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
std::size_t extractScanNumberFromNativeId (bool *is_ok) const
 try to find scan id in the native id string
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 40 of file massspectrumid.h.

Constructor & Destructor Documentation

◆ MassSpectrumId() [1/4]

pappso::MassSpectrumId::MassSpectrumId ( )

Definition at line 33 of file massspectrumid.cpp.

34{
35}

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

◆ MassSpectrumId() [2/4]

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

Definition at line 38 of file massspectrumid.cpp.

38 : mcsp_msRunId(msRunId)
39{
40}
pappso::MassSpectrumId::mcsp_msRunId
MsRunIdCstSPtr mcsp_msRunId
Definition massspectrumid.h:76

References mcsp_msRunId.

◆ MassSpectrumId() [3/4]

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

Definition at line 43 of file massspectrumid.cpp.

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

References m_nativeId, m_spectrumIndex, and mcsp_msRunId.

◆ MassSpectrumId() [4/4]

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

Definition at line 49 of file massspectrumid.cpp.

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

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

◆ ~MassSpectrumId()

pappso::MassSpectrumId::~MassSpectrumId ( )

Definition at line 57 of file massspectrumid.cpp.

58{
59}

Member Function Documentation

◆ extractScanNumberFromNativeId()

std::size_t pappso::MassSpectrumId::extractScanNumberFromNativeId ( bool * is_ok) const

try to find scan id in the native id string

Parameters
is_oktrue if scan number is found
Returns
integer of the scan number

Definition at line 145 of file massspectrumid.cpp.

146{
147 *is_ok = false;
148
149 QRegularExpression regexp_scan("scan=([0-9]+)");
150 QRegularExpressionMatch match = regexp_scan.match(m_nativeId);
151 if(match.hasMatch())
152 {
153 return match.captured(0).toInt(is_ok);
154 }
155 return 0;
156}

References m_nativeId.

Referenced by pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum().

◆ getMsRunIdCstSPtr()

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

Definition at line 85 of file massspectrumid.cpp.

86{
87 return mcsp_msRunId;
88};

References mcsp_msRunId.

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

◆ getNativeId()

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

Definition at line 99 of file massspectrumid.cpp.

100{
101 return m_nativeId;
102}

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 113 of file massspectrumid.cpp.

114{
115 return m_spectrumIndex;
116}

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 126 of file massspectrumid.cpp.

127{
128 return mcsp_msRunId->isValid() && m_spectrumIndex != std::numeric_limits<std::size_t>::max();
129}

References m_spectrumIndex, and mcsp_msRunId.

◆ operator=()

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

Definition at line 63 of file massspectrumid.cpp.

64{
65 if(&other == this)
66 return *this;
67
68 mcsp_msRunId = other.mcsp_msRunId;
69 m_spectrumIndex = other.m_spectrumIndex;
70 m_nativeId = other.m_nativeId;
71
72 return *this;
73}

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

◆ operator==()

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

Definition at line 120 of file massspectrumid.cpp.

121{
122 return (mcsp_msRunId == other.mcsp_msRunId && m_spectrumIndex == other.m_spectrumIndex);
123}

References MassSpectrumId(), m_spectrumIndex, and mcsp_msRunId.

◆ setMsRunId()

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

Definition at line 77 of file massspectrumid.cpp.

78{
79
80 mcsp_msRunId = other;
81};

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 92 of file massspectrumid.cpp.

93{
94 m_nativeId = native_id;
95}

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 106 of file massspectrumid.cpp.

107{
108 m_spectrumIndex = index;
109}

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 133 of file massspectrumid.cpp.

134{
135 return QString(
136 "ms run id: %1 \n"
137 "native id: %2 \n"
138 "m_spectrumIndex: %3\n")
139 .arg(mcsp_msRunId != nullptr ? mcsp_msRunId->toString() : "nullptr")
140 .arg(m_nativeId)
141 .arg(m_spectrumIndex);
142}

References m_nativeId, m_spectrumIndex, and mcsp_msRunId.

Member Data Documentation

◆ m_nativeId

QString pappso::MassSpectrumId::m_nativeId
private

Definition at line 85 of file massspectrumid.h.

Referenced by MassSpectrumId(), MassSpectrumId(), extractScanNumberFromNativeId(), 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 90 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 76 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: