libpappsomspp
Library for mass spectrometry
Loading...
Searching...
No Matches
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.
 
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 92 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 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 388 of file qualifiedmassspectrum.cpp.

390{
391 // Sort the PrecursorIonData instances by increasing mz values.
392 // Then craft the string using the mz values.
393
394 std::vector<PrecursorIonData> sorted_vector =
396
397 return getPrecursorDataChargeValuesAsString(sorted_vector, separator);
398}
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 324 of file qualifiedmassspectrum.cpp.

326{
327 // Sort the PrecursorIonData instances by increasing mz values.
328 // Then craft the string using the mz values.
329
330 std::vector<PrecursorIonData> sorted_vector =
332
333 return getPrecursorDataMzValuesAsString(sorted_vector, separator);
334}
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 497 of file qualifiedmassspectrum.cpp.

499{
500 auto it = m_paramsMap.find(parameter);
501 if(it == m_paramsMap.end())
502 {
503 return QVariant();
504 }
505 else
506 {
507 return it->second;
508 }
509}

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 339 of file qualifiedmassspectrum.cpp.

340{
341 if(!m_precursorIonData.size())
342 {
343 if(ok_p != nullptr)
344 *ok_p = false;
345 return std::numeric_limits<unsigned int>::max();
346 }
347
348 if(ok_p != nullptr)
349 *ok_p = true;
350
351 return m_precursorIonData.front().charge;
352}

References m_precursorIonData.

Referenced by 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 356 of file qualifiedmassspectrum.cpp.

359{
360 QString text;
361
362 // We do not want to use the separator if there is only one precursor in the
363 // vector.
364
365 if(precursor_ion_data_vector.size() == 1)
366 return QString("%1").arg(precursor_ion_data_vector.front().charge);
367
368 // If there are more than one precursor, then we should list them joined with
369 // the separator.
370 for(auto item : precursor_ion_data_vector)
371 {
372 text += QString("%1%2").arg(item.charge).arg(separator);
373 }
374
375 return text;
376}

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 281 of file qualifiedmassspectrum.cpp.

284{
285 QString text;
286
287 // We do not want to use the separator if there is only one precursor in the
288 // vector.
289
290 if(precursor_ion_data_vector.size() == 1)
291 return QString("%1").arg(precursor_ion_data_vector.front().mz, 0, 'f', 6);
292
293 // If there are more than one precursor, then we should list them joined with
294 // the separator.
295
296 using iterator = std::vector<pappso::PrecursorIonData>::const_iterator;
297
298 iterator begin_iterator = precursor_ion_data_vector.begin();
299 iterator pre_end_iterator = std::prev(precursor_ion_data_vector.end());
300
301 for(; begin_iterator != precursor_ion_data_vector.end(); ++begin_iterator)
302 {
303 if(begin_iterator == pre_end_iterator)
304 // No separator at the end of the string
305 text += QString("%1").arg(begin_iterator->mz, 0, 'f', 6);
306 else
307 text +=
308 QString("%1%2").arg(begin_iterator->mz, 0, 'f', 6).arg(separator);
309 }
310
311 return text;
312}

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 403 of file qualifiedmassspectrum.cpp.

404{
405 if(!m_precursorIonData.size())
406 {
407 if(ok_p != nullptr)
408 *ok_p = false;
409 return std::numeric_limits<double>::max();
410 }
411
412 if(ok_p != nullptr)
413 *ok_p = true;
414
415 return m_precursorIonData.front().intensity;
416}

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 466 of file qualifiedmassspectrum.cpp.

467{
468 std::vector<PrecursorIonData> new_vector;
469 new_vector.assign(m_precursorIonData.begin(), m_precursorIonData.end());
470
471 std::sort(new_vector.begin(),
472 new_vector.end(),
473 [](const PrecursorIonData &a, const PrecursorIonData &b) -> bool {
474 return a.mz < b.mz;
475 });
476
477 return new_vector;
478}

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 258 of file qualifiedmassspectrum.cpp.

259{
260 if(ok_p != nullptr)
261 *ok_p = false;
262 bool ok_precmz = false;
263 double mz_prec = getPrecursorMz(&ok_precmz);
264 if(ok_precmz)
265 {
266 uint charge = getPrecursorCharge(&ok_precmz);
267 if(ok_precmz)
268 {
269 // compute precursor mass given the charge state
270 mz_prec = mz_prec * (double)charge;
271 mz_prec -= MHPLUS * (double)charge;
272 if(ok_p != nullptr)
273 *ok_p = true;
274 return mz_prec;
275 }
276 }
277 return std::numeric_limits<double>::max();
278}
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().

◆ 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 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 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 430 of file qualifiedmassspectrum.cpp.

431{
433}

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{
174}

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)

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::readSpectrumCollection2().

◆ setEmptyMassSpectrum()

◆ setMassSpectrumId()

◆ setMassSpectrumSPtr()

◆ setMsLevel()

◆ setParameterValue()

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

◆ 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 513 of file qualifiedmassspectrum.cpp.

514{
515 if(msp_massSpectrum == nullptr)
516 {
517 throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
518 }
519 return msp_massSpectrum.get()->size();
520}

References msp_massSpectrum.

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

◆ toString()

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

Definition at line 524 of file qualifiedmassspectrum.cpp.

525{
526 QString text;
527
528 if(msp_massSpectrum != nullptr && msp_massSpectrum.get() != nullptr)
529 {
530 QString pointer_string =
531 QString("msp_massSpectrum.get(): %1 ")
532 .arg(Utils::pointerToString((void *)msp_massSpectrum.get()));
533
534 text += pointer_string;
535 }
536 else
537 text += QString("msp_massSpectrum is nullptr ");
538
539 // qDebug() << text;
540
541 QString precursor_mz_values_string;
542
543 if(m_precursorIonData.size())
544 precursor_mz_values_string += "Precursor mz values: ";
545
546 precursor_mz_values_string += getMzSortedPrecursorDataMzValuesAsString();
547
548 precursor_mz_values_string += "\n";
549
550 text +=
551 QString(
552 "; m_massSpectrumId : %1 \n"
553 "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
554 "index: %5 ; %6")
556 .arg(m_msLevel)
557 .arg(getRtInMinutes(), 0, 'f', 2)
558 .arg(m_dt, 0, 'f', 5)
559 .arg(m_precursorSpectrumIndex != std::numeric_limits<std::size_t>::max()
561 : -1)
562 .arg(precursor_mz_values_string);
563
564 if(with_data)
565 {
566 text += msp_massSpectrum->toString();
567 }
568
569 return text;
570}
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 205 of file qualifiedmassspectrum.h.

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

◆ m_isEmptyMassSpectrum

bool pappso::QualifiedMassSpectrum::m_isEmptyMassSpectrum = false
protected

Definition at line 196 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 194 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 199 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 221 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 213 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 209 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 202 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 191 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: