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)
 
const QualifiedMassSpectrumcloneMassSpectrumSPtr ()
 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 MassSpectrumIdgetMassSpectrumId () 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< PrecursorIonDatagetPrecursorIonDataSortedWithMz () 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< PrecursorIonDatam_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 84 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 }
MassSpectrumId m_massSpectrumId
Id of the mass spectrum.

◆ 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 }
MassSpectrumSPtr msp_massSpectrum
Shared pointer to the mass spectrum.

◆ 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_precursorIonData(other.m_precursorIonData),
69  m_paramsMap(other.m_paramsMap)
70 {
71  // qDebug();
72 }
std::vector< PrecursorIonData > m_precursorIonData
std::size_t m_precursorSpectrumIndex
Index of the spectrum of the precusor ion that was fragmented to yield.
unsigned int m_msLevel
Mass spectrometry level of this mass spectrum.
pappso_double m_rt
Retention time (in seconds) at which this mass spectrum was acquired.
pappso_double m_dt
Drift time (in milliseconds) at which this mass spectrum was acquired.
std::map< QualifiedMassSpectrumParameter, QVariant > m_paramsMap
map containing any parameter value for this spectrum
QString m_precursorNativeId
Native XML id of the spectrum relative to the mz data native file.

◆ ~QualifiedMassSpectrum()

pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum ( )

Destruct this QualifiedMassSpectrum.

Definition at line 76 of file qualifiedmassspectrum.cpp.

77 {
78  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
79 }

Member Function Documentation

◆ appendPrecursorIonData()

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

◆ cloneMassSpectrumSPtr()

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

clone the mass spectrum contained in Qualified Mass Spectrum

Definition at line 101 of file qualifiedmassspectrum.cpp.

102 {
103  this->msp_massSpectrum =
104  std::make_shared<MassSpectrum>(*this->msp_massSpectrum.get());
105  return *this;
106 }

References msp_massSpectrum.

◆ getDtInMilliSeconds()

pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds ( ) const

Get the drift time in milliseconds.

Definition at line 230 of file qualifiedmassspectrum.cpp.

231 {
232  return m_dt;
233 }

References m_dt.

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId()

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getMzSortedPrecursorDataChargeValuesAsString()

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

Definition at line 366 of file qualifiedmassspectrum.cpp.

368 {
369  // Sort the PrecursorIonData instances by increasing mz values.
370  // Then craft the string using the mz values.
371 
372  std::vector<PrecursorIonData> sorted_vector =
374 
375  return getPrecursorDataChargeValuesAsString(sorted_vector, separator);
376 }
std::vector< PrecursorIonData > getPrecursorIonDataSortedWithMz() const
QString getPrecursorDataChargeValuesAsString(const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const

References getPrecursorDataChargeValuesAsString(), and getPrecursorIonDataSortedWithMz().

◆ getMzSortedPrecursorDataMzValuesAsString()

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

Definition at line 301 of file qualifiedmassspectrum.cpp.

303 {
304  // Sort the PrecursorIonData instances by increasing mz values.
305  // Then craft the string using the mz values.
306 
307  std::vector<PrecursorIonData> sorted_vector =
309 
310  return getPrecursorDataMzValuesAsString(sorted_vector, separator);
311 }
QString getPrecursorDataMzValuesAsString(const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const

References getPrecursorDataMzValuesAsString(), and getPrecursorIonDataSortedWithMz().

Referenced by toString().

◆ getParameterValue()

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

Definition at line 476 of file qualifiedmassspectrum.cpp.

478 {
479  auto it = m_paramsMap.find(parameter);
480  if(it == m_paramsMap.end())
481  {
482  return QVariant();
483  }
484  else
485  {
486  return it->second;
487  }
488 }

References m_paramsMap.

◆ getPrecursorCharge()

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

Get the precursor charge.

Definition at line 316 of file qualifiedmassspectrum.cpp.

317 {
318  if(!m_precursorIonData.size())
319  {
320  return std::numeric_limits<unsigned int>::max();
321 
322  if(ok_p != nullptr)
323  *ok_p = false;
324  }
325 
326  if(ok_p != nullptr)
327  *ok_p = true;
328 
329  return m_precursorIonData.front().charge;
330 }

References m_precursorIonData.

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 358 of file qualifiedmassspectrum.cpp.

360 {
362 }

References getPrecursorDataChargeValuesAsString(), and m_precursorIonData.

◆ getPrecursorDataChargeValuesAsString() [2/2]

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

Definition at line 334 of file qualifiedmassspectrum.cpp.

