pappso::MassSpectrumId Class Reference

#include <massspectrumid.h>

Public Member Functions
	MassSpectrumId ()
	MassSpectrumId (const MsRunIdCstSPtr &msrun_id)
	MassSpectrumId (const MsRunIdCstSPtr &msrun_id, std::size_t spectrum_index)
	MassSpectrumId (const MassSpectrumId &other)
	~MassSpectrumId ()
MassSpectrumId &	operator= (const MassSpectrumId &other)
void	setMsRunId (MsRunIdCstSPtr other)
const MsRunIdCstSPtr &	getMsRunIdCstSPtr () const
void	setNativeId (const QString &native_id)
const QString &	getNativeId () const
void	setSpectrumIndex (std::size_t index)
std::size_t	getSpectrumIndex () const
bool	operator== (const MassSpectrumId &other) const
bool	isValid () const
QString	toString () const

Private Attributes
MsRunIdCstSPtr	mcsp_msRunId = nullptr
QString	m_nativeId
std::size_t	m_spectrumIndex = std::numeric_limits<std::size_t>::max()

Detailed Description

Definition at line 39 of file massspectrumid.h.

Constructor & Destructor Documentation

MassSpectrumId() [1/4]

pappso::MassSpectrumId::MassSpectrumId

(

)

Definition at line 34 of file massspectrumid.cpp.

{
}

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

MassSpectrumId() [2/4]

pappso::MassSpectrumId::MassSpectrumId

(

const MsRunIdCstSPtr &

msrun_id

)

Definition at line 39 of file massspectrumid.cpp.

  : mcsp_msRunId(msRunId)
{
}

References mcsp_msRunId.

MassSpectrumId() [3/4]

pappso::MassSpectrumId::MassSpectrumId	(	const MsRunIdCstSPtr &	msrun_id,
		std::size_t	spectrum_index )

Definition at line 45 of file massspectrumid.cpp.

  : mcsp_msRunId(msRunId), m_nativeId(""), m_spectrumIndex(spectrum_index)
{
}

References m_nativeId, m_spectrumIndex, and mcsp_msRunId.

MassSpectrumId() [4/4]

pappso::MassSpectrumId::MassSpectrumId

(

const MassSpectrumId &

other

)

Definition at line 52 of file massspectrumid.cpp.

  : mcsp_msRunId(other.mcsp_msRunId),
    m_nativeId(other.m_nativeId),
    m_spectrumIndex(other.m_spectrumIndex)
{
}

References MassSpectrumId(), m_nativeId, m_spectrumIndex, and mcsp_msRunId.

~MassSpectrumId()

pappso::MassSpectrumId::~MassSpectrumId

(

)

Definition at line 60 of file massspectrumid.cpp.

{
}

Member Function Documentation

getMsRunIdCstSPtr()

const MsRunIdCstSPtr & pappso::MassSpectrumId::getMsRunIdCstSPtr

(

)

const

Definition at line 88 of file massspectrumid.cpp.

{
  return mcsp_msRunId;
};

References mcsp_msRunId.

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

getNativeId()

const QString & pappso::MassSpectrumId::getNativeId

(

)

const

Definition at line 102 of file massspectrumid.cpp.

{
  return m_nativeId;
}

References m_nativeId.

Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum(), pappso::MsRunQualifiedSpectrumLoader::setQualifiedMassSpectrum(), pappso::MsRunReaderRetentionTimeLine::setQualifiedMassSpectrum(), and pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum().

getSpectrumIndex()

std::size_t pappso::MassSpectrumId::getSpectrumIndex

(

)

const

Definition at line 116 of file massspectrumid.cpp.

{
  return m_spectrumIndex;
}

References m_spectrumIndex.

Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum(), pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MgfOutput::write().

isValid()

bool pappso::MassSpectrumId::isValid

(

)

const

Definition at line 130 of file massspectrumid.cpp.

{
  return mcsp_msRunId->isValid() &&
         m_spectrumIndex != std::numeric_limits<std::size_t>::max();
}

References m_spectrumIndex, and mcsp_msRunId.

operator=()

MassSpectrumId & pappso::MassSpectrumId::operator=

(

const MassSpectrumId &

other

)

Definition at line 66 of file massspectrumid.cpp.

{
  if(&other == this)
    return *this;
 
  mcsp_msRunId    = other.mcsp_msRunId;
  m_spectrumIndex = other.m_spectrumIndex;
  m_nativeId      = other.m_nativeId;
 
  return *this;
}

References MassSpectrumId(), m_nativeId, m_spectrumIndex, and mcsp_msRunId.

operator==()

bool pappso::MassSpectrumId::operator==

(

const MassSpectrumId &

other

)

const

Definition at line 123 of file massspectrumid.cpp.

{
  return (mcsp_msRunId == other.mcsp_msRunId &&
          m_spectrumIndex == other.m_spectrumIndex);
}

References MassSpectrumId(), m_spectrumIndex, and mcsp_msRunId.

setMsRunId()

void pappso::MassSpectrumId::setMsRunId

(

MsRunIdCstSPtr

other

)

Definition at line 80 of file massspectrumid.cpp.

{
 
  mcsp_msRunId = other;
};

References mcsp_msRunId.

Referenced by pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

setNativeId()

void pappso::MassSpectrumId::setNativeId

(

const QString &

native_id

)

Definition at line 95 of file massspectrumid.cpp.

{
  m_nativeId = native_id;
}

References m_nativeId.

Referenced by pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

setSpectrumIndex()

void pappso::MassSpectrumId::setSpectrumIndex

(

std::size_t

index

)

Definition at line 109 of file massspectrumid.cpp.

{
  m_spectrumIndex = index;
}

References m_spectrumIndex.

Referenced by pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

toString()

QString pappso::MassSpectrumId::toString

(

)

const

Definition at line 138 of file massspectrumid.cpp.

{
  return QString(
           "ms run id: %1 \n"
           "native id: %2 \n"
           "m_spectrumIndex: %3\n")
    .arg(mcsp_msRunId != nullptr ? mcsp_msRunId->toString() : "nullptr")
    .arg(m_nativeId)
    .arg(m_spectrumIndex);
}

References m_nativeId, m_spectrumIndex, and mcsp_msRunId.

Member Data Documentation

m_nativeId

QString pappso::MassSpectrumId::m_nativeId

private

Definition at line 51 of file massspectrumid.h.

Referenced by MassSpectrumId(), MassSpectrumId(), getNativeId(), operator=(), setNativeId(), and toString().

m_spectrumIndex

std::size_t pappso::MassSpectrumId::m_spectrumIndex = std::numeric_limits<std::size_t>::max()

private

Definition at line 56 of file massspectrumid.h.

Referenced by MassSpectrumId(), MassSpectrumId(), getSpectrumIndex(), isValid(), operator=(), operator==(), setSpectrumIndex(), and toString().

mcsp_msRunId

MsRunIdCstSPtr pappso::MassSpectrumId::mcsp_msRunId = nullptr

private

Definition at line 42 of file massspectrumid.h.

Referenced by MassSpectrumId(), MassSpectrumId(), MassSpectrumId(), getMsRunIdCstSPtr(), isValid(), operator=(), operator==(), setMsRunId(), and toString().

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

• pappsomspp/core/massspectrum/massspectrumid.h
• pappsomspp/core/massspectrum/massspectrumid.cpp