Class representing a fully specified mass spectrum. More...

#include <qualifiedmassspectrum.h>

Public Member Functions
	QualifiedMassSpectrum ()
	Construct an uninitialized QualifiedMassSpectrum.
	QualifiedMassSpectrum (const MassSpectrumId &id)
	Construct a QualifiedMassSpectrum using a MassSpectrumId;.
	QualifiedMassSpectrum (MassSpectrumSPtr mass_spectrum_SPtr)
	QualifiedMassSpectrum (const QualifiedMassSpectrum &other)
	Construct a QualifiedMassSpectrum as a copy of `other`.
	~QualifiedMassSpectrum ()
	Destruct this QualifiedMassSpectrum.
QualifiedMassSpectrum &	operator= (const QualifiedMassSpectrum &other)
const QualifiedMassSpectrum &	cloneMassSpectrumSPtr ()
	clone the mass spectrum contained in Qualified Mass Spectrum
QualifiedMassSpectrumSPtr	makeQualifiedMassSpectrumSPtr () const
QualifiedMassSpectrumCstSPtr	makeQualifiedMassSpectrumCstSPtr () const
void	setMassSpectrumSPtr (MassSpectrumSPtr massSpectrum)
	Set the MassSpectrumSPtr.
MassSpectrumSPtr	getMassSpectrumSPtr () const
	Get the MassSpectrumSPtr.
MassSpectrumCstSPtr	getMassSpectrumCstSPtr () const
	Get the MassSpectrumCstSPtr.
void	setMassSpectrumId (const MassSpectrumId &iD)
	Set the MassSpectrumId.
const MassSpectrumId &	getMassSpectrumId () const
	Get the MassSpectrumId.
MassSpectrumId &	getMassSpectrumId ()
void	setEmptyMassSpectrum (bool is_empty_mass_spectrum)
bool	isEmptyMassSpectrum () const
void	setMsLevel (uint ms_level)
	Set the mass spectrum level.
uint	getMsLevel () const
	Get the mass spectrum level.
void	setRtInSeconds (pappso_double rt)
	Set the retention time in seconds.
pappso_double	getRtInSeconds () const
	Get the retention time in seconds.
pappso_double	getRtInMinutes () const
	Get the retention time in minutes.
void	setDtInMilliSeconds (pappso_double rt)
	Set the drift time in milliseconds.
pappso_double	getDtInMilliSeconds () const
	Get the drift time in milliseconds.
pappso_double	getPrecursorMz (bool *ok=nullptr) const
	get precursor mz
double	getPrecursorMass (bool *ok_p=nullptr) const
	get precursor mass given the charge stats and precursor mz
QString	getPrecursorDataMzValuesAsString (const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const
QString	getPrecursorDataMzValuesAsString (const QString &separator="\n") const
QString	getMzSortedPrecursorDataMzValuesAsString (const QString &separator="\n") const
uint	getPrecursorCharge (bool *ok=nullptr) const
	get precursor charge
QString	getPrecursorDataChargeValuesAsString (const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const
QString	getPrecursorDataChargeValuesAsString (const QString &separator="\n") const
QString	getMzSortedPrecursorDataChargeValuesAsString (const QString &separator="\n") const
pappso_double	getPrecursorIntensity (bool *ok=nullptr) const
	get precursor intensity
void	setPrecursorSpectrumIndex (std::size_t precursor_scan_num)
	Set the scan number of the precursor ion.
std::size_t	getPrecursorSpectrumIndex () const
	Get the scan number of the precursor ion.
void	setPrecursorNativeId (const QString &native_id)
	Set the scan native id of the precursor ion.
const QString &	getPrecursorNativeId () const
void	appendPrecursorIonData (const PrecursorIonData &precursor_ion_data)
const std::vector< PrecursorIonData > &	getPrecursorIonData () const
std::vector< PrecursorIonData >	getPrecursorIonDataSortedWithMz () const
void	setParameterValue (QualifiedMassSpectrumParameter parameter, const QVariant &value)
const QVariant	getParameterValue (QualifiedMassSpectrumParameter parameter) const
std::size_t	size () const
QString	toString (bool with_data=false) const

Protected Attributes
MassSpectrumSPtr	msp_massSpectrum = nullptr
	Shared pointer to the mass spectrum.
MassSpectrumId	m_massSpectrumId
	Id of the mass spectrum.
bool	m_isEmptyMassSpectrum = false
unsigned int	m_msLevel = 0
	Mass spectrometry level of this mass spectrum.
pappso_double	m_rt = -1
	Retention time (in seconds) at which this mass spectrum was acquired.
pappso_double	m_dt = -1
	Drift time (in milliseconds) at which this mass spectrum was acquired.
std::size_t	m_precursorSpectrumIndex
	Index of the spectrum of the precusor ion that was fragmented to yield.
QString	m_precursorNativeId
	Native XML id of the spectrum relative to the mz data native file.
std::vector< PrecursorIonData >	m_precursorIonData
	vector of precursor ion data of the precursors that were fragmented to yield this mass spectrum.
std::map< QualifiedMassSpectrumParameter, QVariant >	m_paramsMap
	map containing any parameter value for this spectrum

Detailed Description

Class representing a fully specified mass spectrum.

The member data that qualify the MassSpectrum msp_massSpectrum member allow to unambiguously characterize the mass spectrum.

See also: MassSpectrum

Definition at line 98 of file qualifiedmassspectrum.h.

Constructor & Destructor Documentation

◆ QualifiedMassSpectrum() [1/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( )

Construct an uninitialized QualifiedMassSpectrum.

Definition at line 39 of file qualifiedmassspectrum.cpp.

40{

41}

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

◆ QualifiedMassSpectrum() [2/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( const MassSpectrumId & id )

Construct a QualifiedMassSpectrum using a MassSpectrumId;.

Definition at line 45 of file qualifiedmassspectrum.cpp.

                                                                     : m_massSpectrumId(id)
{
}

References m_massSpectrumId.

◆ QualifiedMassSpectrum() [3/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( MassSpectrumSPtr mass_spectrum_SPtr )

Definition at line 50 of file qualifiedmassspectrum.cpp.

  : msp_massSpectrum{mass_spectrum_SPtr}
{
}

References msp_massSpectrum.

◆ QualifiedMassSpectrum() [4/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( const QualifiedMassSpectrum & other )

Construct a QualifiedMassSpectrum as a copy of other.

Definition at line 57 of file qualifiedmassspectrum.cpp.

  : msp_massSpectrum(other.msp_massSpectrum),
    m_massSpectrumId(other.m_massSpectrumId),
    m_isEmptyMassSpectrum(other.m_isEmptyMassSpectrum),
    m_msLevel(other.m_msLevel),
    m_rt(other.m_rt),
    m_dt(other.m_dt),
    m_precursorSpectrumIndex(other.m_precursorSpectrumIndex),
    m_precursorNativeId(other.m_precursorNativeId),
    m_precursorIonData(other.m_precursorIonData),
    m_paramsMap(other.m_paramsMap)
{
  // qDebug();
}

References QualifiedMassSpectrum(), m_dt, m_isEmptyMassSpectrum, m_massSpectrumId, m_msLevel, m_paramsMap, m_precursorIonData, m_precursorNativeId, m_precursorSpectrumIndex, m_rt, and msp_massSpectrum.

◆ ~QualifiedMassSpectrum()

pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum ( )

Destruct this QualifiedMassSpectrum.

Definition at line 74 of file qualifiedmassspectrum.cpp.

{
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
}

Member Function Documentation

◆ appendPrecursorIonData()

void pappso::QualifiedMassSpectrum::appendPrecursorIonData ( const PrecursorIonData & precursor_ion_data )

Definition at line 443 of file qualifiedmassspectrum.cpp.

{
  m_precursorIonData.push_back(precursor_ion_data);
}

References m_precursorIonData.

Referenced by pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ cloneMassSpectrumSPtr()

const QualifiedMassSpectrum & pappso::QualifiedMassSpectrum::cloneMassSpectrumSPtr ( )

clone the mass spectrum contained in Qualified Mass Spectrum

Definition at line 99 of file qualifiedmassspectrum.cpp.

{
  this->msp_massSpectrum = std::make_shared<MassSpectrum>(*this->msp_massSpectrum.get());
  return *this;
}

References msp_massSpectrum.

◆ getDtInMilliSeconds()

pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds ( ) const

Get the drift time in milliseconds.

Definition at line 232 of file qualifiedmassspectrum.cpp.

