libpappsomspp
Library for mass spectrometry
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pappso::QualifiedMassSpectrum Class Reference

Class representing a fully specified mass spectrum. More...

#include <qualifiedmassspectrum.h>

Public Member Functions

 QualifiedMassSpectrum ()
 Construct an uninitialized QualifiedMassSpectrum.
 
 QualifiedMassSpectrum (const MassSpectrumId &id)
 Construct a QualifiedMassSpectrum using a MassSpectrumId;.
 
 QualifiedMassSpectrum (MassSpectrumSPtr mass_spectrum_SPtr)
 
 QualifiedMassSpectrum (const QualifiedMassSpectrum &other)
 Construct a QualifiedMassSpectrum as a copy of other.
 
 ~QualifiedMassSpectrum ()
 Destruct this QualifiedMassSpectrum.
 
QualifiedMassSpectrumoperator= (const QualifiedMassSpectrum &other)
 
const QualifiedMassSpectrumcloneMassSpectrumSPtr ()
 clone the mass spectrum contained in Qualified Mass Spectrum
 
QualifiedMassSpectrumSPtr makeQualifiedMassSpectrumSPtr () const
 
QualifiedMassSpectrumCstSPtr makeQualifiedMassSpectrumCstSPtr () const
 
void setMassSpectrumSPtr (MassSpectrumSPtr massSpectrum)
 Set the MassSpectrumSPtr.
 
MassSpectrumSPtr getMassSpectrumSPtr () const
 Get the MassSpectrumSPtr.
 
MassSpectrumCstSPtr getMassSpectrumCstSPtr () const
 Get the MassSpectrumCstSPtr.
 
void setMassSpectrumId (const MassSpectrumId &iD)
 Set the MassSpectrumId.
 
const MassSpectrumIdgetMassSpectrumId () const
 Get the MassSpectrumId.
 
MassSpectrumIdgetMassSpectrumId ()
 
void setEmptyMassSpectrum (bool is_empty_mass_spectrum)
 
bool isEmptyMassSpectrum () const
 
void setMsLevel (uint ms_level)
 Set the mass spectrum level.
 
uint getMsLevel () const
 Get the mass spectrum level.
 
void setRtInSeconds (pappso_double rt)
 Set the retention time in seconds.
 
pappso_double getRtInSeconds () const
 Get the retention time in seconds.
 
pappso_double getRtInMinutes () const
 Get the retention time in minutes.
 
void setDtInMilliSeconds (pappso_double rt)
 Set the drift time in milliseconds.
 
pappso_double getDtInMilliSeconds () const
 Get the drift time in milliseconds.
 
pappso_double getPrecursorMz (bool *ok=nullptr) const
 get precursor mz
 
double getPrecursorMass (bool *ok_p=nullptr) const
 get precursor mass given the charge stats and precursor mz
 
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 precursor charge
 
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 precursor intensity
 
void setPrecursorSpectrumIndex (std::size_t precursor_scan_num)
 Set the scan number of the precursor ion.
 
std::size_t getPrecursorSpectrumIndex () const
 Get the scan number of the precursor ion.
 
void setPrecursorNativeId (const QString &native_id)
 Set the scan native id of the precursor ion.
 
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 (bool with_data=false) const
 

Protected Attributes

MassSpectrumSPtr msp_massSpectrum = nullptr
 Shared pointer to the mass spectrum.
 
MassSpectrumId m_massSpectrumId
 Id of the mass spectrum.
 
bool m_isEmptyMassSpectrum = false
 
unsigned int m_msLevel = 0
 Mass spectrometry level of this mass spectrum.
 
pappso_double m_rt = -1
 Retention time (in seconds) at which this mass spectrum was acquired.
 
pappso_double m_dt = -1
 Drift time (in milliseconds) at which this mass spectrum was acquired.
 
std::size_t m_precursorSpectrumIndex
 Index of the spectrum of the precusor ion that was fragmented to yield.
 
QString m_precursorNativeId
 Native XML id of the spectrum relative to the mz data native file.
 
std::vector< PrecursorIonDatam_precursorIonData
 
std::map< QualifiedMassSpectrumParameter, QVariant > m_paramsMap
 map containing any parameter value for this spectrum
 

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 98 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.

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()

◆ 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 235 of file qualifiedmassspectrum.cpp.

236{
237 return m_dt;
238}

References m_dt.

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumId() [1/2]

MassSpectrumId & pappso::QualifiedMassSpectrum::getMassSpectrumId ( )

Definition at line 163 of file qualifiedmassspectrum.cpp.

164{
165 return m_massSpectrumId;
166}

References m_massSpectrumId.

◆ getMassSpectrumId() [2/2]

◆ getMassSpectrumSPtr()

◆ getMsLevel()

◆ getMzSortedPrecursorDataChargeValuesAsString()

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

Definition at line 393 of file qualifiedmassspectrum.cpp.

