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
MsRunId &	operator= (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
const QString &	getXmlId () const
void	setSampleName (const QString &name)
	set a sample name for this MsRunId
const QString &	getSampleName () const
void	setMsDataFormat (Enums::MsDataFormat format)
Enums::MsDataFormat	getMsDataFormat () const
QString	toString () const
bool	isValid () const

Private Attributes
QString	m_fileName = "NOT_SET"
QString	m_runId
QString	m_xmlId
QString	m_sampleName
Enums::MsDataFormat	m_mzFormat = Enums::MsDataFormat::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 53 of file msrunid.h.

Constructor & Destructor Documentation

◆ MsRunId() [1/4]

pappso::MsRunId::MsRunId ( )

Definition at line 38 of file msrunid.cpp.

39{

40}

Referenced by MsRunId(), MsRunId(), operator=(), and operator==().

◆ MsRunId() [2/4]

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

Definition at line 43 of file msrunid.cpp.

                                         : m_fileName(file_name)
{
  // by default, the sample name is given by the file name
  QFileInfo fileinfo(m_fileName);
  if(fileinfo.fileName() == "analysis.tdf")
    {
      m_fileName = fileinfo.absoluteDir().absolutePath();
    }
  m_sampleName = QFileInfo(m_fileName).baseName();
}

References m_fileName, and m_sampleName.

◆ MsRunId() [3/4]

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

Definition at line 55 of file msrunid.cpp.

                                                                : MsRunId(file_name)
{
  m_runId = run_id;
}

References MsRunId(), and m_runId.

◆ MsRunId() [4/4]

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

Definition at line 61 of file msrunid.cpp.

  : m_fileName(other.m_fileName),
    m_runId(other.m_runId),
    m_xmlId(other.m_xmlId),
    m_sampleName(other.m_sampleName),
    m_mzFormat(other.m_mzFormat)
{
}

References MsRunId(), m_fileName, m_mzFormat, m_runId, m_sampleName, and m_xmlId.

◆ ~MsRunId()

pappso::MsRunId::~MsRunId ( )

virtual

Definition at line 71 of file msrunid.cpp.

72{

73}

Member Function Documentation

◆ getFileName()

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

Definition at line 161 of file msrunid.cpp.

{
  return m_fileName;
}

References m_fileName.

Referenced by pappso::MzxmlOutput::writeHeader().

◆ getMsDataFormat()

Enums::MsDataFormat pappso::MsRunId::getMsDataFormat ( ) const

Definition at line 175 of file msrunid.cpp.

{
  return m_mzFormat;
}

References m_mzFormat.

◆ getRunId()

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

Definition at line 140 of file msrunid.cpp.

{
  return m_runId;
}

References m_runId.

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

◆ getSampleName()

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

Definition at line 84 of file msrunid.cpp.

{
  return m_sampleName;
}

References m_sampleName.

Referenced by pappso::MgfOutput::write().

◆ getXmlId()

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

Definition at line 154 of file msrunid.cpp.

{
  return m_xmlId;
}

References m_xmlId.

Referenced by pappso::IonMobilityGrid::storeObservedIdentityBetween(), and pappso::IonMobilityGrid::translateXicCoordFromTo().

◆ isValid()

bool pappso::MsRunId::isValid ( ) const

Definition at line 220 of file msrunid.cpp.

{
  return !m_fileName.isEmpty() && !m_runId.isEmpty() && !m_xmlId.isEmpty() &&
         m_mzFormat != Enums::MsDataFormat::unknown;
}

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

◆ operator=()

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

Definition at line 191 of file msrunid.cpp.

{
  m_xmlId      = other.m_xmlId;
  m_fileName   = other.m_fileName;
  m_sampleName = other.m_sampleName;
  m_mzFormat   = other.m_mzFormat;
 
  return *this;
}

References MsRunId(), m_fileName, m_mzFormat, m_sampleName, and m_xmlId.

◆ operator==()

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

Definition at line 182 of file msrunid.cpp.

{
  if(m_xmlId == other.m_xmlId)
    return true;
  return false;
}

References MsRunId(), and m_xmlId.

