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)

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

QualifiedMassSpectrumSPtr	makeQualifiedMassSpectrumSPtr () const

QualifiedMassSpectrumCstSPtr	makeQualifiedMassSpectrumCstSPtr () const

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

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

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

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

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

void	setEmptyMassSpectrum (bool is_empty_mass_spectrum)

bool	isEmptyMassSpectrum () const

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

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

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...

pappso_double	getPrecursorMz (bool *ok=nullptr) const
	Get the precursor m/z ratio. More...

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 the precursor charge. More...

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 the intensity of the precursor ion. 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	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 () 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...

std::vector< PrecursorIonData >	m_precursorIonData

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 102 of file qualifiedmassspectrum.h.

Constructor & Destructor Documentation

◆ QualifiedMassSpectrum() [1/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( )

Construct an uninitialized QualifiedMassSpectrum.

Definition at line 57 of file qualifiedmassspectrum.cpp.

60 : msp_massSpectrum(other.msp_massSpectrum),

◆ QualifiedMassSpectrum() [2/4]

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

Construct a QualifiedMassSpectrum using a MassSpectrumId;.

Definition at line 63 of file qualifiedmassspectrum.cpp.

70 {

◆ QualifiedMassSpectrum() [3/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( MassSpectrumSPtr mass_spectrum_SPtr )

Definition at line 69 of file qualifiedmassspectrum.cpp.

 {
   // qDebug();
 }
  

◆ QualifiedMassSpectrum() [4/4]

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

Construct a QualifiedMassSpectrum as a copy of other.

Definition at line 77 of file qualifiedmassspectrum.cpp.

 {
   // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
 }
  
  
 QualifiedMassSpectrum &
 QualifiedMassSpectrum::operator=(const QualifiedMassSpectrum &other)
 {
   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;

◆ ~QualifiedMassSpectrum()

pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum ( )

Destruct this QualifiedMassSpectrum.

Definition at line 94 of file qualifiedmassspectrum.cpp.

Member Function Documentation

◆ appendPrecursorIonData()

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

Definition at line 448 of file qualifiedmassspectrum.cpp.

452 {

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

◆ cloneMassSpectrumSPtr()

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

clone the mass spectrum contained in Qualified Mass Spectrum

Definition at line 119 of file qualifiedmassspectrum.cpp.

◆ getDtInMilliSeconds()

pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds ( ) const

Get the drift time in milliseconds.

Definition at line 248 of file qualifiedmassspectrum.cpp.

◆ getMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr ( ) const

Get the MassSpectrumCstSPtr.

Definition at line 159 of file qualifiedmassspectrum.cpp.

Referenced by pappso::PwizMsRunReader::accept(), 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 175 of file qualifiedmassspectrum.cpp.

References m_msLevel.

Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum(), and pappso::MgfOutput::write().

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr ( ) const

Get the MassSpectrumSPtr.

Definition at line 151 of file qualifiedmassspectrum.cpp.

Referenced by pappso::TimsMsRunReaderMs2::massSpectrumCstSPtr(), pappso::TimsMsRunReaderMs2Selected::massSpectrumCstSPtr(), pappso::XyMsRunReader::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2::massSpectrumSPtr(), and pappso::TimsMsRunReaderMs2Selected::massSpectrumSPtr().

◆ getMsLevel()

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

Get the mass spectrum level.

Definition at line 205 of file qualifiedmassspectrum.cpp.

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

◆ getMzSortedPrecursorDataChargeValuesAsString()

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

Definition at line 384 of file qualifiedmassspectrum.cpp.

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

◆ getMzSortedPrecursorDataMzValuesAsString()

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

Definition at line 319 of file qualifiedmassspectrum.cpp.

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

◆ getParameterValue()

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

Definition at line 494 of file qualifiedmassspectrum.cpp.

     {
       throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
     }
   return msp_massSpectrum.get()->size();
 }
  
  
 QString
 QualifiedMassSpectrum::toString() const
 {
   QString text;
  

◆ getPrecursorCharge()

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

Get the precursor charge.

Definition at line 334 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)

Referenced by 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.

◆ getPrecursorDataChargeValuesAsString() [2/2]

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

Definition at line 352 of file qualifiedmassspectrum.cpp.

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

◆ getPrecursorDataMzValuesAsString() [1/2]

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

Definition at line 311 of file qualifiedmassspectrum.cpp.

◆ getPrecursorDataMzValuesAsString() [2/2]

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

Definition at line 276 of file qualifiedmassspectrum.cpp.

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

◆ getPrecursorIntensity()

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

Get the intensity of the precursor ion.

Definition at line 399 of file qualifiedmassspectrum.cpp.

 {
   m_precursorSpectrumIndex = precursor_spectrum_index;
 }
  
  
 //! Get the scan number of the precursor ion.
 std::size_t
 QualifiedMassSpectrum::getPrecursorSpectrumIndex() const
 {
   return m_precursorSpectrumIndex;
 }
  

References m_precursorSpectrumIndex.

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

◆ getPrecursorIonData()

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

Definition at line 456 of file qualifiedmassspectrum.cpp.

◆ getPrecursorIonDataSortedWithMz()

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

Definition at line 463 of file qualifiedmassspectrum.cpp.

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

References m_paramsMap.

◆ getPrecursorMz()

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

Get the precursor m/z ratio.

Definition at line 256 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.
  

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

◆ getPrecursorNativeId()

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

Definition at line 441 of file qualifiedmassspectrum.cpp.

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

◆ getPrecursorSpectrumIndex()

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

Get the scan number of the precursor ion.

Definition at line 427 of file qualifiedmassspectrum.cpp.