395{
396 // Sort the PrecursorIonData instances by increasing mz values.
397 // Then craft the string using the mz values.
398
399 std::vector<PrecursorIonData> sorted_vector =
401
402 return getPrecursorDataChargeValuesAsString(sorted_vector, separator);
403}
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 329 of file qualifiedmassspectrum.cpp.

331{
332 // Sort the PrecursorIonData instances by increasing mz values.
333 // Then craft the string using the mz values.
334
335 std::vector<PrecursorIonData> sorted_vector =
337
338 return getPrecursorDataMzValuesAsString(sorted_vector, separator);
339}
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 502 of file qualifiedmassspectrum.cpp.

504{
505 auto it = m_paramsMap.find(parameter);
506 if(it == m_paramsMap.end())
507 {
508 return QVariant();
509 }
510 else
511 {
512 return it->second;
513 }
514}

References m_paramsMap.

◆ getPrecursorCharge()

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

get precursor charge

Get the precursor charge.

Parameters
okpointer on boolean, false if precursor charge is not defined
Returns
precursor charge

Definition at line 344 of file qualifiedmassspectrum.cpp.

345{
346 if(!m_precursorIonData.size())
347 {
348 if(ok_p != nullptr)
349 *ok_p = false;
350 return std::numeric_limits<unsigned int>::max();
351 }
352
353 if(ok_p != nullptr)
354 *ok_p = true;
355
356 return m_precursorIonData.front().charge;
357}

References m_precursorIonData.

Referenced by pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), getPrecursorMass(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().

◆ getPrecursorDataChargeValuesAsString() [1/2]

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

◆ getPrecursorDataChargeValuesAsString() [2/2]

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

Definition at line 361 of file qualifiedmassspectrum.cpp.

364{
365 QString text;
366
367 // We do not want to use the separator if there is only one precursor in the
368 // vector.
369
370 if(precursor_ion_data_vector.size() == 1)
371 return QString("%1").arg(precursor_ion_data_vector.front().charge);
372
373 // If there are more than one precursor, then we should list them joined with
374 // the separator.
375 for(auto item : precursor_ion_data_vector)
376 {
377 text += QString("%1%2").arg(item.charge).arg(separator);
378 }
379
380 return text;
381}

Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getPrecursorDataChargeValuesAsString().

◆ getPrecursorDataMzValuesAsString() [1/2]

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

◆ getPrecursorDataMzValuesAsString() [2/2]

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

Definition at line 286 of file qualifiedmassspectrum.cpp.

289{
290 QString text;
291
292 // We do not want to use the separator if there is only one precursor in the
293 // vector.
294
295 if(precursor_ion_data_vector.size() == 1)
296 return QString("%1").arg(precursor_ion_data_vector.front().mz, 0, 'f', 6);
297
298 // If there are more than one precursor, then we should list them joined with
299 // the separator.
300
301 using iterator = std::vector<pappso::PrecursorIonData>::const_iterator;
302
303 iterator begin_iterator = precursor_ion_data_vector.begin();
304 iterator pre_end_iterator = std::prev(precursor_ion_data_vector.end());
305
306 for(; begin_iterator != precursor_ion_data_vector.end(); ++begin_iterator)
307 {
308 if(begin_iterator == pre_end_iterator)
309 // No separator at the end of the string
310 text += QString("%1").arg(begin_iterator->mz, 0, 'f', 6);
311 else
312 text +=
313 QString("%1%2").arg(begin_iterator->mz, 0, 'f', 6).arg(separator);
314 }
315
316 return text;
317}

Referenced by getMzSortedPrecursorDataMzValuesAsString(), and getPrecursorDataMzValuesAsString().

◆ getPrecursorIntensity()

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

get precursor intensity

Get the intensity of the precursor ion.

Parameters
okpointer on boolean, false if precursor intensity is not defined
Returns
precursor intensity

Definition at line 408 of file qualifiedmassspectrum.cpp.

409{
410 if(!m_precursorIonData.size())
411 {
412 if(ok_p != nullptr)
413 *ok_p = false;
414 return std::numeric_limits<double>::max();
415 }
416
417 if(ok_p != nullptr)
418 *ok_p = true;
419
420 return m_precursorIonData.front().intensity;
421}

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

◆ getPrecursorIonDataSortedWithMz()

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

Definition at line 471 of file qualifiedmassspectrum.cpp.

472{
473 std::vector<PrecursorIonData> new_vector;
474 new_vector.assign(m_precursorIonData.begin(), m_precursorIonData.end());
475
476 std::sort(new_vector.begin(),
477 new_vector.end(),
478 [](const PrecursorIonData &a, const PrecursorIonData &b) -> bool {
479 return a.mz < b.mz;
480 });
481
482 return new_vector;
483}

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

Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getMzSortedPrecursorDataMzValuesAsString().

◆ getPrecursorMass()

double pappso::QualifiedMassSpectrum::getPrecursorMass ( bool * ok_p = nullptr) const

get precursor mass given the charge stats and precursor mz

Get the precursor mass ratio.

Parameters
okpointer on boolean, false if precursor mz is not defined
Returns
precursor mass (neutral mass without H+)

Definition at line 263 of file qualifiedmassspectrum.cpp.

264{
265 if(ok_p != nullptr)
266 *ok_p = false;
267 bool ok_precmz = false;
268 double mz_prec = getPrecursorMz(&ok_precmz);
269 if(ok_precmz)
270 {
271 uint charge = getPrecursorCharge(&ok_precmz);
272 if(ok_precmz)
273 {
274 // compute precursor mass given the charge state
275 mz_prec = mz_prec * (double)charge;
276 mz_prec -= (MHPLUS * (double)charge);
277 if(ok_p != nullptr)
278 *ok_p = true;
279 return mz_prec;
280 }
281 }
282 return std::numeric_limits<double>::max();
283}
uint getPrecursorCharge(bool *ok=nullptr) const
get precursor charge
pappso_double getPrecursorMz(bool *ok=nullptr) const
get precursor mz
const pappso_double MHPLUS(1.007276466879)
unsigned int uint
Definition types.h:57

References getPrecursorCharge(), getPrecursorMz(), and pappso::MHPLUS().

Referenced by pappso::specglob::PeptideModel::PeptideModel().

◆ getPrecursorMz()

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

get precursor mz

Get the precursor m/z ratio.

Parameters
okpointer on boolean, false if precursor mz is not defined
Returns
precursor mz

Definition at line 243 of file qualifiedmassspectrum.cpp.

244{
245 if(!m_precursorIonData.size())
246 {
247 if(ok_p != nullptr)
248 *ok_p = false;
249
250 return std::numeric_limits<double>::max();
251 }
252
253 if(ok_p != nullptr)
254 *ok_p = true;
255
256 // qDebug() << "Returning precursor mz value: " <<
257 // m_precursorIonData.front().mz;
258 return m_precursorIonData.front().mz;
259}

References m_precursorIonData.

Referenced by pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), getPrecursorMass(), 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 435 of file qualifiedmassspectrum.cpp.

436{
438}

References m_precursorSpectrumIndex.

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

◆ getRtInMinutes()

pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes ( ) const

Get the retention time in minutes.

Definition at line 216 of file qualifiedmassspectrum.cpp.

217{
218 return m_rt / 60;
219}

References m_rt.

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

◆ getRtInSeconds()

◆ isEmptyMassSpectrum()

bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum ( ) const

Definition at line 176 of file qualifiedmassspectrum.cpp.

177{
179}

References m_isEmptyMassSpectrum.

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

◆ 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)

◆ setEmptyMassSpectrum()

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

◆ setPrecursorNativeId()

◆ setPrecursorSpectrumIndex()

◆ setRtInSeconds()

◆ size()

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

◆ toString()

QString pappso::QualifiedMassSpectrum::toString ( bool with_data = false) const

Definition at line 529 of file qualifiedmassspectrum.cpp.

530{
531 QString text;
532
533 if(msp_massSpectrum != nullptr && msp_massSpectrum.get() != nullptr)
534 {
535 QString pointer_string =
536 QString("msp_massSpectrum.get(): %1 ")
537 .arg(Utils::pointerToString((void *)msp_massSpectrum.get()));
538
539 text += pointer_string;
540 }
541 else
542 text += QString("msp_massSpectrum is nullptr ");
543
544 // qDebug() << text;
545
546 QString precursor_mz_values_string;
547
548 if(m_precursorIonData.size())
549 precursor_mz_values_string += "Precursor mz values: ";
550
551 precursor_mz_values_string += getMzSortedPrecursorDataMzValuesAsString();
552
553 precursor_mz_values_string += "\n";
554
555 text +=
556 QString(
557 "; m_massSpectrumId : %1 \n"
558 "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
559 "index: %5 ; %6")
561 .arg(m_msLevel)
562 .arg(getRtInMinutes(), 0, 'f', 2)
563 .arg(m_dt, 0, 'f', 5)
564 .arg(m_precursorSpectrumIndex != std::numeric_limits<std::size_t>::max()
566 : -1)
567 .arg(precursor_mz_values_string);
568
569 if(with_data)
570 {
571 text += msp_massSpectrum->toString();
572 }
573
574 return text;
575}
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:295

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 212 of file qualifiedmassspectrum.h.

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

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false
protected

Definition at line 203 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 201 of file qualifiedmassspectrum.h.

Referenced by getMassSpectrumId(), 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 206 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 227 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 220 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 216 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 209 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 198 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: