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. 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... | |
QualifiedMassSpectrum & | operator= (const QualifiedMassSpectrum &other) |
QualifiedMassSpectrumSPtr | makeQualifiedMassSpectrumSPtr () const |
QualifiedMassSpectrumCstSPtr | makeQualifiedMassSpectrumCstSPtr () const |
void | setMassSpectrumId (const MassSpectrumId &iD) |
Set the MassSpectrumId. More... | |
const MassSpectrumId & | getMassSpectrumId () const |
Get the MassSpectrumId. More... | |
void | setMassSpectrumSPtr (MassSpectrumSPtr massSpectrum) |
Set the MassSpectrumSPtr. More... | |
MassSpectrumSPtr | getMassSpectrumSPtr () const |
Get the MassSpectrumSPtr. More... | |
MassSpectrumCstSPtr | getMassSpectrumCstSPtr () const |
Get the MassSpectrumCstSPtr. More... | |
const QualifiedMassSpectrum & | cloneMassSpectrumSPtr () |
clone the mass spectrum contained in Qualified Mass Spectrum More... | |
void | setEmptyMassSpectrum (bool is_empty_mass_spectrum) |
bool | isEmptyMassSpectrum () const |
void | setPrecursorCharge (uint precursor_charge) |
Set the precursor charge. More... | |
uint | getPrecursorCharge () const |
Get the precursor charge. More... | |
void | setPrecursorMz (pappso_double precursor_mz) |
Set the precursor m/z ratio. More... | |
pappso_double | getPrecursorMz () const |
Get the precursor m/z ratio. More... | |
void | setMsLevel (uint ms_level) |
Set the mass spectrum level. More... | |
uint | getMsLevel () const |
Get the mass spectrum level. 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 | 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... | |
void | setPrecursorIntensity (pappso_double intensity) |
Set the intensity of the precursor ion. More... | |
pappso_double | getPrecursorIntensity () const |
Get the intensity of the precursor ion. More... | |
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... | |
pappso_double | m_precursorMz = std::numeric_limits<double>::max() |
unsigned int | m_precursorCharge = std::numeric_limits<unsigned int>::max() |
Charge of the precursor that was fragmented to yield this mass spectrum. More... | |
pappso_double | m_precursorIntensity = std::numeric_limits<double>::max() |
std::map< QualifiedMassSpectrumParameter, QVariant > | m_paramsMap |
map containing any parameter value for this spectrum More... | |
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 67 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 77 of file qualifiedmassspectrum.cpp.
const QualifiedMassSpectrum & pappso::QualifiedMassSpectrum::cloneMassSpectrumSPtr | ( | ) |
clone the mass spectrum contained in Qualified Mass Spectrum
Definition at line 390 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
pappso_double pappso::QualifiedMassSpectrum::getDtInMilliSeconds | ( | ) | const |
Get the drift time in milliseconds.
Definition at line 257 of file qualifiedmassspectrum.cpp.
References m_dt.
MassSpectrumCstSPtr pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr | ( | ) | const |
Get the MassSpectrumCstSPtr.
Definition at line 152 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::PwizMsRunReader::massSpectrumCstSPtr(), pappso::XyMsRunReader::massSpectrumCstSPtr(), pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
const MassSpectrumId & pappso::QualifiedMassSpectrum::getMassSpectrumId | ( | ) | const |
Get the MassSpectrumId.
Definition at line 128 of file qualifiedmassspectrum.cpp.
References m_massSpectrumId.
Referenced by pappso::MzxmlOutput::getScanNumber(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MgfOutput::write().
MassSpectrumSPtr pappso::QualifiedMassSpectrum::getMassSpectrumSPtr | ( | ) | const |
Get the MassSpectrumSPtr.
Definition at line 144 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::TimsMsRunReaderMs2::massSpectrumCstSPtr(), pappso::PwizMsRunReader::massSpectrumSPtr(), pappso::TimsMsRunReaderMs2::massSpectrumSPtr(), and pappso::XyMsRunReader::massSpectrumSPtr().
unsigned int pappso::QualifiedMassSpectrum::getMsLevel | ( | ) | const |
Get the mass spectrum level.
Definition at line 214 of file qualifiedmassspectrum.cpp.
References m_msLevel.
Referenced by pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunSimpleStatistics::setQualifiedMassSpectrum(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
const QVariant pappso::QualifiedMassSpectrum::getParameterValue | ( | QualifiedMassSpectrumParameter | parameter | ) | const |
unsigned int pappso::QualifiedMassSpectrum::getPrecursorCharge | ( | ) | const |
Get the precursor charge.
Definition at line 182 of file qualifiedmassspectrum.cpp.
References m_precursorCharge.
Referenced by pappso::MassSpectrumWidget::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
pappso_double pappso::QualifiedMassSpectrum::getPrecursorIntensity | ( | ) | const |
Get the intensity of the precursor ion.
Definition at line 301 of file qualifiedmassspectrum.cpp.
References m_precursorIntensity.
Referenced by pappso::MsRunRetentionTime< T >::addPeptideAsSeamark(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
pappso_double pappso::QualifiedMassSpectrum::getPrecursorMz | ( | ) | const |
Get the precursor m/z ratio.
Definition at line 198 of file qualifiedmassspectrum.cpp.
References m_precursorMz.
Referenced by pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
const QString & pappso::QualifiedMassSpectrum::getPrecursorNativeId | ( | ) | const |
Definition at line 286 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 273 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 238 of file qualifiedmassspectrum.cpp.
References m_rt.
Referenced by toString().
pappso_double pappso::QualifiedMassSpectrum::getRtInSeconds | ( | ) | const |
Get the retention time in seconds.
Definition at line 230 of file qualifiedmassspectrum.cpp.
References m_rt.
Referenced by pappso::MsRunRetentionTime< T >::addPeptideAsSeamark(), pappso::PwizMsRunReader::qualifiedMassSpectrum(), RetentionTimeReader::setQualifiedMassSpectrum(), pappso::MsRunXicExtractorInterface::MsRunXicExtractorReadPoints::setQualifiedMassSpectrum(), pappso::MgfOutput::write(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
bool pappso::QualifiedMassSpectrum::isEmptyMassSpectrum | ( | ) | const |
Definition at line 166 of file qualifiedmassspectrum.cpp.
References m_isEmptyMassSpectrum.
QualifiedMassSpectrumCstSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumCstSPtr | ( | ) | const |
Definition at line 112 of file qualifiedmassspectrum.cpp.
QualifiedMassSpectrumSPtr pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr | ( | ) | const |
Definition at line 105 of file qualifiedmassspectrum.cpp.
QualifiedMassSpectrum & pappso::QualifiedMassSpectrum::operator= | ( | const QualifiedMassSpectrum & | other | ) |
Definition at line 84 of file qualifiedmassspectrum.cpp.
References m_dt, m_isEmptyMassSpectrum, m_massSpectrumId, m_msLevel, m_paramsMap, m_precursorCharge, m_precursorIntensity, m_precursorMz, 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 246 of file qualifiedmassspectrum.cpp.
References m_dt.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
void pappso::QualifiedMassSpectrum::setEmptyMassSpectrum | ( | bool | is_empty_mass_spectrum | ) |
Definition at line 159 of file qualifiedmassspectrum.cpp.
References m_isEmptyMassSpectrum.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::readSpectrumCollection().
void pappso::QualifiedMassSpectrum::setMassSpectrumId | ( | const MassSpectrumId & | iD | ) |
Set the MassSpectrumId.
Definition at line 120 of file qualifiedmassspectrum.cpp.
References m_massSpectrumId.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), and pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum().
void pappso::QualifiedMassSpectrum::setMassSpectrumSPtr | ( | MassSpectrumSPtr | massSpectrum | ) |
Set the MassSpectrumSPtr.
Definition at line 136 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().
void pappso::QualifiedMassSpectrum::setMsLevel | ( | uint | ms_level | ) |
Set the mass spectrum level.
Definition at line 206 of file qualifiedmassspectrum.cpp.
References m_msLevel.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().
void pappso::QualifiedMassSpectrum::setParameterValue | ( | QualifiedMassSpectrumParameter | parameter, |
const QVariant & | value | ||
) |
Definition at line 362 of file qualifiedmassspectrum.cpp.
References m_paramsMap.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), and pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId().
void pappso::QualifiedMassSpectrum::setPrecursorCharge | ( | uint | precursor_charge | ) |
Set the precursor charge.
Definition at line 174 of file qualifiedmassspectrum.cpp.
References m_precursorCharge.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
void pappso::QualifiedMassSpectrum::setPrecursorIntensity | ( | pappso_double | intensity | ) |
Set the intensity of the precursor ion.
Definition at line 293 of file qualifiedmassspectrum.cpp.
References m_precursorIntensity.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
void pappso::QualifiedMassSpectrum::setPrecursorMz | ( | pappso_double | precursor_mz | ) |
Set the precursor m/z ratio.
Definition at line 190 of file qualifiedmassspectrum.cpp.
References m_precursorMz.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
void pappso::QualifiedMassSpectrum::setPrecursorNativeId | ( | const QString & | native_id | ) |
Set the scan native id of the precursor ion.
Definition at line 280 of file qualifiedmassspectrum.cpp.
References m_precursorNativeId.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
void pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex | ( | std::size_t | precursor_scan_num | ) |
Set the scan number of the precursor ion.
Definition at line 265 of file qualifiedmassspectrum.cpp.
References m_precursorSpectrumIndex.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr().
void pappso::QualifiedMassSpectrum::setRtInSeconds | ( | pappso_double | rt | ) |
Set the retention time in seconds.
Definition at line 222 of file qualifiedmassspectrum.cpp.
References m_rt.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), and pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile().
std::size_t pappso::QualifiedMassSpectrum::size | ( | ) | const |
Definition at line 308 of file qualifiedmassspectrum.cpp.
References msp_massSpectrum.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), and pappso::MzxmlOutput::writeQualifiedMassSpectrum().
QString pappso::QualifiedMassSpectrum::toString | ( | ) | const |
Definition at line 319 of file qualifiedmassspectrum.cpp.
References getRtInMinutes(), m_dt, m_massSpectrumId, m_msLevel, m_precursorCharge, m_precursorIntensity, m_precursorMz, 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 146 of file qualifiedmassspectrum.h.
Referenced by getDtInMilliSeconds(), operator=(), setDtInMilliSeconds(), and toString().
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Definition at line 137 of file qualifiedmassspectrum.h.
Referenced by isEmptyMassSpectrum(), operator=(), and setEmptyMassSpectrum().
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Id of the mass spectrum.
Definition at line 135 of file qualifiedmassspectrum.h.
Referenced by getMassSpectrumId(), operator=(), setMassSpectrumId(), and toString().
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Mass spectrometry level of this mass spectrum.
Definition at line 140 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 168 of file qualifiedmassspectrum.h.
Referenced by getParameterValue(), operator=(), and setParameterValue().
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Charge of the precursor that was fragmented to yield this mass spectrum.
Definition at line 161 of file qualifiedmassspectrum.h.
Referenced by getPrecursorCharge(), operator=(), setPrecursorCharge(), and toString().
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Intensity of the precursor that was fragmented to yield this mass spectrum.
Definition at line 165 of file qualifiedmassspectrum.h.
Referenced by getPrecursorIntensity(), operator=(), setPrecursorIntensity(), and toString().
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m/z ratio of the precursor that was fragmented to yield this mass spectrum.
Definition at line 158 of file qualifiedmassspectrum.h.
Referenced by getPrecursorMz(), operator=(), setPrecursorMz(), and toString().
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Native XML id of the spectrum relative to the mz data native file.
Definition at line 154 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 150 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 143 of file qualifiedmassspectrum.h.
Referenced by getRtInMinutes(), getRtInSeconds(), operator=(), and setRtInSeconds().
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Shared pointer to the mass spectrum.
Definition at line 132 of file qualifiedmassspectrum.h.
Referenced by cloneMassSpectrumSPtr(), getMassSpectrumCstSPtr(), getMassSpectrumSPtr(), operator=(), setMassSpectrumSPtr(), size(), and toString().