432 {

References m_precursorIonData.

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

◆ getRtInMinutes()

pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes ( ) const

Get the retention time in minutes.

Definition at line 229 of file qualifiedmassspectrum.cpp.

231 {

232 return m_dt;

References m_dt.

◆ getRtInSeconds()

pappso_double pappso::QualifiedMassSpectrum::getRtInSeconds ( ) const

Get the retention time in seconds.

Definition at line 221 of file qualifiedmassspectrum.cpp.

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

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 189 of file qualifiedmassspectrum.cpp.

◆ makeQualifiedMassSpectrumCstSPtr()

QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr ( ) const

Definition at line 135 of file qualifiedmassspectrum.cpp.

◆ makeQualifiedMassSpectrumSPtr()

QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr ( ) const

Definition at line 128 of file qualifiedmassspectrum.cpp.

◆ operator=()

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

Definition at line 101 of file qualifiedmassspectrum.cpp.

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

References msp_massSpectrum.

◆ setDtInMilliSeconds()

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

Set the drift time in milliseconds.

Definition at line 237 of file qualifiedmassspectrum.cpp.

 {
   if(!m_precursorIonData.size())
     {
       if(ok_p != nullptr)
         *ok_p = false;

References m_precursorIonData.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex().

◆ setEmptyMassSpectrum()

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

Definition at line 182 of file qualifiedmassspectrum.cpp.

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

◆ setMassSpectrumId()

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

Set the MassSpectrumId.

Definition at line 167 of file qualifiedmassspectrum.cpp.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), and pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().

◆ setMassSpectrumSPtr()

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

Set the MassSpectrumSPtr.

Definition at line 143 of file qualifiedmassspectrum.cpp.

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

◆ setMsLevel()

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

Set the mass spectrum level.

Definition at line 197 of file qualifiedmassspectrum.cpp.

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

◆ setParameterValue()

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

Definition at line 479 of file qualifiedmassspectrum.cpp.

     {
       return QVariant();
     }
   else
     {
       return it->second;
     }
 }
  
  

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

◆ setPrecursorNativeId()

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

Set the scan native id of the precursor ion.

Definition at line 435 of file qualifiedmassspectrum.cpp.

439 {

References m_precursorIonData.

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

◆ setPrecursorSpectrumIndex()

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

Set the scan number of the precursor ion.

Definition at line 418 of file qualifiedmassspectrum.cpp.

 {
   m_precursorNativeId = native_id;
 }
  
 const QString &

References m_precursorNativeId.

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

◆ setRtInSeconds()

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

Set the retention time in seconds.

Definition at line 213 of file qualifiedmassspectrum.cpp.

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

◆ size()

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

Definition at line 510 of file qualifiedmassspectrum.cpp.

                                        : %1 ")
           .arg(Utils::pointerToString((void *)msp_massSpectrum.get()));
  
       text += pointer_string;
     }
   else
     text += QString("msp_massSpectrum is nullptr ");
  

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( ) const

Definition at line 521 of file qualifiedmassspectrum.cpp.

                                                       : ";
  
   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);
  
   return text;
 }
  
  
 } // namespace pappso

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 195 of file qualifiedmassspectrum.h.

Referenced by getRtInMinutes().

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false

protected

Definition at line 186 of file qualifiedmassspectrum.h.

◆ m_massSpectrumId

MassSpectrumId pappso::QualifiedMassSpectrum::m_massSpectrumId

protected

Id of the mass spectrum.

Definition at line 184 of file qualifiedmassspectrum.h.

◆ m_msLevel

unsigned int pappso::QualifiedMassSpectrum::m_msLevel = 0

protected

Mass spectrometry level of this mass spectrum.

Definition at line 189 of file qualifiedmassspectrum.h.

Referenced by getMassSpectrumId().

◆ m_paramsMap

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

protected

map containing any parameter value for this spectrum

Definition at line 211 of file qualifiedmassspectrum.h.

Referenced by getPrecursorIonDataSortedWithMz().

◆ 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 208 of file qualifiedmassspectrum.h.

Referenced by getPrecursorSpectrumIndex(), setDtInMilliSeconds(), and setPrecursorNativeId().

◆ m_precursorNativeId

QString pappso::QualifiedMassSpectrum::m_precursorNativeId

protected

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

Definition at line 203 of file qualifiedmassspectrum.h.

Referenced by setPrecursorSpectrumIndex().

◆ 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 199 of file qualifiedmassspectrum.h.

Referenced by getPrecursorIntensity().

◆ m_rt

pappso_double pappso::QualifiedMassSpectrum::m_rt = -1

protected

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

Definition at line 192 of file qualifiedmassspectrum.h.

◆ msp_massSpectrum

MassSpectrumSPtr pappso::QualifiedMassSpectrum::msp_massSpectrum = nullptr

protected

Shared pointer to the mass spectrum.

Definition at line 181 of file qualifiedmassspectrum.h.

Referenced by operator=().

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

◆ appendPrecursorIonData()

◆ cloneMassSpectrumSPtr()

◆ getDtInMilliSeconds()

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId()

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getMzSortedPrecursorDataChargeValuesAsString()

◆ getMzSortedPrecursorDataMzValuesAsString()

◆ getParameterValue()

◆ getPrecursorCharge()

◆ getPrecursorDataChargeValuesAsString() [1/2]

◆ getPrecursorDataChargeValuesAsString() [2/2]

◆ getPrecursorDataMzValuesAsString() [1/2]

◆ getPrecursorDataMzValuesAsString() [2/2]

◆ getPrecursorIntensity()

◆ getPrecursorIonData()

◆ getPrecursorIonDataSortedWithMz()

◆ 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