◆ setFileName()

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

Definition at line 91 of file msrunid.cpp.

{
 
  QFileInfo fileinfo(file_name);
  if(fileinfo.fileName() == "analysis.tdf")
    {
      m_fileName = fileinfo.absoluteDir().absolutePath();
    }
  else
    {
      m_fileName = file_name;
    }
 
  QString extension = fileinfo.suffix();
 
  if(m_sampleName.isEmpty())
    {
      // set sample name by default :
      m_sampleName = QFileInfo(m_fileName).baseName();
    }
 
  m_mzFormat = Enums::MsDataFormat::unknown;
 
  if(extension.toLower() == "mzxml")
    {
      m_mzFormat = Enums::MsDataFormat::mzXML;
    }
  else if(extension.toLower() == "mgf")
    {
      m_mzFormat = Enums::MsDataFormat::MGF;
    }
  else if(extension.toLower() == "mzml")
    {
      m_mzFormat = Enums::MsDataFormat::mzML;
    }
  else if((extension.toLower() == "mzcbor") || (extension.toLower() == "cbor"))
    {
      m_mzFormat = Enums::MsDataFormat::mzcbor;
    }
}

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

◆ setMsDataFormat()

void pappso::MsRunId::setMsDataFormat ( Enums::MsDataFormat format )

Definition at line 168 of file msrunid.cpp.

{
  m_mzFormat = format;
}

References m_mzFormat.

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

◆ setRunId()

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

Definition at line 133 of file msrunid.cpp.

{
  m_runId = run_id;
}

References m_runId.

Referenced by pappso::BafAsciiFileReader::getMsRunIds(), 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 77 of file msrunid.cpp.

{
  m_sampleName = name;
}

References m_sampleName.

Referenced by pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::BafAsciiFileReader::getMsRunIds(), pappso::MzcborMsFileReader::getMsRunIds(), 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_id this id must respect XML constraints (no space characters)

Definition at line 147 of file msrunid.cpp.

{
  m_xmlId = xml_id;
}

References m_xmlId.

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

◆ toString()

QString pappso::MsRunId::toString ( ) const

Definition at line 203 of file msrunid.cpp.

{
  QString text = QString(
                   "file name: '%1'\n"
                   "run id: '%2'\n"
                   "xml id: '%3'\n"
                   "sample name: '%4'\n")
                   .arg(m_fileName)
                   .arg(m_runId)
                   .arg(m_xmlId)
                   .arg(m_sampleName);
 
  return text;
}

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 90 of file msrunid.h.

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

◆ m_mzFormat

Enums::MsDataFormat pappso::MsRunId::m_mzFormat = Enums::MsDataFormat::mzXML

private

Definition at line 94 of file msrunid.h.

Referenced by MsRunId(), getMsDataFormat(), isValid(), operator=(), setFileName(), and setMsDataFormat().

◆ m_runId

QString pappso::MsRunId::m_runId

private

Definition at line 91 of file msrunid.h.

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

◆ m_sampleName

QString pappso::MsRunId::m_sampleName

private

Definition at line 93 of file msrunid.h.

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

◆ m_xmlId

QString pappso::MsRunId::m_xmlId

private

Definition at line 92 of file msrunid.h.

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

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

pappsomspp/core/msrun/msrunid.h
pappsomspp/core/msrun/msrunid.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MsRunId() [1/4]

◆ MsRunId() [2/4]

◆ MsRunId() [3/4]

◆ MsRunId() [4/4]

◆ ~MsRunId()

Member Function Documentation

◆ getFileName()

◆ getMsDataFormat()

◆ getRunId()

◆ getSampleName()

◆ getXmlId()

◆ isValid()

◆ operator=()

◆ operator==()

◆ setFileName()

◆ setMsDataFormat()

◆ setRunId()

◆ setSampleName()

◆ setXmlId()

◆ toString()

Member Data Documentation

◆ m_fileName

◆ m_mzFormat

◆ m_runId

◆ m_sampleName

◆ m_xmlId