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 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.

70 {
71  // qDebug();
72 }
73 

◆ 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.

77 {
78  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
79 }
80 
81 
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;

◆ ~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)

◆ 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()

◆ getMassSpectrumId()

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getMzSortedPrecursorDataChargeValuesAsString()

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

Definition at line 384 of file qualifiedmassspectrum.cpp.

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;

◆ getMzSortedPrecursorDataMzValuesAsString()

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

Definition at line 319 of file qualifiedmassspectrum.cpp.

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;

◆ getParameterValue()

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

Definition at line 494 of file qualifiedmassspectrum.cpp.

495  {
496  throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
497  }
498  return msp_massSpectrum.get()->size();
499 }
500 
501 
502 QString
504 {
505  QString text;
506 

◆ getPrecursorCharge()

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

Get the precursor charge.

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)

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.

360 {
362 }
363 
364 
365 QString
367  const QString &separator) const
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 =

◆ 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.

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 }
290 
291 
292 QString
294  const QString &separator) const
295 {
297 }
298 
299 
300 QString
302  const QString &separator) const
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 =

◆ 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.

402 {
403  m_precursorSpectrumIndex = precursor_spectrum_index;
404 }
405 
406 
407 //! Get the scan number of the precursor ion.
408 std::size_t
410 {
412 }
413 

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.

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 }
473 
474 
475 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.

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 

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 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

◆ 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.

102 {
103  this->msp_massSpectrum =
104  std::make_shared<MassSpectrum>(*this->msp_massSpectrum.get());
105  return *this;
106 }
107 
108 
111 {
112  return std::make_shared<QualifiedMassSpectrum>(*this);
113 }
114 
115 

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.

239 {
240  if(!m_precursorIonData.size())
241  {
242  if(ok_p != nullptr)
243  *ok_p = false;

References m_precursorIonData.

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

◆ 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 479 of file qualifiedmassspectrum.cpp.

481  {
482  return QVariant();
483  }
484  else
485  {
486  return it->second;
487  }
488 }
489 
490 

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.

418 {
419  m_precursorNativeId = native_id;
420 }
421 
422 const QString &

References m_precursorNativeId.

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

◆ setRtInSeconds()

◆ size()

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

Definition at line 510 of file qualifiedmassspectrum.cpp.

510  : %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 

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

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( ) const

Definition at line 521 of file qualifiedmassspectrum.cpp.

523  : ";
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()
539  ? m_precursorSpectrumIndex
540  : -1)
541  .arg(precursor_mz_values_string);
542 
543  return text;
544 }
545 
546 
547 } // 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:
pappso::QualifiedMassSpectrum::m_dt
pappso_double m_dt
Drift time (in milliseconds) at which this mass spectrum was acquired.
Definition: qualifiedmassspectrum.h:195
pappso::QualifiedMassSpectrum::getPrecursorDataChargeValuesAsString
QString getPrecursorDataChargeValuesAsString(const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const
Definition: qualifiedmassspectrum.cpp:352
pappso::QualifiedMassSpectrumSPtr
std::shared_ptr< QualifiedMassSpectrum > QualifiedMassSpectrumSPtr
Definition: qualifiedmassspectrum.h:59
pappso::QualifiedMassSpectrum::operator=
QualifiedMassSpectrum & operator=(const QualifiedMassSpectrum &other)
Definition: qualifiedmassspectrum.cpp:101
pappso::QualifiedMassSpectrum::m_paramsMap
std::map< QualifiedMassSpectrumParameter, QVariant > m_paramsMap
map containing any parameter value for this spectrum
Definition: qualifiedmassspectrum.h:211
pappso::QualifiedMassSpectrum::m_rt
pappso_double m_rt
Retention time (in seconds) at which this mass spectrum was acquired.
Definition: qualifiedmassspectrum.h:192
pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr
QualifiedMassSpectrumSPtr makeQualifiedMassSpectrumSPtr() const
Definition: qualifiedmassspectrum.cpp:128
pappso::QualifiedMassSpectrum::getPrecursorDataMzValuesAsString
QString getPrecursorDataMzValuesAsString(const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const
Definition: qualifiedmassspectrum.cpp:276
pappso::QualifiedMassSpectrum::msp_massSpectrum
MassSpectrumSPtr msp_massSpectrum
Shared pointer to the mass spectrum.
Definition: qualifiedmassspectrum.h:181
pappso::QualifiedMassSpectrum::m_massSpectrumId
MassSpectrumId m_massSpectrumId
Id of the mass spectrum.
Definition: qualifiedmassspectrum.h:184
pappso::QualifiedMassSpectrum::m_precursorIonData
std::vector< PrecursorIonData > m_precursorIonData
Definition: qualifiedmassspectrum.h:208
pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum
bool m_isEmptyMassSpectrum
Definition: qualifiedmassspectrum.h:186
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:199
pappso::QualifiedMassSpectrum::QualifiedMassSpectrum
QualifiedMassSpectrum()
Construct an uninitialized QualifiedMassSpectrum.
Definition: qualifiedmassspectrum.cpp:57
pappso::QualifiedMassSpectrum::m_precursorNativeId
QString m_precursorNativeId
Native XML id of the spectrum relative to the mz data native file.
Definition: qualifiedmassspectrum.h:203
pappso::QualifiedMassSpectrum::m_msLevel
unsigned int m_msLevel
Mass spectrometry level of this mass spectrum.
Definition: qualifiedmassspectrum.h:189
pappso::QualifiedMassSpectrum::toString
QString toString() const
Definition: qualifiedmassspectrum.cpp:521
pappso::QualifiedMassSpectrum::getMzSortedPrecursorDataMzValuesAsString
QString getMzSortedPrecursorDataMzValuesAsString(const QString &separator="\n") const
Definition: qualifiedmassspectrum.cpp:319
pappso::QualifiedMassSpectrum::getPrecursorSpectrumIndex
std::size_t getPrecursorSpectrumIndex() const
Get the scan number of the precursor ion.
Definition: qualifiedmassspectrum.cpp:427
pappso::QualifiedMassSpectrum::getMzSortedPrecursorDataChargeValuesAsString
QString getMzSortedPrecursorDataChargeValuesAsString(const QString &separator="\n") const
Definition: qualifiedmassspectrum.cpp:384
pappso::PappsoException
Definition: pappsoexception.h:63