libpappsomspp
Library for mass spectrometry
pappso::QualifiedMassSpectrum Class Reference

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...
 
QualifiedMassSpectrumoperator= (const QualifiedMassSpectrum &other)
 
QualifiedMassSpectrumSPtr makeQualifiedMassSpectrumSPtr () const
 
QualifiedMassSpectrumCstSPtr makeQualifiedMassSpectrumCstSPtr () const
 
void setMassSpectrumId (const MassSpectrumId &iD)
 Set the MassSpectrumId. More...
 
const MassSpectrumIdgetMassSpectrumId () 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...
 
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 85 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.

72 {

◆ QualifiedMassSpectrum() [3/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( MassSpectrumSPtr  mass_spectrum_SPtr)

Definition at line 69 of file qualifiedmassspectrum.cpp.

72 {
73  // 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.

78 {
79  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
80 }
81 
82 
85 {
86  msp_massSpectrum = other.msp_massSpectrum;
87  m_massSpectrumId = other.m_massSpectrumId;
88  m_isEmptyMassSpectrum = other.m_isEmptyMassSpectrum;
89  m_msLevel = other.m_msLevel;
90  m_rt = other.m_rt;
91  m_dt = other.m_dt;
92  m_precursorSpectrumIndex = other.m_precursorSpectrumIndex;

◆ ~QualifiedMassSpectrum()

pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum ( )

Destruct this QualifiedMassSpectrum.

Definition at line 95 of file qualifiedmassspectrum.cpp.

Member Function Documentation

◆ getDtInMilliSeconds()

pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds ( ) const

Get the drift time in milliseconds.

Definition at line 275 of file qualifiedmassspectrum.cpp.

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId()

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr ( ) const

◆ getMsLevel()

◆ getParameterValue()

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

Definition at line 393 of file qualifiedmassspectrum.cpp.

◆ getPrecursorCharge()

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

◆ getPrecursorIntensity()

pappso_double pappso::QualifiedMassSpectrum::getPrecursorIntensity ( ) const

Get the intensity of the precursor ion.

Definition at line 319 of file qualifiedmassspectrum.cpp.

320 {
321  QString text;
322 

References msp_massSpectrum.

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 216 of file qualifiedmassspectrum.cpp.

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

◆ getPrecursorNativeId()

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

◆ getPrecursorSpectrumIndex()

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

Get the scan number of the precursor ion.

Definition at line 291 of file qualifiedmassspectrum.cpp.

294 {

References m_precursorIntensity.

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

◆ getRtInMinutes()

pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes ( ) const

Get the retention time in minutes.

Definition at line 256 of file qualifiedmassspectrum.cpp.

258 {
259  return m_dt;

References m_dt.

◆ getRtInSeconds()

pappso_double pappso::QualifiedMassSpectrum::getRtInSeconds ( ) const

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 184 of file qualifiedmassspectrum.cpp.

◆ makeQualifiedMassSpectrumCstSPtr()

QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr ( ) const

Definition at line 130 of file qualifiedmassspectrum.cpp.

◆ makeQualifiedMassSpectrumSPtr()

QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr ( ) const

Definition at line 123 of file qualifiedmassspectrum.cpp.

◆ operator=()

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

Definition at line 102 of file qualifiedmassspectrum.cpp.

106 {
107  return std::make_shared<QualifiedMassSpectrum>(*this);
108 }
109 
110 
113 {
114  return std::make_shared<const QualifiedMassSpectrum>(*this);
115 }
116 
117 
118 //! Set the MassSpectrumId.
119 void

◆ setDtInMilliSeconds()

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

Set the drift time in milliseconds.

Definition at line 264 of file qualifiedmassspectrum.cpp.

267 {
268  m_precursorSpectrumIndex = precursor_spectrum_index;
269 }
270 

References m_precursorSpectrumIndex.

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

◆ setEmptyMassSpectrum()

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

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

Definition at line 380 of file qualifiedmassspectrum.cpp.

380  {
381  return QVariant();
382  }
383  else
384  {
385  return it->second;
386  }
387 }
388 
389 } // namespace pappso

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

◆ setPrecursorCharge()

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

◆ setPrecursorIntensity()

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

Set the intensity of the precursor ion.

Definition at line 311 of file qualifiedmassspectrum.cpp.

311  {
312  throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
313  }
314  return msp_massSpectrum.get()->size();

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

◆ setPrecursorMz()

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

◆ setPrecursorNativeId()

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

Set the scan native id of the precursor ion.

Definition at line 298 of file qualifiedmassspectrum.cpp.

302 {

References m_precursorIntensity.

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

◆ setPrecursorSpectrumIndex()

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

◆ setRtInSeconds()

◆ size()

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

Definition at line 326 of file qualifiedmassspectrum.cpp.

326  : %1 ")
327  .arg(Utils::pointerToString((void *)msp_massSpectrum.get()));
328 
329  text += pointer_string;
330  }
331  else
332  text += QString("msp_massSpectrum is nullptr ");
333 

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

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( ) const

Definition at line 337 of file qualifiedmassspectrum.cpp.

