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

#include <qualifiedmassspectrum.h>

Public Member Functions
	QualifiedMassSpectrum ()
	Construct an uninitialized QualifiedMassSpectrum. More...

	QualifiedMassSpectrum (const MassSpectrumId &id)
	Construct a QualifiedMassSpectrum using a MassSpectrumId;. More...

	QualifiedMassSpectrum (MassSpectrumSPtr mass_spectrum_SPtr)

	QualifiedMassSpectrum (const QualifiedMassSpectrum &other)
	Construct a QualifiedMassSpectrum as a copy of `other`. More...

	~QualifiedMassSpectrum ()
	Destruct this QualifiedMassSpectrum. More...

QualifiedMassSpectrum &	operator= (const QualifiedMassSpectrum &other)

QualifiedMassSpectrumSPtr	makeQualifiedMassSpectrumSPtr () const

QualifiedMassSpectrumCstSPtr	makeQualifiedMassSpectrumCstSPtr () const

void	setMassSpectrumId (const MassSpectrumId &iD)
	Set the MassSpectrumId. More...

const MassSpectrumId &	getMassSpectrumId () const
	Get the MassSpectrumId. More...

void	setMassSpectrumSPtr (MassSpectrumSPtr massSpectrum)
	Set the MassSpectrumSPtr. More...

MassSpectrumSPtr	getMassSpectrumSPtr () const
	Get the MassSpectrumSPtr. More...

MassSpectrumCstSPtr	getMassSpectrumCstSPtr () const
	Get the MassSpectrumCstSPtr. More...

const QualifiedMassSpectrum &	cloneMassSpectrumSPtr ()
	clone the mass spectrum contained in Qualified Mass Spectrum More...

void	setEmptyMassSpectrum (bool is_empty_mass_spectrum)

bool	isEmptyMassSpectrum () const

void	setPrecursorCharge (uint precursor_charge)
	Set the precursor charge. More...

uint	getPrecursorCharge () const
	Get the precursor charge. More...

void	setPrecursorMz (pappso_double precursor_mz)
	Set the precursor m/z ratio. More...

pappso_double	getPrecursorMz () const
	Get the precursor m/z ratio. More...

void	setMsLevel (uint ms_level)
	Set the mass spectrum level. More...

uint	getMsLevel () const
	Get the mass spectrum level. More...

void	setPrecursorSpectrumIndex (std::size_t precursor_scan_num)
	Set the scan number of the precursor ion. More...

std::size_t	getPrecursorSpectrumIndex () const
	Get the scan number of the precursor ion. More...

void	setPrecursorNativeId (const QString &native_id)
	Set the scan native id of the precursor ion. More...

const QString &	getPrecursorNativeId () const

void	setRtInSeconds (pappso_double rt)
	Set the retention time in seconds. More...

pappso_double	getRtInSeconds () const
	Get the retention time in seconds. More...

pappso_double	getRtInMinutes () const
	Get the retention time in minutes. More...

void	setDtInMilliSeconds (pappso_double rt)
	Set the drift time in milliseconds. More...

pappso_double	getDtInMilliSeconds () const
	Get the drift time in milliseconds. More...

void	setPrecursorIntensity (pappso_double intensity)
	Set the intensity of the precursor ion. More...

pappso_double	getPrecursorIntensity () const
	Get the intensity of the precursor ion. More...

void	setParameterValue (QualifiedMassSpectrumParameter parameter, const QVariant &value)

const QVariant	getParameterValue (QualifiedMassSpectrumParameter parameter) const

std::size_t	size () const

QString	toString () const

Protected Attributes
MassSpectrumSPtr	msp_massSpectrum = nullptr
	Shared pointer to the mass spectrum. More...

MassSpectrumId	m_massSpectrumId
	Id of the mass spectrum. More...

bool	m_isEmptyMassSpectrum = false

unsigned int	m_msLevel = 0
	Mass spectrometry level of this mass spectrum. More...

pappso_double	m_rt = -1
	Retention time (in seconds) at which this mass spectrum was acquired. More...

pappso_double	m_dt = -1
	Drift time (in milliseconds) at which this mass spectrum was acquired. More...

std::size_t	m_precursorSpectrumIndex
	Index of the spectrum of the precusor ion that was fragmented to yield. More...

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

pappso_double	m_precursorMz = std::numeric_limits<double>::max()

unsigned int	m_precursorCharge = std::numeric_limits<unsigned int>::max()
	Charge of the precursor that was fragmented to yield this mass spectrum. More...

pappso_double	m_precursorIntensity = std::numeric_limits<double>::max()

std::map< QualifiedMassSpectrumParameter, QVariant >	m_paramsMap
	map containing any parameter value for this spectrum More...

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 67 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 }

◆ 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)
 {
 }

◆ QualifiedMassSpectrum() [3/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( MassSpectrumSPtr mass_spectrum_SPtr )

Definition at line 51 of file qualifiedmassspectrum.cpp.

   : msp_massSpectrum{mass_spectrum_SPtr}
 {
 }

◆ QualifiedMassSpectrum() [4/4]

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

Construct a QualifiedMassSpectrum as a copy of other.

Definition at line 59 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_precursorMz(other.m_precursorMz),
     m_precursorCharge(other.m_precursorCharge),
     m_precursorIntensity(other.m_precursorIntensity),
     m_paramsMap(other.m_paramsMap)
 {
   // qDebug();
 }

◆ ~QualifiedMassSpectrum()

pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum ( )

Destruct this QualifiedMassSpectrum.

Definition at line 77 of file qualifiedmassspectrum.cpp.

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

Member Function Documentation

◆ cloneMassSpectrumSPtr()

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

clone the mass spectrum contained in Qualified Mass Spectrum

Definition at line 390 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 257 of file qualifiedmassspectrum.cpp.

 {
   return m_dt;
 }

References m_dt.

◆ getMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr ( ) const

Get the MassSpectrumCstSPtr.

Definition at line 152 of file qualifiedmassspectrum.cpp.

 {
   return msp_massSpectrum;
 }

References msp_massSpectrum.

Referenced by pappso::PwizMsRunReader::massSpectrumCstSPtr(), pappso::XyMsRunReader::massSpectrumCstSPtr(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getMassSpectrumId()

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

Get the MassSpectrumId.

Definition at line 128 of file qualifiedmassspectrum.cpp.

 {
   return m_massSpectrumId;
 }

References m_massSpectrumId.

Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MgfOutput::write().

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr ( ) const

Get the MassSpectrumSPtr.

Definition at line 144 of file qualifiedmassspectrum.cpp.

 {
   return msp_massSpectrum;
 }

References msp_massSpectrum.

Referenced by pappso::TimsMsRunReaderMs2::massSpectrumCstSPtr(), pappso::PwizMsRunReader::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2::massSpectrumSPtr(), and pappso::XyMsRunReader::massSpectrumSPtr().

◆ getMsLevel()

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

Get the mass spectrum level.

Definition at line 214 of file qualifiedmassspectrum.cpp.

 {
   return m_msLevel;
 }

References m_msLevel.

Referenced by pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunSimpleStatistics::setQualifiedMassSpectrum(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getParameterValue()

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

Definition at line 375 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 ( ) const

Get the precursor charge.

Definition at line 182 of file qualifiedmassspectrum.cpp.

 {
   return m_precursorCharge;
 }

References m_precursorCharge.

Referenced by pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorIntensity()

pappso_double pappso::QualifiedMassSpectrum::getPrecursorIntensity ( ) const

Get the intensity of the precursor ion.

Definition at line 301 of file qualifiedmassspectrum.cpp.

 {
   return m_precursorIntensity;
 }

References m_precursorIntensity.

Referenced by pappso::MsRunRetentionTime< T >::addPeptideAsSeamark(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorMz()

pappso_double pappso::QualifiedMassSpectrum::getPrecursorMz ( ) const

Get the precursor m/z ratio.

Definition at line 198 of file qualifiedmassspectrum.cpp.

 {
   return m_precursorMz;
 }

References m_precursorMz.

Referenced by pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorNativeId()

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

Definition at line 286 of file qualifiedmassspectrum.cpp.

 {
   return m_precursorNativeId;
 }

References m_precursorNativeId.

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

◆ getPrecursorSpectrumIndex()

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

Get the scan number of the precursor ion.

Definition at line 273 of file qualifiedmassspectrum.cpp.

 {
   return m_precursorSpectrumIndex;
 }

References m_precursorSpectrumIndex.

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

◆ getRtInMinutes()

pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes ( ) const

Get the retention time in minutes.

Definition at line 238 of file qualifiedmassspectrum.cpp.

 {
   return m_rt / 60;
 }

References m_rt.

Referenced by toString().

◆ getRtInSeconds()

pappso_double pappso::QualifiedMassSpectrum::getRtInSeconds ( ) const

Get the retention time in seconds.

Definition at line 230 of file qualifiedmassspectrum.cpp.

 {
   return m_rt;
 }

References m_rt.

Referenced by pappso::MsRunRetentionTime< T >::addPeptideAsSeamark(), pappso::PwizMsRunReader::qualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 166 of file qualifiedmassspectrum.cpp.

 {
   return m_isEmptyMassSpectrum;
 }

References m_isEmptyMassSpectrum.

◆ makeQualifiedMassSpectrumCstSPtr()

QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr ( ) const

Definition at line 112 of file qualifiedmassspectrum.cpp.

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

◆ makeQualifiedMassSpectrumSPtr()

QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr ( ) const

Definition at line 105 of file qualifiedmassspectrum.cpp.

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

◆ operator=()

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

Definition at line 84 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_precursorMz            = other.m_precursorMz;
   m_precursorCharge        = other.m_precursorCharge;
   m_precursorIntensity     = other.m_precursorIntensity;
  
   m_paramsMap = other.m_paramsMap;
  
   return *this;
 }

References m_dt, m_isEmptyMassSpectrum, m_massSpectrumId, m_msLevel, m_paramsMap, m_precursorCharge, m_precursorIntensity, m_precursorMz, 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 246 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::getQualifiedMassSpectrumByRawIndex(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ setEmptyMassSpectrum()

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

Definition at line 159 of file qualifiedmassspectrum.cpp.

 {
   m_isEmptyMassSpectrum = is_empty_mass_spectrum;
 }

References m_isEmptyMassSpectrum.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::readSpectrumCollection().

◆ setMassSpectrumId()

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

Set the MassSpectrumId.

Definition at line 120 of file qualifiedmassspectrum.cpp.

 {
   m_massSpectrumId = iD;
 }

References m_massSpectrumId.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), and pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum().

◆ setMassSpectrumSPtr()

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

Set the MassSpectrumSPtr.

Definition at line 136 of file qualifiedmassspectrum.cpp.

 {
   msp_massSpectrum = massSpectrum;
 }

References msp_massSpectrum.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().

◆ setMsLevel()

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

Set the mass spectrum level.

Definition at line 206 of file qualifiedmassspectrum.cpp.

 {
   m_msLevel = level;
 }

References m_msLevel.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().

◆ setParameterValue()

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

Definition at line 362 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::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), and pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId().

◆ setPrecursorCharge()

void pappso::QualifiedMassSpectrum::setPrecursorCharge ( uint precursor_charge )

Set the precursor charge.

Definition at line 174 of file qualifiedmassspectrum.cpp.

 {
   m_precursorCharge = precursor_charge;
 }

References m_precursorCharge.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ setPrecursorIntensity()

void pappso::QualifiedMassSpectrum::setPrecursorIntensity ( pappso_double intensity )

Set the intensity of the precursor ion.

Definition at line 293 of file qualifiedmassspectrum.cpp.

 {
   m_precursorIntensity = intensity;
 }

References m_precursorIntensity.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ setPrecursorMz()

void pappso::QualifiedMassSpectrum::setPrecursorMz ( pappso_double precursor_mz )

Set the precursor m/z ratio.

Definition at line 190 of file qualifiedmassspectrum.cpp.

 {
   m_precursorMz = precursor_mz;
 }

References m_precursorMz.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ setPrecursorNativeId()

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

Set the scan native id of the precursor ion.

Definition at line 280 of file qualifiedmassspectrum.cpp.

 {
   m_precursorNativeId = native_id;
 }

References m_precursorNativeId.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ setPrecursorSpectrumIndex()

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

Set the scan number of the precursor ion.

Definition at line 265 of file qualifiedmassspectrum.cpp.

 {
   m_precursorSpectrumIndex = precursor_spectrum_index;
 }

References m_precursorSpectrumIndex.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().

◆ setRtInSeconds()

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

Set the retention time in seconds.

Definition at line 222 of file qualifiedmassspectrum.cpp.

 {
   m_rt = rt_in_seconds;
 }

References m_rt.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().

◆ size()

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

Definition at line 308 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::getQualifiedMassSpectrumByRawIndex(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( ) const

Definition at line 319 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((void *)msp_massSpectrum.get()));
  
       text += pointer_string;
     }
   else
     text += QString("msp_massSpectrum is nullptr ");
  
   // qDebug() << text;
  
   text +=
     QString(
       "; m_massSpectrumId : %1 \n"
       "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
       "index: %5 ; prec. mz: %6 ; prec. z: %7 ; prec. int.: %8")
       .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(m_precursorMz != std::numeric_limits<double>::max() ? m_precursorMz
                                                                : -1)
       .arg(m_precursorCharge != std::numeric_limits<unsigned int>::max()
              ? m_precursorCharge
              : -1)
       .arg(m_precursorIntensity != std::numeric_limits<double>::max()
              ? m_precursorIntensity
              : -1);
  
   return text;
 }

References getRtInMinutes(), m_dt, m_massSpectrumId, m_msLevel, m_precursorCharge, m_precursorIntensity, m_precursorMz, m_precursorSpectrumIndex, msp_massSpectrum, pappso::Utils::pointerToString(), and pappso::MassSpectrumId::toString().

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 146 of file qualifiedmassspectrum.h.

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

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false

protected

Definition at line 137 of file qualifiedmassspectrum.h.

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

◆ m_massSpectrumId

MassSpectrumId pappso::QualifiedMassSpectrum::m_massSpectrumId

protected

Id of the mass spectrum.

Definition at line 135 of file qualifiedmassspectrum.h.

Referenced by 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 140 of file qualifiedmassspectrum.h.

Referenced by 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 168 of file qualifiedmassspectrum.h.

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

◆ m_precursorCharge

unsigned int pappso::QualifiedMassSpectrum::m_precursorCharge = std::numeric_limits<unsigned int>::max()

protected

Charge of the precursor that was fragmented to yield this mass spectrum.

Definition at line 161 of file qualifiedmassspectrum.h.

Referenced by getPrecursorCharge(), operator=(), setPrecursorCharge(), and toString().

◆ m_precursorIntensity

pappso_double pappso::QualifiedMassSpectrum::m_precursorIntensity = std::numeric_limits<double>::max()

protected

Intensity of the precursor that was fragmented to yield this mass spectrum.

Definition at line 165 of file qualifiedmassspectrum.h.

Referenced by getPrecursorIntensity(), operator=(), setPrecursorIntensity(), and toString().

◆ m_precursorMz

pappso_double pappso::QualifiedMassSpectrum::m_precursorMz = std::numeric_limits<double>::max()

protected

m/z ratio of the precursor that was fragmented to yield this mass spectrum.

Definition at line 158 of file qualifiedmassspectrum.h.

Referenced by getPrecursorMz(), operator=(), setPrecursorMz(), 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 154 of file qualifiedmassspectrum.h.

Referenced by 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 150 of file qualifiedmassspectrum.h.

Referenced by 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 143 of file qualifiedmassspectrum.h.

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

◆ msp_massSpectrum

MassSpectrumSPtr pappso::QualifiedMassSpectrum::msp_massSpectrum = nullptr

protected

Shared pointer to the mass spectrum.

Definition at line 132 of file qualifiedmassspectrum.h.

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

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

pappsomspp/massspectrum/qualifiedmassspectrum.h
pappsomspp/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

◆ cloneMassSpectrumSPtr()

◆ getDtInMilliSeconds()

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId()

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getParameterValue()

◆ getPrecursorCharge()

◆ getPrecursorIntensity()

◆ getPrecursorMz()

◆ getPrecursorNativeId()

◆ getPrecursorSpectrumIndex()

◆ getRtInMinutes()

◆ getRtInSeconds()

◆ isEmptyMassSpectrum()

◆ makeQualifiedMassSpectrumCstSPtr()

◆ makeQualifiedMassSpectrumSPtr()

◆ operator=()

◆ setDtInMilliSeconds()

◆ setEmptyMassSpectrum()

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

◆ setPrecursorCharge()

◆ setPrecursorIntensity()

◆ setPrecursorMz()

◆ setPrecursorNativeId()

◆ setPrecursorSpectrumIndex()

◆ setRtInSeconds()

◆ size()

◆ toString()

Member Data Documentation

◆ m_dt

◆ m_isEmptyMassSpectrum

◆ m_massSpectrumId

◆ m_msLevel

◆ m_paramsMap

◆ m_precursorCharge

◆ m_precursorIntensity

◆ m_precursorMz

◆ m_precursorNativeId

◆ m_precursorSpectrumIndex

◆ m_rt

◆ msp_massSpectrum