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...
 
const QualifiedMassSpectrumcloneMassSpectrumSPtr ()
 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.

46  : m_massSpectrumId(id)
47 {
48 }

◆ QualifiedMassSpectrum() [3/4]

pappso::QualifiedMassSpectrum::QualifiedMassSpectrum ( MassSpectrumSPtr  mass_spectrum_SPtr)

Definition at line 51 of file qualifiedmassspectrum.cpp.

53  : msp_massSpectrum{mass_spectrum_SPtr}
54 {
55 }

◆ 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.

60  : msp_massSpectrum(other.msp_massSpectrum),
61  m_massSpectrumId(other.m_massSpectrumId),
62  m_isEmptyMassSpectrum(other.m_isEmptyMassSpectrum),
63  m_msLevel(other.m_msLevel),
64  m_rt(other.m_rt),
65  m_dt(other.m_dt),
66  m_precursorSpectrumIndex(other.m_precursorSpectrumIndex),
67  m_precursorNativeId(other.m_precursorNativeId),
68  m_precursorMz(other.m_precursorMz),
69  m_precursorCharge(other.m_precursorCharge),
70  m_precursorIntensity(other.m_precursorIntensity),
71  m_paramsMap(other.m_paramsMap)
72 {
73  // qDebug();
74 }

◆ ~QualifiedMassSpectrum()

pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum ( )

Destruct this QualifiedMassSpectrum.

Definition at line 77 of file qualifiedmassspectrum.cpp.

78 {
79  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
80 }

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.

391 {
392  this->msp_massSpectrum =
393  std::make_shared<MassSpectrum>(*this->msp_massSpectrum.get());
394  return *this;
395 }

References msp_massSpectrum.

◆ getDtInMilliSeconds()

pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds ( ) const

Get the drift time in milliseconds.

Definition at line 257 of file qualifiedmassspectrum.cpp.

258 {
259  return m_dt;
260 }

References m_dt.

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId()

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr ( ) const

◆ getMsLevel()

◆ getParameterValue()

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

Definition at line 375 of file qualifiedmassspectrum.cpp.

377 {
378  auto it = m_paramsMap.find(parameter);
379  if(it == m_paramsMap.end())
380  {
381  return QVariant();
382  }
383  else
384  {
385  return it->second;
386  }
387 }

References m_paramsMap.

◆ getPrecursorCharge()

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

◆ getPrecursorIntensity()

pappso_double pappso::QualifiedMassSpectrum::getPrecursorIntensity ( ) const

Get the intensity of the precursor ion.

Definition at line 301 of file qualifiedmassspectrum.cpp.

302 {
303  return m_precursorIntensity;
304 }

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.

199 {
200  return m_precursorMz;
201 }

References m_precursorMz.

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 273 of file qualifiedmassspectrum.cpp.

274 {
276 }

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.

239 {
240  return m_rt / 60;
241 }

References m_rt.

Referenced by toString().

◆ getRtInSeconds()

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 166 of file qualifiedmassspectrum.cpp.

167 {
168  return m_isEmptyMassSpectrum;
169 }

References m_isEmptyMassSpectrum.

◆ makeQualifiedMassSpectrumCstSPtr()

QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr ( ) const

Definition at line 112 of file qualifiedmassspectrum.cpp.

113 {
114  return std::make_shared<const QualifiedMassSpectrum>(*this);
115 }

◆ makeQualifiedMassSpectrumSPtr()

QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr ( ) const

Definition at line 105 of file qualifiedmassspectrum.cpp.

106 {
107  return std::make_shared<QualifiedMassSpectrum>(*this);
108 }

◆ operator=()

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

Definition at line 84 of file qualifiedmassspectrum.cpp.

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;
93  m_precursorNativeId = other.m_precursorNativeId;
94  m_precursorMz = other.m_precursorMz;
95  m_precursorCharge = other.m_precursorCharge;
96  m_precursorIntensity = other.m_precursorIntensity;
97 
98  m_paramsMap = other.m_paramsMap;
99 
100  return *this;
101 }

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.