338  : %1 \n"
339  "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
340  "index: %5 ; prec. mz: %6 ; prec. z: %7 ; prec. int.: %8")
341  .arg(m_massSpectrumId.toString())
342  .arg(m_msLevel)
343  .arg(getRtInMinutes(), 0, 'f', 2)
344  .arg(m_dt, 0, 'f', 5)
345  .arg(m_precursorSpectrumIndex != std::numeric_limits<std::size_t>::max()
346  ? m_precursorSpectrumIndex
347  : -1)
348  .arg(m_precursorMz != std::numeric_limits<double>::max() ? m_precursorMz
349  : -1)
350  .arg(m_precursorCharge != std::numeric_limits<unsigned int>::max()
351  ? m_precursorCharge
352  : -1)
353  .arg(m_precursorIntensity != std::numeric_limits<double>::max()
354  ? m_precursorIntensity
355  : -1);
356 
357  return text;
358 }
359 
360 
361 void
362 QualifiedMassSpectrum::setParameterValue(
363  QualifiedMassSpectrumParameter parameter, const QVariant &value)
364 {
365 
366  auto ret = m_paramsMap.insert(
367  std::pair<QualifiedMassSpectrumParameter, QVariant>(parameter, value));
368 
369  if(ret.second == false)
370  {
371  ret.first->second = value;
372  }
373 }
374 const QVariant
375 QualifiedMassSpectrum::getParameterValue(
376  QualifiedMassSpectrumParameter parameter) const

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 160 of file qualifiedmassspectrum.h.

Referenced by getRtInMinutes().

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false
protected

Definition at line 151 of file qualifiedmassspectrum.h.

◆ m_massSpectrumId

MassSpectrumId pappso::QualifiedMassSpectrum::m_massSpectrumId
protected

Id of the mass spectrum.

Definition at line 149 of file qualifiedmassspectrum.h.

◆ m_msLevel

unsigned int pappso::QualifiedMassSpectrum::m_msLevel = 0
protected

Mass spectrometry level of this mass spectrum.

Definition at line 154 of file qualifiedmassspectrum.h.

◆ m_paramsMap

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

map containing any parameter value for this spectrum

Definition at line 182 of file qualifiedmassspectrum.h.

◆ 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 175 of file qualifiedmassspectrum.h.

Referenced by getMassSpectrumCstSPtr().

◆ 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 179 of file qualifiedmassspectrum.h.

Referenced by getPrecursorSpectrumIndex(), and setPrecursorNativeId().

◆ 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 172 of file qualifiedmassspectrum.h.

◆ m_precursorNativeId

QString pappso::QualifiedMassSpectrum::m_precursorNativeId
protected

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

Definition at line 168 of file qualifiedmassspectrum.h.

◆ 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 164 of file qualifiedmassspectrum.h.

Referenced by setDtInMilliSeconds().

◆ m_rt

pappso_double pappso::QualifiedMassSpectrum::m_rt = -1
protected

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

Definition at line 157 of file qualifiedmassspectrum.h.

◆ msp_massSpectrum

MassSpectrumSPtr pappso::QualifiedMassSpectrum::msp_massSpectrum = nullptr
protected

Shared pointer to the mass spectrum.

Definition at line 146 of file qualifiedmassspectrum.h.

Referenced by getPrecursorIntensity().


The documentation for this class was generated from the following files:
pappso::QualifiedMassSpectrum::m_dt
pappso_double m_dt
Drift time (in milliseconds) at which this mass spectrum was acquired.
Definition: qualifiedmassspectrum.h:160
pappso::QualifiedMassSpectrum::operator=
QualifiedMassSpectrum & operator=(const QualifiedMassSpectrum &other)
Definition: qualifiedmassspectrum.cpp:102
pappso::QualifiedMassSpectrum::m_rt
pappso_double m_rt
Retention time (in seconds) at which this mass spectrum was acquired.
Definition: qualifiedmassspectrum.h:157
pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr
QualifiedMassSpectrumCstSPtr makeQualifiedMassSpectrumCstSPtr() const
Definition: qualifiedmassspectrum.cpp:130
pappso::QualifiedMassSpectrum::msp_massSpectrum
MassSpectrumSPtr msp_massSpectrum
Shared pointer to the mass spectrum.
Definition: qualifiedmassspectrum.h:146
pappso::QualifiedMassSpectrum::m_massSpectrumId
MassSpectrumId m_massSpectrumId
Id of the mass spectrum.
Definition: qualifiedmassspectrum.h:149
pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum
bool m_isEmptyMassSpectrum
Definition: qualifiedmassspectrum.h:151
pappso::QualifiedMassSpectrum::m_precursorSpectrumIndex
std::size_t m_precursorSpectrumIndex
Index of the spectrum of the precusor ion that was fragmented to yield.
Definition: qualifiedmassspectrum.h:164
pappso::QualifiedMassSpectrum::QualifiedMassSpectrum
QualifiedMassSpectrum()
Construct an uninitialized QualifiedMassSpectrum.
Definition: qualifiedmassspectrum.cpp:57
pappso::QualifiedMassSpectrumCstSPtr
std::shared_ptr< const QualifiedMassSpectrum > QualifiedMassSpectrumCstSPtr
Definition: qualifiedmassspectrum.h:63
pappso::QualifiedMassSpectrum::m_msLevel
unsigned int m_msLevel
Mass spectrometry level of this mass spectrum.
Definition: qualifiedmassspectrum.h:154
pappso::PeptideIonCter::z
@ z
pappso::PrecisionUnit::mz
@ mz
pappso::PappsoException
Definition: pappsoexception.h:62