libpappsomspp
Library for mass spectrometry
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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. | |
QualifiedMassSpectrum & | operator= (const QualifiedMassSpectrum &other) |
const QualifiedMassSpectrum & | cloneMassSpectrumSPtr () |
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 MassSpectrumId & | getMassSpectrumId () const |
Get the MassSpectrumId. | |
MassSpectrumId & | getMassSpectrumId () |
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< PrecursorIonData > | getPrecursorIonDataSortedWithMz () 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< PrecursorIonData > | m_precursorIonData |
std::map< QualifiedMassSpectrumParameter, QVariant > | m_paramsMap |
map containing any parameter value for this spectrum | |
Class representing a fully specified mass spectrum.
The member data that qualify the MassSpectrum msp_massSpectrum
member allow to unambiguously characterize the mass spectrum.
Definition at line 94 of file qualifiedmassspectrum.h.
pappso::QualifiedMassSpectrum::QualifiedMassSpectrum | ( | ) |
Construct an uninitialized QualifiedMassSpectrum.
Definition at line 39 of file qualifiedmassspectrum.cpp.
pappso::QualifiedMassSpectrum::QualifiedMassSpectrum | ( | const MassSpectrumId & | id | ) |
Construct a QualifiedMassSpectrum using a MassSpectrumId;.
Definition at line 45 of file qualifiedmassspectrum.cpp.
pappso::QualifiedMassSpectrum::QualifiedMassSpectrum | ( | MassSpectrumSPtr | mass_spectrum_SPtr | ) |
Definition at line 51 of file qualifiedmassspectrum.cpp.
pappso::QualifiedMassSpectrum::QualifiedMassSpectrum | ( | const QualifiedMassSpectrum & | other | ) |
Construct a QualifiedMassSpectrum as a copy of other
.
Definition at line 59 of file qualifiedmassspectrum.cpp.
pappso::QualifiedMassSpectrum::~QualifiedMassSpectrum | ( | ) |
Destruct this QualifiedMassSpectrum.
Definition at line 76 of file qualifiedmassspectrum.cpp.
void pappso::QualifiedMassSpectrum::appendPrecursorIonData | ( | const PrecursorIonData & | precursor_ion_data | ) |
Definition at line 456 of file qualifiedmassspectrum.cpp.
References m_precursorIonData.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::TimsData::rawReaderSpectrumCollectionByMsLevel().
const QualifiedMassSpectrum & pappso::QualifiedMassSpectrum::cloneMassSpectrumSPtr | ( | ) |
clone the mass spectrum contained in Qualified Mass Spectrum
Definition at line 101 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds | ( | ) | const |
Get the drift time in milliseconds.
Definition at line 235 of file qualifiedmassspectrum.cpp.
References m_dt.
MassSpectrumCstSPtr pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr | ( | ) | const |
Get the MassSpectrumCstSPtr.
Definition at line 141 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::specglob::PeptideModel::PeptideModel(), pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), pappso::specglob::ExperimentalSpectrum::findMz(), pappso::BafAsciiMsRunReader::massSpectrumCstSPtr(), pappso::PwizMsRunReader::massSpectrumCstSPtr(), pappso::XyMsRunReader::massSpectrumCstSPtr(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
MassSpectrumId & pappso::QualifiedMassSpectrum::getMassSpectrumId | ( | ) |
Definition at line 163 of file qualifiedmassspectrum.cpp.
References m_massSpectrumId.
const MassSpectrumId & pappso::QualifiedMassSpectrum::getMassSpectrumId | ( | ) | const |
Get the MassSpectrumId.
Definition at line 157 of file qualifiedmassspectrum.cpp.
References m_massSpectrumId.
Referenced by pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), pappso::MzxmlOutput::getScanNumber(), pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::MsRunReaderQualifiedSpectrumList::setQualifiedMassSpectrum(), pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum(), pappso::MsRunReaderRetentionTimeLine::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MgfOutput::write().
MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr | ( | ) | const |
Get the MassSpectrumSPtr.