247 {
248  if(std::isinf(dt_in_milli_seconds))
249  m_dt = -1;
250  else
251  m_dt = dt_in_milli_seconds;
252 }

References m_dt.

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

◆ setEmptyMassSpectrum()

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

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

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

Definition at line 362 of file qualifiedmassspectrum.cpp.

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 }

References m_paramsMap.

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)

◆ setPrecursorMz()

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

◆ setPrecursorNativeId()

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

◆ setPrecursorSpectrumIndex()

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

◆ setRtInSeconds()

◆ size()

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

Definition at line 308 of file qualifiedmassspectrum.cpp.

309 {
310  if(msp_massSpectrum == nullptr)
311  {
312  throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
313  }
314  return msp_massSpectrum.get()->size();
315 }

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.

320 {
321  QString text;
322 
323  if(msp_massSpectrum != nullptr && msp_massSpectrum.get() != nullptr)
324  {
325  QString pointer_string =
326  QString("msp_massSpectrum.get(): %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 
334  // qDebug() << text;
335 
336  text +=
337  QString(
338  "; m_massSpectrumId : %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()
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()
352  : -1)
353  .arg(m_precursorIntensity != std::numeric_limits<double>::max()
355  : -1);
356 
357  return text;
358 }

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:
pappso::QualifiedMassSpectrum::m_precursorCharge
unsigned int m_precursorCharge
Charge of the precursor that was fragmented to yield this mass spectrum.
Definition: qualifiedmassspectrum.h:161
pappso::QualifiedMassSpectrum::m_dt
pappso_double m_dt
Drift time (in milliseconds) at which this mass spectrum was acquired.
Definition: qualifiedmassspectrum.h:146
pappso::QualifiedMassSpectrum::m_paramsMap
std::map< QualifiedMassSpectrumParameter, QVariant > m_paramsMap
map containing any parameter value for this spectrum
Definition: qualifiedmassspectrum.h:168
pappso::QualifiedMassSpectrum::m_rt
pappso_double m_rt
Retention time (in seconds) at which this mass spectrum was acquired.
Definition: qualifiedmassspectrum.h:143
pappso::QualifiedMassSpectrum::m_precursorMz
pappso_double m_precursorMz
Definition: qualifiedmassspectrum.h:158
pappso::QualifiedMassSpectrum::msp_massSpectrum
MassSpectrumSPtr msp_massSpectrum
Shared pointer to the mass spectrum.
Definition: qualifiedmassspectrum.h:132
pappso::QualifiedMassSpectrum::getRtInMinutes
pappso_double getRtInMinutes() const
Get the retention time in minutes.
Definition: qualifiedmassspectrum.cpp:238
pappso::QualifiedMassSpectrum::m_massSpectrumId
MassSpectrumId m_massSpectrumId
Id of the mass spectrum.
Definition: qualifiedmassspectrum.h:135
pappso::Utils::pointerToString
static QString pointerToString(const void *const pointer)
Definition: utils.cpp:223
pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum
bool m_isEmptyMassSpectrum
Definition: qualifiedmassspectrum.h:137
pappso::MassSpectrumId::toString
QString toString() const
Definition: massspectrumid.cpp:132
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:150
pappso::QualifiedMassSpectrum::m_precursorNativeId
QString m_precursorNativeId
Native XML id of the spectrum relative to the mz data native file.
Definition: qualifiedmassspectrum.h:154
pappso::QualifiedMassSpectrum::m_msLevel
unsigned int m_msLevel
Mass spectrometry level of this mass spectrum.
Definition: qualifiedmassspectrum.h:140
pappso::QualifiedMassSpectrum::m_precursorIntensity
pappso_double m_precursorIntensity
Definition: qualifiedmassspectrum.h:165
pappso::PappsoException
Definition: pappsoexception.h:42