libpappsomspp
Library for mass spectrometry
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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.

35{
36}

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

◆ MassSpectrumId() [2/4]

pappso::MassSpectrumId::MassSpectrumId ( const MsRunIdCstSPtr & msrun_id)

Definition at line 39 of file massspectrumid.cpp.

39 : mcsp_msRunId(msRunId)
40{
41}
pappso::MassSpectrumId::mcsp_msRunId
MsRunIdCstSPtr mcsp_msRunId
Definition massspectrumid.h:42

References mcsp_msRunId.

◆ MassSpectrumId() [3/4]

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

Definition at line 44 of file massspectrumid.cpp.

45 : mcsp_msRunId(msRunId), m_nativeId(""), m_spectrumIndex(spectrum_index)
46{
47}

References m_nativeId, m_spectrumIndex, and mcsp_msRunId.

◆ MassSpectrumId() [4/4]

pappso::MassSpectrumId::MassSpectrumId ( const MassSpectrumId & other)

Definition at line 50 of file massspectrumid.cpp.

51 : mcsp_msRunId(other.mcsp_msRunId),
52 m_nativeId(other.m_nativeId),
53 m_spectrumIndex(other.m_spectrumIndex)
54{
55}

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

◆ ~MassSpectrumId()

pappso::MassSpectrumId::~MassSpectrumId ( )

Definition at line 58 of file massspectrumid.cpp.

59{
60}

Member Function Documentation

◆ getMsRunIdCstSPtr()

const MsRunIdCstSPtr & pappso::MassSpectrumId::getMsRunIdCstSPtr ( ) const

Definition at line 86 of file massspectrumid.cpp.

87{
88 return mcsp_msRunId;
89};

References mcsp_msRunId.

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

◆ getNativeId()

const QString & pappso::MassSpectrumId::getNativeId ( ) const

Definition at line 100 of file massspectrumid.cpp.

101{
102 return m_nativeId;
103}

References m_nativeId.

Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), 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 114 of file massspectrumid.cpp.

115{
116 return m_spectrumIndex;
117}

References m_spectrumIndex.

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

◆ isValid()

bool pappso::MassSpectrumId::isValid ( ) const

Definition at line 127 of file massspectrumid.cpp.

128{
129 return mcsp_msRunId->isValid() && m_spectrumIndex != std::numeric_limits<std::size_t>::max();
130}

References m_spectrumIndex, and mcsp_msRunId.

◆ operator=()

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

Definition at line 64 of file massspectrumid.cpp.

65{
66 if(&other == this)
67 return *this;
68
69 mcsp_msRunId = other.mcsp_msRunId;
70 m_spectrumIndex = other.m_spectrumIndex;
71 m_nativeId = other.m_nativeId;
72
73 return *this;
74}

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

◆ operator==()

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

Definition at line 121 of file massspectrumid.cpp.

122{
123 return (mcsp_msRunId == other.mcsp_msRunId && m_spectrumIndex == other.m_spectrumIndex);
124}

References MassSpectrumId(), m_spectrumIndex, and mcsp_msRunId.

◆ setMsRunId()

void pappso::MassSpectrumId::setMsRunId ( MsRunIdCstSPtr other)

Definition at line 78 of file massspectrumid.cpp.

79{
80
81 mcsp_msRunId = other;
82};

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 93 of file massspectrumid.cpp.

94{
95 m_nativeId = native_id;
96}

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::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), 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 107 of file massspectrumid.cpp.

108{
109 m_spectrumIndex = index;
110}

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::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ toString()

QString pappso::MassSpectrumId::toString ( ) const

Definition at line 134 of file massspectrumid.cpp.

135{
136 return QString(
137 "ms run id: %1 \n"
138 "native id: %2 \n"
139 "m_spectrumIndex: %3\n")
140 .arg(mcsp_msRunId != nullptr ? mcsp_msRunId->toString() : "nullptr")
141 .arg(m_nativeId)
142 .arg(m_spectrumIndex);
143}

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().

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