{
  return m_dt;
}

References m_dt.

◆ getMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr ( ) const

Get the MassSpectrumCstSPtr.

Definition at line 138 of file qualifiedmassspectrum.cpp.

{
  return msp_massSpectrum;
}

References msp_massSpectrum.

Referenced by pappso::specglob::PeptideModel::PeptideModel(), pappso::BafAsciiMsRunReader::massSpectrumCstSPtr(), pappso::PwizMsRunReader::massSpectrumCstSPtr(), pappso::XyMsRunReader::massSpectrumCstSPtr(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrumAndPeakList(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getMassSpectrumId() [1/2]

MassSpectrumId & pappso::QualifiedMassSpectrum::getMassSpectrumId ( )

Definition at line 160 of file qualifiedmassspectrum.cpp.

{
  return m_massSpectrumId;
}

References m_massSpectrumId.

◆ getMassSpectrumId() [2/2]

const MassSpectrumId & pappso::QualifiedMassSpectrum::getMassSpectrumId ( ) const

Get the MassSpectrumId.

Definition at line 154 of file qualifiedmassspectrum.cpp.

{
  return m_massSpectrumId;
}

References m_massSpectrumId.

Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum(), pappso::MsRunQualifiedSpectrumLoader::setQualifiedMassSpectrum(), pappso::MsRunReaderRetentionTimeLine::setQualifiedMassSpectrum(), pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MgfOutput::write().

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr ( ) const

Get the MassSpectrumSPtr.

Definition at line 130 of file qualifiedmassspectrum.cpp.

{
  return msp_massSpectrum;
}

References msp_massSpectrum.

Referenced by pappso::TimsMsRunReaderMs2::massSpectrumCstSPtr(), pappso::TimsMsRunReaderMs2Selected::massSpectrumCstSPtr(), pappso::BafAsciiMsRunReader::massSpectrumSPtr(), pappso::PwizMsRunReader::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2Selected::massSpectrumSPtr(), pappso::XyMsRunReader::massSpectrumSPtr(), and pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum().

◆ getMsLevel()

unsigned int pappso::QualifiedMassSpectrum::getMsLevel ( ) const

Get the mass spectrum level.

Definition at line 189 of file qualifiedmassspectrum.cpp.

{
  return m_msLevel;
}

References m_msLevel.

Referenced by pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::XyMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig(), pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum(), pappso::MsRunSimpleStatistics::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getMzSortedPrecursorDataChargeValuesAsString()

QString pappso::QualifiedMassSpectrum::getMzSortedPrecursorDataChargeValuesAsString ( const QString & separator = "\n" ) const

Definition at line 383 of file qualifiedmassspectrum.cpp.

{
  // Sort the PrecursorIonData instances by increasing mz values.
  // Then craft the string using the mz values.
 
  std::vector<PrecursorIonData> sorted_vector = getPrecursorIonDataSortedWithMz();
 
  return getPrecursorDataChargeValuesAsString(sorted_vector, separator);
}

References getPrecursorDataChargeValuesAsString(), and getPrecursorIonDataSortedWithMz().

◆ getMzSortedPrecursorDataMzValuesAsString()

QString pappso::QualifiedMassSpectrum::getMzSortedPrecursorDataMzValuesAsString ( const QString & separator = "\n" ) const

Definition at line 323 of file qualifiedmassspectrum.cpp.

{
  // Sort the PrecursorIonData instances by increasing mz values.
  // Then craft the string using the mz values.
 
  std::vector<PrecursorIonData> sorted_vector = getPrecursorIonDataSortedWithMz();
 
  return getPrecursorDataMzValuesAsString(sorted_vector, separator);
}

References getPrecursorDataMzValuesAsString(), and getPrecursorIonDataSortedWithMz().

Referenced by toString().

◆ getParameterValue()

const QVariant pappso::QualifiedMassSpectrum::getParameterValue ( QualifiedMassSpectrumParameter parameter ) const

Definition at line 487 of file qualifiedmassspectrum.cpp.

{
  auto it = m_paramsMap.find(parameter);
  if(it == m_paramsMap.end())
    {
      return QVariant();
    }
  else
    {
      return it->second;
    }
}

References m_paramsMap.

◆ getPrecursorCharge()

unsigned int pappso::QualifiedMassSpectrum::getPrecursorCharge ( bool * ok = nullptr ) const

get precursor charge

Get the precursor charge.

Parameters

ok	pointer on boolean, false if precursor charge is not defined

Returns: precursor charge

Definition at line 336 of file qualifiedmassspectrum.cpp.

{
  if(!m_precursorIonData.size())
    {
      if(ok_p != nullptr)
        *ok_p = false;
      return std::numeric_limits<unsigned int>::max();
    }
 
  if(ok_p != nullptr)
    *ok_p = true;
 
  return m_precursorIonData.front().charge;
}

References m_precursorIonData.

Referenced by getPrecursorMass(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorDataChargeValuesAsString() [1/2]

QString pappso::QualifiedMassSpectrum::getPrecursorDataChargeValuesAsString ( const QString & separator = "\n" ) const

Definition at line 376 of file qualifiedmassspectrum.cpp.

{
  return getPrecursorDataChargeValuesAsString(m_precursorIonData, separator);
}

References getPrecursorDataChargeValuesAsString(), and m_precursorIonData.

◆ getPrecursorDataChargeValuesAsString() [2/2]

QString pappso::QualifiedMassSpectrum::getPrecursorDataChargeValuesAsString	(	const std::vector< PrecursorIonData > &	precursor_ion_data_vector,
		const QString &	separator = "\n" ) const

Definition at line 353 of file qualifiedmassspectrum.cpp.

{
  QString text;
 
  // We do not want to use the separator if there is only one precursor in the
  // vector.
 
  if(precursor_ion_data_vector.size() == 1)
    return QString("%1").arg(precursor_ion_data_vector.front().charge);
 
  // If there are more than one precursor, then we should list them joined with
  // the separator.
  for(auto item : precursor_ion_data_vector)
    {
      text += QString("%1%2").arg(item.charge).arg(separator);
    }
 
  return text;
}

Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getPrecursorDataChargeValuesAsString().

◆ getPrecursorDataMzValuesAsString() [1/2]

QString pappso::QualifiedMassSpectrum::getPrecursorDataMzValuesAsString ( const QString & separator = "\n" ) const

Definition at line 316 of file qualifiedmassspectrum.cpp.

{
  return getPrecursorDataMzValuesAsString(m_precursorIonData, separator);
}

References getPrecursorDataMzValuesAsString(), and m_precursorIonData.

◆ getPrecursorDataMzValuesAsString() [2/2]

QString pappso::QualifiedMassSpectrum::getPrecursorDataMzValuesAsString	(	const std::vector< PrecursorIonData > &	precursor_ion_data_vector,
		const QString &	separator = "\n" ) const

Definition at line 283 of file qualifiedmassspectrum.cpp.

{
  QString text;
 
  // We do not want to use the separator if there is only one precursor in the
  // vector.
 
  if(precursor_ion_data_vector.size() == 1)
    return QString("%1").arg(precursor_ion_data_vector.front().mz, 0, 'f', 6);
 
  // If there are more than one precursor, then we should list them joined with
  // the separator.
 
  using iterator = std::vector<pappso::PrecursorIonData>::const_iterator;
 
  iterator begin_iterator   = precursor_ion_data_vector.begin();
  iterator pre_end_iterator = std::prev(precursor_ion_data_vector.end());
 
  for(; begin_iterator != precursor_ion_data_vector.end(); ++begin_iterator)
    {
      if(begin_iterator == pre_end_iterator)
        // No separator at the end of the string
        text += QString("%1").arg(begin_iterator->mz, 0, 'f', 6);
      else
        text += QString("%1%2").arg(begin_iterator->mz, 0, 'f', 6).arg(separator);
    }
 
  return text;
}

Referenced by getMzSortedPrecursorDataMzValuesAsString(), and getPrecursorDataMzValuesAsString().

◆ getPrecursorIntensity()

pappso_double pappso::QualifiedMassSpectrum::getPrecursorIntensity ( bool * ok = nullptr ) const

get precursor intensity

Get the intensity of the precursor ion.

Parameters

ok	pointer on boolean, false if precursor intensity is not defined

Returns: precursor intensity

Definition at line 396 of file qualifiedmassspectrum.cpp.

{
  if(!m_precursorIonData.size())
    {
      if(ok_p != nullptr)
        *ok_p = false;
      return std::numeric_limits<double>::max();
    }
 
  if(ok_p != nullptr)
    *ok_p = true;
 
  return m_precursorIonData.front().intensity;
}

References m_precursorIonData.

Referenced by pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorIonData()

const std::vector< PrecursorIonData > & pappso::QualifiedMassSpectrum::getPrecursorIonData ( ) const

Definition at line 450 of file qualifiedmassspectrum.cpp.

{
  return m_precursorIonData;
}

References m_precursorIonData.

Referenced by pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ getPrecursorIonDataSortedWithMz()

std::vector< PrecursorIonData > pappso::QualifiedMassSpectrum::getPrecursorIonDataSortedWithMz ( ) const

Definition at line 457 of file qualifiedmassspectrum.cpp.

{
  std::vector<PrecursorIonData> new_vector;
  new_vector.assign(m_precursorIonData.begin(), m_precursorIonData.end());
 
  std::sort(
    new_vector.begin(),
    new_vector.end(),
    [](const PrecursorIonData &a, const PrecursorIonData &b) -> bool { return a.mz < b.mz; });
 
  return new_vector;
}

References pappso::a, pappso::b, and m_precursorIonData.

Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getMzSortedPrecursorDataMzValuesAsString().

◆ getPrecursorMass()

double pappso::QualifiedMassSpectrum::getPrecursorMass ( bool * ok_p = nullptr ) const

get precursor mass given the charge stats and precursor mz

Get the precursor mass ratio.

Parameters

ok	pointer on boolean, false if precursor mz is not defined

Returns: precursor mass (neutral mass without H+)

Definition at line 260 of file qualifiedmassspectrum.cpp.

{
  if(ok_p != nullptr)
    *ok_p = false;
  bool ok_precmz = false;
  double mz_prec = getPrecursorMz(&ok_precmz);
  if(ok_precmz)
    {
      uint charge = getPrecursorCharge(&ok_precmz);
      if(ok_precmz)
        {
          // compute precursor mass given the charge state
          mz_prec = mz_prec * (double)charge;
          mz_prec -= (MHPLUS * (double)charge);
          if(ok_p != nullptr)
            *ok_p = true;
          return mz_prec;
        }
    }
  return std::numeric_limits<double>::max();
}

References getPrecursorCharge(), getPrecursorMz(), and pappso::MHPLUS().

Referenced by pappso::specglob::PeptideModel::PeptideModel(), and pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum().

◆ getPrecursorMz()

pappso_double pappso::QualifiedMassSpectrum::getPrecursorMz ( bool * ok = nullptr ) const

get precursor mz

Get the precursor m/z ratio.

Parameters

ok	pointer on boolean, false if precursor mz is not defined

Returns: precursor mz

Definition at line 240 of file qualifiedmassspectrum.cpp.

{
  if(!m_precursorIonData.size())
    {
      if(ok_p != nullptr)
        *ok_p = false;
 
      return std::numeric_limits<double>::max();
    }
 
  if(ok_p != nullptr)
    *ok_p = true;
 
  // qDebug() << "Returning precursor mz value: " <<
  // m_precursorIonData.front().mz;
  return m_precursorIonData.front().mz;
}

References m_precursorIonData.

Referenced by getPrecursorMass(), pappso::MzcborMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::PwizMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorNativeId()

const QString & pappso::QualifiedMassSpectrum::getPrecursorNativeId ( ) const

Definition at line 436 of file qualifiedmassspectrum.cpp.

{
  return m_precursorNativeId;
}

References m_precursorNativeId.

Referenced by pappso::MzxmlOutput::getPrecursorScanNumber(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getPrecursorSpectrumIndex()

std::size_t pappso::QualifiedMassSpectrum::getPrecursorSpectrumIndex ( ) const

Get the scan number of the precursor ion.

Definition at line 422 of file qualifiedmassspectrum.cpp.

{
  return m_precursorSpectrumIndex;
}

References m_precursorSpectrumIndex.

Referenced by pappso::MzxmlOutput::getPrecursorScanNumber(), and pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum().

◆ getRtInMinutes()

pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes ( ) const

Get the retention time in minutes.

Definition at line 213 of file qualifiedmassspectrum.cpp.

{
  return m_rt / 60;
}

References m_rt.

Referenced by pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum(), and toString().

◆ getRtInSeconds()

pappso_double pappso::QualifiedMassSpectrum::getRtInSeconds ( ) const

Get the retention time in seconds.

Definition at line 205 of file qualifiedmassspectrum.cpp.

{
  return m_rt;
}

References m_rt.

Referenced by pappso::MzcborMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::PwizMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrum(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig(), pappso::MsRunReaderRetentionTimeLine::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 173 of file qualifiedmassspectrum.cpp.

{
  return m_isEmptyMassSpectrum;
}

References m_isEmptyMassSpectrum.

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

◆ makeQualifiedMassSpectrumCstSPtr()

QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr ( ) const

Definition at line 114 of file qualifiedmassspectrum.cpp.

{
  return std::make_shared<const QualifiedMassSpectrum>(*this);
}

◆ makeQualifiedMassSpectrumSPtr()

QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr ( ) const

Definition at line 107 of file qualifiedmassspectrum.cpp.

{
  return std::make_shared<QualifiedMassSpectrum>(*this);
}

Referenced by pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), and pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr().

◆ operator=()

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

Definition at line 81 of file qualifiedmassspectrum.cpp.

{
  msp_massSpectrum         = other.msp_massSpectrum;
  m_massSpectrumId         = other.m_massSpectrumId;
  m_isEmptyMassSpectrum    = other.m_isEmptyMassSpectrum;
  m_msLevel                = other.m_msLevel;
  m_rt                     = other.m_rt;
  m_dt                     = other.m_dt;
  m_precursorSpectrumIndex = other.m_precursorSpectrumIndex;
  m_precursorNativeId      = other.m_precursorNativeId;
  m_precursorIonData       = other.m_precursorIonData;
  m_paramsMap              = other.m_paramsMap;
 
  return *this;
}

References QualifiedMassSpectrum(), m_dt, m_isEmptyMassSpectrum, m_massSpectrumId, m_msLevel, m_paramsMap, m_precursorIonData, m_precursorNativeId, m_precursorSpectrumIndex, m_rt, and msp_massSpectrum.

◆ setDtInMilliSeconds()

void pappso::QualifiedMassSpectrum::setDtInMilliSeconds ( pappso_double rt )

Set the drift time in milliseconds.

Definition at line 221 of file qualifiedmassspectrum.cpp.

{
  if(std::isinf(dt_in_milli_seconds))
    m_dt = -1;
  else
    m_dt = dt_in_milli_seconds;
}

References m_dt.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::PwizMsRunReader::processDriftTime(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ setEmptyMassSpectrum()

void pappso::QualifiedMassSpectrum::setEmptyMassSpectrum ( bool is_empty_mass_spectrum )

Definition at line 166 of file qualifiedmassspectrum.cpp.

{
  m_isEmptyMassSpectrum = is_empty_mass_spectrum;
}

References m_isEmptyMassSpectrum.

Referenced by pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

◆ setMassSpectrumId()

void pappso::QualifiedMassSpectrum::setMassSpectrumId ( const MassSpectrumId & iD )

Set the MassSpectrumId.

Definition at line 146 of file qualifiedmassspectrum.cpp.

{
  m_massSpectrumId = iD;
}

References m_massSpectrumId.

Referenced by pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ setMassSpectrumSPtr()

void pappso::QualifiedMassSpectrum::setMassSpectrumSPtr ( MassSpectrumSPtr massSpectrum )

Set the MassSpectrumSPtr.

Definition at line 122 of file qualifiedmassspectrum.cpp.

{
  msp_massSpectrum = massSpectrum;
}

References msp_massSpectrum.

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::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().

◆ setMsLevel()

void pappso::QualifiedMassSpectrum::setMsLevel ( uint ms_level )

Set the mass spectrum level.

Definition at line 181 of file qualifiedmassspectrum.cpp.

{
  m_msLevel = level;
}

References m_msLevel.

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::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().

◆ setParameterValue()

void pappso::QualifiedMassSpectrum::setParameterValue	(	QualifiedMassSpectrumParameter	parameter,
		const QVariant &	value )

Definition at line 472 of file qualifiedmassspectrum.cpp.

{
 
  auto ret =
    m_paramsMap.insert(std::pair<QualifiedMassSpectrumParameter, QVariant>(parameter, value));
 
  if(ret.second == false)
    {
      ret.first->second = value;
    }
}

References m_paramsMap.