337 {
338  QString text;
339 
340  // We do not want to use the separator if there is only one precursor in the
341  // vector.
342 
343  if(precursor_ion_data_vector.size() == 1)
344  return QString("%1").arg(precursor_ion_data_vector.front().charge);
345 
346  // If there are more than one precursor, then we should list them joined with
347  // the separator.
348  for(auto item : precursor_ion_data_vector)
349  {
350  text += QString("%1%2").arg(item.charge).arg(separator);
351  }
352 
353  return text;
354 }

Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getPrecursorDataChargeValuesAsString().

◆ getPrecursorDataMzValuesAsString() [1/2]

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

Definition at line 293 of file qualifiedmassspectrum.cpp.

295 {
297 }

References getPrecursorDataMzValuesAsString(), and m_precursorIonData.

◆ getPrecursorDataMzValuesAsString() [2/2]

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

Definition at line 258 of file qualifiedmassspectrum.cpp.

261 {
262  QString text;
263 
264  // We do not want to use the separator if there is only one precursor in the
265  // vector.
266 
267  if(precursor_ion_data_vector.size() == 1)
268  return QString("%1").arg(precursor_ion_data_vector.front().mz, 0, 'f', 6);
269 
270  // If there are more than one precursor, then we should list them joined with
271  // the separator.
272 
273  using iterator = std::vector<pappso::PrecursorIonData>::const_iterator;
274 
275  iterator begin_iterator = precursor_ion_data_vector.begin();
276  iterator pre_end_iterator = std::prev(precursor_ion_data_vector.end());
277 
278  for(; begin_iterator != precursor_ion_data_vector.end(); ++begin_iterator)
279  {
280  if(begin_iterator == pre_end_iterator)
281  // No separator at the end of the string
282  text += QString("%1").arg(begin_iterator->mz, 0, 'f', 6);
283  else
284  text +=
285  QString("%1%2").arg(begin_iterator->mz, 0, 'f', 6).arg(separator);
286  }
287 
288  return text;
289 }

Referenced by getMzSortedPrecursorDataMzValuesAsString(), and getPrecursorDataMzValuesAsString().

◆ getPrecursorIntensity()

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

Get the intensity of the precursor ion.

Definition at line 381 of file qualifiedmassspectrum.cpp.

382 {
383  if(!m_precursorIonData.size())
384  {
385  return std::numeric_limits<double>::max();
386 
387  if(ok_p != nullptr)
388  *ok_p = false;
389  }
390 
391  if(ok_p != nullptr)
392  *ok_p = true;
393 
394  return m_precursorIonData.front().intensity;
395 }

References m_precursorIonData.

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 438 of file qualifiedmassspectrum.cpp.

439 {
440  return m_precursorIonData;
441 }

References m_precursorIonData.

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

◆ getPrecursorIonDataSortedWithMz()

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

Definition at line 445 of file qualifiedmassspectrum.cpp.

446 {
447  std::vector<PrecursorIonData> new_vector;
448  new_vector.assign(m_precursorIonData.begin(), m_precursorIonData.end());
449 
450  std::sort(new_vector.begin(),
451  new_vector.end(),
452  [](const PrecursorIonData &a, const PrecursorIonData &b) -> bool {
453  return a.mz < b.mz;
454  });
455 
456  return new_vector;
457 }

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

Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getMzSortedPrecursorDataMzValuesAsString().

◆ getPrecursorMz()

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

Get the precursor m/z ratio.

Definition at line 238 of file qualifiedmassspectrum.cpp.

239 {
240  if(!m_precursorIonData.size())
241  {
242  if(ok_p != nullptr)
243  *ok_p = false;
244 
245  return std::numeric_limits<double>::max();
246  }
247 
248  if(ok_p != nullptr)
249  *ok_p = true;
250 
251  // qDebug() << "Returning precursor mz value: " <<
252  // m_precursorIonData.front().mz;
253  return m_precursorIonData.front().mz;
254 }

References m_precursorIonData.

Referenced by pappso::PwizMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), 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 409 of file qualifiedmassspectrum.cpp.

410 {
412 }

References m_precursorSpectrumIndex.

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

◆ getRtInMinutes()

pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes ( ) const

Get the retention time in minutes.

Definition at line 211 of file qualifiedmassspectrum.cpp.

212 {
213  return m_rt / 60;
214 }

References m_rt.

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

◆ getRtInSeconds()

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 171 of file qualifiedmassspectrum.cpp.

172 {
173  return m_isEmptyMassSpectrum;
174 }

References m_isEmptyMassSpectrum.

◆ makeQualifiedMassSpectrumCstSPtr()

QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr ( ) const

Definition at line 117 of file qualifiedmassspectrum.cpp.

118 {
119  return std::make_shared<const QualifiedMassSpectrum>(*this);
120 }

◆ makeQualifiedMassSpectrumSPtr()

QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr ( ) const

Definition at line 110 of file qualifiedmassspectrum.cpp.

111 {
112  return std::make_shared<QualifiedMassSpectrum>(*this);
113 }

◆ operator=()

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

Definition at line 83 of file qualifiedmassspectrum.cpp.

84 {
85  msp_massSpectrum = other.msp_massSpectrum;
86  m_massSpectrumId = other.m_massSpectrumId;
87  m_isEmptyMassSpectrum = other.m_isEmptyMassSpectrum;
88  m_msLevel = other.m_msLevel;
89  m_rt = other.m_rt;
90  m_dt = other.m_dt;
91  m_precursorSpectrumIndex = other.m_precursorSpectrumIndex;
92  m_precursorNativeId = other.m_precursorNativeId;
93  m_precursorIonData = other.m_precursorIonData;
94  m_paramsMap = other.m_paramsMap;
95 
96  return *this;
97 }

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

◆ setDtInMilliSeconds()

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

Set the drift time in milliseconds.

Definition at line 219 of file qualifiedmassspectrum.cpp.

220 {
221  if(std::isinf(dt_in_milli_seconds))
222  m_dt = -1;
223  else
224  m_dt = dt_in_milli_seconds;
225 }

References m_dt.

Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::PwizMsRunReader::processDriftTime(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), and pappso::TimsFramesMsRunReader::readSpectrumCollection().

◆ setEmptyMassSpectrum()

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

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

Definition at line 461 of file qualifiedmassspectrum.cpp.

463 {
464 
465  auto ret = m_paramsMap.insert(
466  std::pair<QualifiedMassSpectrumParameter, QVariant>(parameter, value));
467 
468  if(ret.second == false)
469  {
470  ret.first->second = value;
471  }
472 }

References m_paramsMap.

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

◆ 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 492 of file qualifiedmassspectrum.cpp.

493 {
494  if(msp_massSpectrum == nullptr)
495  {
496  throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
497  }
498  return msp_massSpectrum.get()->size();
499 }

References msp_massSpectrum.

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

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( ) const

Definition at line 503 of file qualifiedmassspectrum.cpp.

504 {
505  QString text;
506 
507  if(msp_massSpectrum != nullptr && msp_massSpectrum.get() != nullptr)
508  {
509  QString pointer_string =
510  QString("msp_massSpectrum.get(): %1 ")
511  .arg(Utils::pointerToString((void *)msp_massSpectrum.get()));
512 
513  text += pointer_string;
514  }
515  else
516  text += QString("msp_massSpectrum is nullptr ");
517 
518  // qDebug() << text;
519 
520  QString precursor_mz_values_string;
521 
522  if(m_precursorIonData.size())
523  precursor_mz_values_string += "Precursor mz values: ";
524 
525  precursor_mz_values_string += getMzSortedPrecursorDataMzValuesAsString();
526 
527  precursor_mz_values_string += "\n";
528 
529  text +=
530  QString(
531  "; m_massSpectrumId : %1 \n"
532  "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
533  "index: %5 ; %6")
534  .arg(m_massSpectrumId.toString())
535  .arg(m_msLevel)
536  .arg(getRtInMinutes(), 0, 'f', 2)
537  .arg(m_dt, 0, 'f', 5)
538  .arg(m_precursorSpectrumIndex != std::numeric_limits<std::size_t>::max()
540  : -1)
541  .arg(precursor_mz_values_string);
542 
543  return text;
544 }
QString toString() const
pappso_double getRtInMinutes() const
Get the retention time in minutes.
QString getMzSortedPrecursorDataMzValuesAsString(const QString &separator="\n") const
static QString pointerToString(const void *const pointer)
Definition: utils.cpp:251

References getMzSortedPrecursorDataMzValuesAsString(), getRtInMinutes(), m_dt, m_massSpectrumId, m_msLevel, m_precursorIonData, 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 177 of file qualifiedmassspectrum.h.

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

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false
protected

Definition at line 168 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 166 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 171 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 193 of file qualifiedmassspectrum.h.

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

◆ m_precursorIonData

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

◆ m_precursorNativeId

QString pappso::QualifiedMassSpectrum::m_precursorNativeId
protected

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

Definition at line 185 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 181 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 174 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 163 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: