References m_fileName, and m_sampleName.

◆ MsRunId() [3/4]

pappso::MsRunId::MsRunId ( const QString &  file_name,
const QString &  run_id 
)

Definition at line 56 of file msrunid.cpp.

57  : MsRunId(file_name)
58 {
59  m_runId = run_id;
60 }
QString m_runId
Definition: msrunid.h:90

References m_runId.

◆ MsRunId() [4/4]

pappso::MsRunId::MsRunId ( const MsRunId other)

Definition at line 63 of file msrunid.cpp.

64  : m_fileName(other.m_fileName),
65  m_runId(other.m_runId),
66  m_xmlId(other.m_xmlId),
67  m_sampleName(other.m_sampleName),
68  m_mzFormat(other.m_mzFormat)
69 {
70 }
MzFormat m_mzFormat
Definition: msrunid.h:93
QString m_xmlId
Definition: msrunid.h:91

◆ ~MsRunId()

pappso::MsRunId::~MsRunId ( )
virtual

Definition at line 73 of file msrunid.cpp.

74 {
75 }

Member Function Documentation

◆ getFileName()

const QString & pappso::MsRunId::getFileName ( ) const

Definition at line 151 of file msrunid.cpp.

152 {
153  return m_fileName;
154 }

References m_fileName.

◆ getMzFormat()

MzFormat pappso::MsRunId::getMzFormat ( ) const

Definition at line 165 of file msrunid.cpp.

166 {
167  return m_mzFormat;
168 }

References m_mzFormat.

◆ getRunId()

const QString & pappso::MsRunId::getRunId ( ) const

Definition at line 130 of file msrunid.cpp.

131 {
132  return m_runId;
133 }

References m_runId.

Referenced by pappso::XyMsFileReader::getMsRunIds().

◆ getSampleName()

const QString & pappso::MsRunId::getSampleName ( ) const

Definition at line 86 of file msrunid.cpp.

87 {
88  return m_sampleName;
89 }

References m_sampleName.

◆ getXmlId()

const QString & pappso::MsRunId::getXmlId ( ) const

Definition at line 144 of file msrunid.cpp.

145 {
146  return m_xmlId;
147 }

References m_xmlId.

◆ isValid()

bool pappso::MsRunId::isValid ( ) const

Definition at line 210 of file msrunid.cpp.

211 {
212  return !m_fileName.isEmpty() && !m_runId.isEmpty() && !m_xmlId.isEmpty() &&
214 }
@ unknown
unknown format

References m_fileName, m_mzFormat, m_runId, m_xmlId, and pappso::unknown.

◆ operator=()

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

Definition at line 181 of file msrunid.cpp.

182 {
183  m_xmlId = other.m_xmlId;
184  m_fileName = other.m_fileName;
185  m_sampleName = other.m_sampleName;
186  m_mzFormat = other.m_mzFormat;
187 
188  return *this;
189 }

References m_fileName, m_mzFormat, m_sampleName, and m_xmlId.

◆ operator==()

bool pappso::MsRunId::operator== ( const MsRunId other) const

Definition at line 172 of file msrunid.cpp.

173 {
174  if(m_xmlId == other.m_xmlId)
175  return true;
176  return false;
177 }

References m_xmlId.

◆ setFileName()

void pappso::MsRunId::setFileName ( const QString &  file_name)

Definition at line 93 of file msrunid.cpp.

94 {
95  m_fileName = file_name;
96 
97  QFileInfo file_info(file_name);
98  QString extension = file_info.suffix();
99 
100  if(m_sampleName.isEmpty())
101  {
102  // set sample name by default :
103  m_sampleName = file_info.baseName();
104  }
105 
107 
108  if(extension.toLower() == "mzxml")
109  {
111  }
112  else if(extension.toLower() == "mgf")
113  {
115  }
116  else if(extension.toLower() == "mzml")
117  {
119  }
120 }
@ MGF
Mascot format.

References m_fileName, m_mzFormat, m_sampleName, pappso::MGF, pappso::mzML, pappso::mzXML, and pappso::unknown.

◆ setMzFormat()

void pappso::MsRunId::setMzFormat ( MzFormat  format)

◆ setRunId()

void pappso::MsRunId::setRunId ( const QString &  run_id)

Definition at line 123 of file msrunid.cpp.

124 {
125  m_runId = run_id;
126 }

References m_runId.

Referenced by pappso::TimsMsFileReader::getMsRunIds(), and pappso::XyMsFileReader::getMsRunIds().

◆ setSampleName()

void pappso::MsRunId::setSampleName ( const QString &  name)

set a sample name for this MsRunId

Definition at line 79 of file msrunid.cpp.

80 {
81  m_sampleName = name;
82 }

References m_sampleName.

Referenced by pappso::PwizMsFileReader::getMsRunIds(), pappso::TimsMsFileReader::getMsRunIds(), and pappso::XyMsFileReader::getMsRunIds().

◆ setXmlId()

void pappso::MsRunId::setXmlId ( const QString &  xml_id)

set an XML unique identifier for this MsRunId

Parameters
xml_idthis id must respect XML constraints (no space characters)

Definition at line 137 of file msrunid.cpp.

138 {
139  m_xmlId = xml_id;
140 }

References m_xmlId.

Referenced by pappso::PwizMsFileReader::getMsRunIds(), pappso::TimsMsFileReader::getMsRunIds(), pappso::XyMsFileReader::getMsRunIds(), and pappso::MsFileAccessor::getMsRunReaderSPtrByRunId().

◆ toString()

QString pappso::MsRunId::toString ( ) const

Definition at line 193 of file msrunid.cpp.

194 {
195  QString text = QString(
196  "file name: '%1'\n"
197  "run id: '%2'\n"
198  "xml id: '%3'\n"
199  "sample name: '%4'\n")
200  .arg(m_fileName)
201  .arg(m_runId)
202  .arg(m_xmlId)
203  .arg(m_sampleName);
204 
205  return text;
206 }

References m_fileName, m_runId, m_sampleName, and m_xmlId.

Referenced by pappso::TimsMsFileReader::getMsRunIds().

Member Data Documentation

◆ m_fileName

QString pappso::MsRunId::m_fileName = "NOT_SET"
private

Definition at line 89 of file msrunid.h.

Referenced by MsRunId(), getFileName(), isValid(), operator=(), setFileName(), and toString().

◆ m_mzFormat

MzFormat pappso::MsRunId::m_mzFormat = MzFormat::mzXML
private

Definition at line 93 of file msrunid.h.

Referenced by getMzFormat(), isValid(), operator=(), setFileName(), and setMzFormat().

◆ m_runId

QString pappso::MsRunId::m_runId
private

Definition at line 90 of file msrunid.h.

Referenced by MsRunId(), getRunId(), isValid(), setRunId(), and toString().

◆ m_sampleName

QString pappso::MsRunId::m_sampleName
private

Definition at line 92 of file msrunid.h.

Referenced by MsRunId(), getSampleName(), operator=(), setFileName(), setSampleName(), and toString().

◆ m_xmlId

QString pappso::MsRunId::m_xmlId
private

Definition at line 91 of file msrunid.h.

Referenced by getXmlId(), isValid(), operator=(), operator==(), setXmlId(), and toString().


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