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

◆ setPrecursorNativeId()

void pappso::QualifiedMassSpectrum::setPrecursorNativeId ( const QString & native_id )

Set the scan native id of the precursor ion.

Definition at line 430 of file qualifiedmassspectrum.cpp.

{
  m_precursorNativeId = native_id;
}

References m_precursorNativeId.

Referenced by pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ setPrecursorSpectrumIndex()

void pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex ( std::size_t precursor_scan_num )

Set the scan number of the precursor ion.

Definition at line 414 of file qualifiedmassspectrum.cpp.

{
  m_precursorSpectrumIndex = precursor_spectrum_index;
}

References m_precursorSpectrumIndex.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum().

◆ setRtInSeconds()

void pappso::QualifiedMassSpectrum::setRtInSeconds ( pappso_double rt )

Set the retention time in seconds.

Definition at line 197 of file qualifiedmassspectrum.cpp.

{
  m_rt = rt_in_seconds;
}

References m_rt.

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::processRetentionTime(), pappso::MzcborMsRunReader::qualifiedMassSpectrum(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().

◆ size()

std::size_t pappso::QualifiedMassSpectrum::size ( ) const

Definition at line 502 of file qualifiedmassspectrum.cpp.

{
  if(msp_massSpectrum == nullptr)
    {
      throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
    }
  return msp_massSpectrum.get()->size();
}

References msp_massSpectrum.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( bool with_data = false ) const

Definition at line 513 of file qualifiedmassspectrum.cpp.

{
  QString text;
 
  if(msp_massSpectrum != nullptr && msp_massSpectrum.get() != nullptr)
    {
      QString pointer_string = QString("msp_massSpectrum.get(): %1 ")
                                   .arg(Utils::pointerToString(
                                       static_cast<void *>(msp_massSpectrum.get())));
 
      text += pointer_string;
    }
  else
    text += QString("msp_massSpectrum is nullptr ");
 
  // qDebug() << text;
 
  QString precursor_mz_values_string;
 
  if(m_precursorIonData.size())
    precursor_mz_values_string += "Precursor mz values: ";
 
  precursor_mz_values_string += getMzSortedPrecursorDataMzValuesAsString();
 
  precursor_mz_values_string += "\n";
 
  text += QString(
            "; m_massSpectrumId : %1 \n"
            "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
            "index: %5 ; %6")
            .arg(m_massSpectrumId.toString())
            .arg(m_msLevel)
            .arg(getRtInMinutes(), 0, 'f', 2)
            .arg(m_dt, 0, 'f', 5)
            .arg(m_precursorSpectrumIndex != std::numeric_limits<std::size_t>::max()
                   ? m_precursorSpectrumIndex
                   : -1)
            .arg(precursor_mz_values_string);
 
  if(with_data)
    {
      text += msp_massSpectrum->toString();
    }
 
  return text;
}

References getMzSortedPrecursorDataMzValuesAsString(), getRtInMinutes(), m_dt, m_massSpectrumId, m_msLevel, m_precursorIonData, m_precursorSpectrumIndex, msp_massSpectrum, and pappso::Utils::pointerToString().

Member Data Documentation

◆ m_dt

pappso_double pappso::QualifiedMassSpectrum::m_dt = -1

protected

Drift time (in milliseconds) at which this mass spectrum was acquired.

Definition at line 212 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), getDtInMilliSeconds(), operator=(), setDtInMilliSeconds(), and toString().

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false

protected

Definition at line 203 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), isEmptyMassSpectrum(), operator=(), and setEmptyMassSpectrum().

◆ m_massSpectrumId

MassSpectrumId pappso::QualifiedMassSpectrum::m_massSpectrumId

protected

Id of the mass spectrum.

Definition at line 201 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), QualifiedMassSpectrum(), getMassSpectrumId(), getMassSpectrumId(), operator=(), setMassSpectrumId(), and toString().

◆ m_msLevel

unsigned int pappso::QualifiedMassSpectrum::m_msLevel = 0

protected

Mass spectrometry level of this mass spectrum.

Definition at line 206 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), getMsLevel(), operator=(), setMsLevel(), and toString().

◆ m_paramsMap

std::map<QualifiedMassSpectrumParameter, QVariant> pappso::QualifiedMassSpectrum::m_paramsMap

protected

map containing any parameter value for this spectrum

Definition at line 227 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), getParameterValue(), operator=(), and setParameterValue().

◆ m_precursorIonData

std::vector<PrecursorIonData> pappso::QualifiedMassSpectrum::m_precursorIonData

protected

vector of precursor ion data of the precursors that were fragmented to yield this mass spectrum.

Definition at line 224 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), appendPrecursorIonData(), getPrecursorCharge(), getPrecursorDataChargeValuesAsString(), getPrecursorDataMzValuesAsString(), getPrecursorIntensity(), getPrecursorIonData(), getPrecursorIonDataSortedWithMz(), getPrecursorMz(), operator=(), and toString().

◆ m_precursorNativeId

QString pappso::QualifiedMassSpectrum::m_precursorNativeId

protected

Native XML id of the spectrum relative to the mz data native file.

Definition at line 220 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), getPrecursorNativeId(), operator=(), and setPrecursorNativeId().

◆ m_precursorSpectrumIndex

std::size_t pappso::QualifiedMassSpectrum::m_precursorSpectrumIndex

protected

Initial value:

=

std::numeric_limits<std::size_t>::max()

Index of the spectrum of the precusor ion that was fragmented to yield.

Definition at line 216 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), getPrecursorSpectrumIndex(), operator=(), setPrecursorSpectrumIndex(), and toString().

◆ m_rt

pappso_double pappso::QualifiedMassSpectrum::m_rt = -1

protected

Retention time (in seconds) at which this mass spectrum was acquired.

Definition at line 209 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), getRtInMinutes(), getRtInSeconds(), operator=(), and setRtInSeconds().

◆ msp_massSpectrum

MassSpectrumSPtr pappso::QualifiedMassSpectrum::msp_massSpectrum = nullptr

protected

Shared pointer to the mass spectrum.

Definition at line 198 of file qualifiedmassspectrum.h.

Referenced by QualifiedMassSpectrum(), QualifiedMassSpectrum(), cloneMassSpectrumSPtr(), getMassSpectrumCstSPtr(), getMassSpectrumSPtr(), operator=(), setMassSpectrumSPtr(), size(), and toString().

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

pappsomspp/core/massspectrum/qualifiedmassspectrum.h
pappsomspp/core/massspectrum/qualifiedmassspectrum.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ QualifiedMassSpectrum() [1/4]

◆ QualifiedMassSpectrum() [2/4]

◆ QualifiedMassSpectrum() [3/4]

◆ QualifiedMassSpectrum() [4/4]

◆ ~QualifiedMassSpectrum()

Member Function Documentation

◆ appendPrecursorIonData()

◆ cloneMassSpectrumSPtr()

◆ getDtInMilliSeconds()

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId() [1/2]

◆ getMassSpectrumId() [2/2]

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getMzSortedPrecursorDataChargeValuesAsString()

◆ getMzSortedPrecursorDataMzValuesAsString()

◆ getParameterValue()

◆ getPrecursorCharge()

◆ getPrecursorDataChargeValuesAsString() [1/2]

◆ getPrecursorDataChargeValuesAsString() [2/2]

◆ getPrecursorDataMzValuesAsString() [1/2]

◆ getPrecursorDataMzValuesAsString() [2/2]

◆ getPrecursorIntensity()

◆ getPrecursorIonData()

◆ getPrecursorIonDataSortedWithMz()

◆ getPrecursorMass()

◆ getPrecursorMz()

◆ getPrecursorNativeId()

◆ getPrecursorSpectrumIndex()

◆ getRtInMinutes()

◆ getRtInSeconds()

◆ isEmptyMassSpectrum()

◆ makeQualifiedMassSpectrumCstSPtr()

◆ makeQualifiedMassSpectrumSPtr()

◆ operator=()

◆ setDtInMilliSeconds()

◆ setEmptyMassSpectrum()

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

◆ setPrecursorNativeId()

◆ setPrecursorSpectrumIndex()

◆ setRtInSeconds()

◆ size()

◆ toString()

Member Data Documentation

◆ m_dt

◆ m_isEmptyMassSpectrum

◆ m_massSpectrumId

◆ m_msLevel

◆ m_paramsMap

◆ m_precursorIonData

◆ m_precursorNativeId

◆ m_precursorSpectrumIndex

◆ m_rt

◆ msp_massSpectrum