Definition at line 133 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::TimsMsRunReaderMs2::massSpectrumCstSPtr(), pappso::TimsMsRunReaderMs2Selected::massSpectrumCstSPtr(), pappso::BafAsciiMsRunReader::massSpectrumSPtr(), pappso::PwizMsRunReader::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2Selected::massSpectrumSPtr(), pappso::XyMsRunReader::massSpectrumSPtr(), and pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum().
unsigned int pappso::QualifiedMassSpectrum::getMsLevel | ( | ) | const |
Get the mass spectrum level.
Definition at line 192 of file qualifiedmassspectrum.cpp.
References m_msLevel.
Referenced by pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::XyMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig(), pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MsRunSimpleStatistics::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
QString pappso::QualifiedMassSpectrum::getMzSortedPrecursorDataChargeValuesAsString | ( | const QString & | separator = "\n" | ) | const |
Definition at line 393 of file qualifiedmassspectrum.cpp.
References getPrecursorDataChargeValuesAsString(), and getPrecursorIonDataSortedWithMz().
QString pappso::QualifiedMassSpectrum::getMzSortedPrecursorDataMzValuesAsString | ( | const QString & | separator = "\n" | ) | const |
Definition at line 329 of file qualifiedmassspectrum.cpp.
References getPrecursorDataMzValuesAsString(), and getPrecursorIonDataSortedWithMz().
Referenced by toString().
const QVariant pappso::QualifiedMassSpectrum::getParameterValue | ( | QualifiedMassSpectrumParameter | parameter | ) | const |
Definition at line 502 of file qualifiedmassspectrum.cpp.
References m_paramsMap.
unsigned int pappso::QualifiedMassSpectrum::getPrecursorCharge | ( | bool * | ok = nullptr | ) | const |
get precursor charge
Get the precursor charge.
ok | pointer on boolean, false if precursor charge is not defined |
Definition at line 344 of file qualifiedmassspectrum.cpp.
References m_precursorIonData.
Referenced by pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), getPrecursorMass(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
QString pappso::QualifiedMassSpectrum::getPrecursorDataChargeValuesAsString | ( | const QString & | separator = "\n" | ) | const |
Definition at line 385 of file qualifiedmassspectrum.cpp.
References getPrecursorDataChargeValuesAsString(), and m_precursorIonData.
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.
Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getPrecursorDataChargeValuesAsString().
QString pappso::QualifiedMassSpectrum::getPrecursorDataMzValuesAsString | ( | const QString & | separator = "\n" | ) | const |
Definition at line 321 of file qualifiedmassspectrum.cpp.
References getPrecursorDataMzValuesAsString(), and m_precursorIonData.
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.
Referenced by getMzSortedPrecursorDataMzValuesAsString(), and getPrecursorDataMzValuesAsString().
pappso_double pappso::QualifiedMassSpectrum::getPrecursorIntensity | ( | bool * | ok = nullptr | ) | const |
get precursor intensity
Get the intensity of the precursor ion.
ok | pointer on boolean, false if precursor intensity is not defined |
Definition at line 408 of file qualifiedmassspectrum.cpp.
References m_precursorIonData.
Referenced by pappso::MsRunRetentionTime< T >::addPeptideAsSeamark(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
const std::vector< PrecursorIonData > & pappso::QualifiedMassSpectrum::getPrecursorIonData | ( | ) | const |
Definition at line 464 of file qualifiedmassspectrum.cpp.
References m_precursorIonData.
Referenced by pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
std::vector< PrecursorIonData > pappso::QualifiedMassSpectrum::getPrecursorIonDataSortedWithMz | ( | ) | const |
Definition at line 471 of file qualifiedmassspectrum.cpp.
References pappso::a, pappso::b, and m_precursorIonData.
Referenced by getMzSortedPrecursorDataChargeValuesAsString(), and getMzSortedPrecursorDataMzValuesAsString().
double pappso::QualifiedMassSpectrum::getPrecursorMass | ( | bool * | ok_p = nullptr | ) | const |
get precursor mass given the charge stats and precursor mz
Get the precursor mass ratio.
ok | pointer on boolean, false if precursor mz is not defined |
Definition at line 263 of file qualifiedmassspectrum.cpp.
References getPrecursorCharge(), getPrecursorMz(), and pappso::MHPLUS().
Referenced by pappso::specglob::PeptideModel::PeptideModel().
pappso_double pappso::QualifiedMassSpectrum::getPrecursorMz | ( | bool * | ok = nullptr | ) | const |
get precursor mz
Get the precursor m/z ratio.
ok | pointer on boolean, false if precursor mz is not defined |
Definition at line 243 of file qualifiedmassspectrum.cpp.
References m_precursorIonData.
Referenced by pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), getPrecursorMass(), pappso::PwizMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
const QString & pappso::QualifiedMassSpectrum::getPrecursorNativeId | ( | ) | const |
Definition at line 449 of file qualifiedmassspectrum.cpp.
References m_precursorNativeId.
Referenced by pappso::MzxmlOutput::getPrecursorScanNumber(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
std::size_t pappso::QualifiedMassSpectrum::getPrecursorSpectrumIndex | ( | ) | const |
Get the scan number of the precursor ion.
Definition at line 435 of file qualifiedmassspectrum.cpp.
References m_precursorSpectrumIndex.
Referenced by pappso::MzxmlOutput::getPrecursorScanNumber().
pappso_double pappso::QualifiedMassSpectrum::getRtInMinutes | ( | ) | const |
Get the retention time in minutes.
Definition at line 216 of file qualifiedmassspectrum.cpp.
References m_rt.
Referenced by pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum(), and toString().
pappso_double pappso::QualifiedMassSpectrum::getRtInSeconds | ( | ) | const |
Get the retention time in seconds.
Definition at line 208 of file qualifiedmassspectrum.cpp.
References m_rt.
Referenced by pappso::MsRunRetentionTime< T >::addPeptideAsSeamark(), pappso::PwizMsRunReader::newXicCoordSPtrFromQualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig(), pappso::MsRunReaderRetentionTimeLine::setQualifiedMassSpectrum(), pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum | ( | ) | const |
Definition at line 176 of file qualifiedmassspectrum.cpp.
References m_isEmptyMassSpectrum.
Referenced by pappso::MzxmlOutput::writeQualifiedMassSpectrum().
QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr | ( | ) | const |
Definition at line 117 of file qualifiedmassspectrum.cpp.
QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr | ( | ) | const |
Definition at line 110 of file qualifiedmassspectrum.cpp.
QualifiedMassSpectrum & pappso::QualifiedMassSpectrum::operator= | ( | const QualifiedMassSpectrum & | other | ) |
Definition at line 83 of file qualifiedmassspectrum.cpp.
References m_dt, m_isEmptyMassSpectrum, m_massSpectrumId, m_msLevel, m_paramsMap, m_precursorIonData, m_precursorNativeId, m_precursorSpectrumIndex, m_rt, and msp_massSpectrum.
void pappso::QualifiedMassSpectrum::setDtInMilliSeconds | ( | pappso_double | rt | ) |
Set the drift time in milliseconds.
Definition at line 224 of file qualifiedmassspectrum.cpp.
References m_dt.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::PwizMsRunReader::processDriftTime(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().
void pappso::QualifiedMassSpectrum::setEmptyMassSpectrum | ( | bool | is_empty_mass_spectrum | ) |
Definition at line 169 of file qualifiedmassspectrum.cpp.
References m_isEmptyMassSpectrum.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().
void pappso::QualifiedMassSpectrum::setMassSpectrumId | ( | const MassSpectrumId & | iD | ) |
Set the MassSpectrumId.
Definition at line 149 of file qualifiedmassspectrum.cpp.
References m_massSpectrumId.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().
void pappso::QualifiedMassSpectrum::setMassSpectrumSPtr | ( | MassSpectrumSPtr | massSpectrum | ) |
Set the MassSpectrumSPtr.
Definition at line 125 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().
void pappso::QualifiedMassSpectrum::setMsLevel | ( | uint | ms_level | ) |
Set the mass spectrum level.
Definition at line 184 of file qualifiedmassspectrum.cpp.
References m_msLevel.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().
void pappso::QualifiedMassSpectrum::setParameterValue | ( | QualifiedMassSpectrumParameter | parameter, |
const QVariant & | value | ||
) |
Definition at line 487 of file qualifiedmassspectrum.cpp.
References m_paramsMap.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().
void pappso::QualifiedMassSpectrum::setPrecursorNativeId | ( | const QString & | native_id | ) |
Set the scan native id of the precursor ion.
Definition at line 443 of file qualifiedmassspectrum.cpp.
References m_precursorNativeId.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::TimsData::rawReaderSpectrumCollectionByMsLevel().
void pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex | ( | std::size_t | precursor_scan_num | ) |
Set the scan number of the precursor ion.
Definition at line 426 of file qualifiedmassspectrum.cpp.
References m_precursorSpectrumIndex.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::TimsData::rawReaderSpectrumCollectionByMsLevel().
void pappso::QualifiedMassSpectrum::setRtInSeconds | ( | pappso_double | rt | ) |
Set the retention time in seconds.
Definition at line 200 of file qualifiedmassspectrum.cpp.
References m_rt.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::processRetentionTime(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), and pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel().
std::size_t pappso::QualifiedMassSpectrum::size | ( | ) | const |
Definition at line 518 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::rawReaderSpectrumCollectionByMsLevel(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
QString pappso::QualifiedMassSpectrum::toString | ( | bool | with_data = false | ) | const |
Definition at line 529 of file qualifiedmassspectrum.cpp.
References getMzSortedPrecursorDataMzValuesAsString(), getRtInMinutes(), m_dt, m_massSpectrumId, m_msLevel, m_precursorIonData, m_precursorSpectrumIndex, msp_massSpectrum, pappso::Utils::pointerToString(), and pappso::MassSpectrumId::toString().
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Drift time (in milliseconds) at which this mass spectrum was acquired.
Definition at line 208 of file qualifiedmassspectrum.h.
Referenced by getDtInMilliSeconds(), operator=(), setDtInMilliSeconds(), and toString().
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Definition at line 199 of file qualifiedmassspectrum.h.
Referenced by isEmptyMassSpectrum(), operator=(), and setEmptyMassSpectrum().
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Id of the mass spectrum.
Definition at line 197 of file qualifiedmassspectrum.h.
Referenced by getMassSpectrumId(), getMassSpectrumId(), operator=(), setMassSpectrumId(), and toString().
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Mass spectrometry level of this mass spectrum.
Definition at line 202 of file qualifiedmassspectrum.h.
Referenced by getMsLevel(), operator=(), setMsLevel(), and toString().
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map containing any parameter value for this spectrum
Definition at line 223 of file qualifiedmassspectrum.h.
Referenced by getParameterValue(), operator=(), and setParameterValue().
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vector of precursor ion data of the precursors that were fragmented to yield this mass spectrum.
Definition at line 220 of file qualifiedmassspectrum.h.
Referenced by appendPrecursorIonData(), getPrecursorCharge(), getPrecursorDataChargeValuesAsString(), getPrecursorDataMzValuesAsString(), getPrecursorIntensity(), getPrecursorIonData(), getPrecursorIonDataSortedWithMz(), getPrecursorMz(), operator=(), and toString().
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Native XML id of the spectrum relative to the mz data native file.
Definition at line 216 of file qualifiedmassspectrum.h.
Referenced by getPrecursorNativeId(), operator=(), and setPrecursorNativeId().
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Index of the spectrum of the precusor ion that was fragmented to yield.
Definition at line 212 of file qualifiedmassspectrum.h.
Referenced by getPrecursorSpectrumIndex(), operator=(), setPrecursorSpectrumIndex(), and toString().
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Retention time (in seconds) at which this mass spectrum was acquired.
Definition at line 205 of file qualifiedmassspectrum.h.
Referenced by getRtInMinutes(), getRtInSeconds(), operator=(), and setRtInSeconds().
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Shared pointer to the mass spectrum.
Definition at line 194 of file qualifiedmassspectrum.h.
Referenced by cloneMassSpectrumSPtr(), getMassSpectrumCstSPtr(), getMassSpectrumSPtr(), operator=(), setMassSpectrumSPtr(), size(), and toString().