libpappsomspp
Library for mass spectrometry
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The MzIntegrationParams class provides the parameters definining how m/z ! More...
#include <mzintegrationparams.h>
Private Member Functions | |
std::vector< double > | createArbitraryBins () |
std::vector< double > | createDataBasedBins (pappso::MassSpectrumCstSPtr massSpectrum) |
Private Attributes | |
pappso::pappso_double | m_smallestMz = std::numeric_limits<double>::max() |
pappso::pappso_double | m_greatestMz = std::numeric_limits<double>::min() |
BinningType | m_binningType = BinningType::NONE |
int | m_decimalPlaces = -1 |
pappso::PrecisionPtr | mp_precision |
bool | m_applyMzShift = false |
pappso::pappso_double | m_mzShift = 0 |
bool | m_removeZeroValDataPoints = true |
The MzIntegrationParams class provides the parameters definining how m/z !
Depending on the various mass spectrometer vendors, the mass spectrometry data files are structured in different ways and the software for mass data format conversion from raw files to mzML or mzXML produce mass data characterized by different behaviours.
The different characteristics of mass spectrometry data set are:
The size of the various mass spectra in the file is constant or variable;
The first m/z value of the various spectra is identical or not (that is, the spectra are root in a constant or variable root m/z value);
The m/z delta between two consecutive m/z values of a given spectrum are constant or variable;
The spectra contain or not 0-value m/z data points;
Definition at line 84 of file mzintegrationparams.h.
pappso::MzIntegrationParams::MzIntegrationParams | ( | ) |
Definition at line 66 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), m_binningType, mp_precision, and pappso::NONE.
pappso::MzIntegrationParams::MzIntegrationParams | ( | pappso::pappso_double | minMz, |
pappso::pappso_double | maxMz, | ||
BinningType | binningType, | ||
int | decimalPlaces, | ||
pappso::PrecisionPtr | precisionPtr, | ||
bool | applyMzShift, | ||
pappso::pappso_double | mzShift, | ||
bool | removeZeroValDataPoints | ||
) |
Definition at line 73 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), and mp_precision.
pappso::MzIntegrationParams::MzIntegrationParams | ( | const MzIntegrationParams & | other | ) |
Definition at line 95 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), and mp_precision.
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Definition at line 110 of file mzintegrationparams.cpp.
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Definition at line 383 of file mzintegrationparams.cpp.
References pappso::PrecisionBase::delta(), m_decimalPlaces, m_greatestMz, m_smallestMz, mp_precision, and pappso::Utils::zeroDecimalsInValue().
Referenced by createBins().
std::vector< double > pappso::MzIntegrationParams::createBins | ( | ) |
Definition at line 323 of file mzintegrationparams.cpp.
References pappso::ARBITRARY, createArbitraryBins(), pappso::DATA_BASED, m_binningType, and pappso::NONE.
std::vector< double > pappso::MzIntegrationParams::createBins | ( | pappso::MassSpectrumCstSPtr | mass_spectrum_csp | ) |
Definition at line 352 of file mzintegrationparams.cpp.
References pappso::ARBITRARY, createArbitraryBins(), createDataBasedBins(), pappso::DATA_BASED, m_binningType, and pappso::NONE.
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Definition at line 543 of file mzintegrationparams.cpp.
References m_decimalPlaces, m_smallestMz, and pappso::MassSpectrum::sortMz().
Referenced by createBins().
BinningType pappso::MzIntegrationParams::getBinningType | ( | ) | const |
Definition at line 187 of file mzintegrationparams.cpp.
References m_binningType.
int pappso::MzIntegrationParams::getDecimalPlaces | ( | ) | const |
Definition at line 200 of file mzintegrationparams.cpp.
References m_decimalPlaces.
pappso::pappso_double pappso::MzIntegrationParams::getGreatestMz | ( | ) | const |
Definition at line 175 of file mzintegrationparams.cpp.
References m_greatestMz.
double pappso::MzIntegrationParams::getMzShift | ( | ) | const |
Definition at line 257 of file mzintegrationparams.cpp.
References m_mzShift.
pappso::PrecisionPtr pappso::MzIntegrationParams::getPrecision | ( | ) | const |
Definition at line 215 of file mzintegrationparams.cpp.
References mp_precision.
pappso::pappso_double pappso::MzIntegrationParams::getSmallestMz | ( | ) | const |
Definition at line 154 of file mzintegrationparams.cpp.
References m_smallestMz.
bool pappso::MzIntegrationParams::hasValidMzRange | ( | ) | const |
Definition at line 315 of file mzintegrationparams.cpp.
References m_greatestMz, and m_smallestMz.
bool pappso::MzIntegrationParams::isApplyMzShift | ( | ) | const |
Definition at line 229 of file mzintegrationparams.cpp.
References m_applyMzShift.
bool pappso::MzIntegrationParams::isRemoveZeroValDataPoints | ( | ) | const |
Definition at line 243 of file mzintegrationparams.cpp.
References m_removeZeroValDataPoints.
bool pappso::MzIntegrationParams::isValid | ( | ) | const |
Definition at line 281 of file mzintegrationparams.cpp.
References m_binningType, m_greatestMz, m_smallestMz, mp_precision, and pappso::NONE.
MzIntegrationParams & pappso::MzIntegrationParams::operator= | ( | const MzIntegrationParams & | other | ) |
Definition at line 116 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), m_applyMzShift, m_binningType, m_decimalPlaces, m_greatestMz, m_mzShift, m_removeZeroValDataPoints, m_smallestMz, and mp_precision.
void pappso::MzIntegrationParams::reset | ( | ) |
Reset the instance to default values.
Definition at line 265 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), m_applyMzShift, m_binningType, m_greatestMz, m_mzShift, m_removeZeroValDataPoints, m_smallestMz, mp_precision, and pappso::NONE.
void pappso::MzIntegrationParams::setApplyMzShift | ( | bool | applyMzShift | ) |
Definition at line 222 of file mzintegrationparams.cpp.
References m_applyMzShift.
void pappso::MzIntegrationParams::setBinningType | ( | BinningType | binningType | ) |
Definition at line 181 of file mzintegrationparams.cpp.
References m_binningType.
void pappso::MzIntegrationParams::setDecimalPlaces | ( | int | decimal_places | ) |
Definition at line 193 of file mzintegrationparams.cpp.
References m_decimalPlaces.
void pappso::MzIntegrationParams::setGreatestMz | ( | pappso::pappso_double | value | ) |
Definition at line 161 of file mzintegrationparams.cpp.
References m_greatestMz.
void pappso::MzIntegrationParams::setMzShift | ( | double | value | ) |
Definition at line 250 of file mzintegrationparams.cpp.
References m_mzShift.
void pappso::MzIntegrationParams::setPrecision | ( | pappso::PrecisionPtr | precisionPtr | ) |
Definition at line 206 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getDaltonInstance(), and mp_precision.
void pappso::MzIntegrationParams::setRemoveZeroValDataPoints | ( | bool | removeOrNot = true | ) |
Definition at line 236 of file mzintegrationparams.cpp.
References m_removeZeroValDataPoints.
void pappso::MzIntegrationParams::setSmallestMz | ( | pappso::pappso_double | value | ) |
Definition at line 140 of file mzintegrationparams.cpp.
References m_smallestMz.
QString pappso::MzIntegrationParams::toString | ( | int | offset = 0 , |
const QString & | spacer = QString() |
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) | const |
Definition at line 658 of file mzintegrationparams.cpp.
References pappso::ARBITRARY, pappso::binningTypeMap, pappso::PrecisionBase::getNominal(), m_applyMzShift, m_binningType, m_decimalPlaces, m_greatestMz, m_mzShift, m_removeZeroValDataPoints, m_smallestMz, mp_precision, and pappso::PrecisionBase::toString().
void pappso::MzIntegrationParams::updateGreatestMz | ( | pappso::pappso_double | value | ) |
Definition at line 168 of file mzintegrationparams.cpp.
References m_greatestMz.
void pappso::MzIntegrationParams::updateSmallestMz | ( | pappso::pappso_double | value | ) |
Definition at line 147 of file mzintegrationparams.cpp.
References m_smallestMz.
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Definition at line 159 of file mzintegrationparams.h.
Referenced by isApplyMzShift(), operator=(), reset(), setApplyMzShift(), and toString().
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Definition at line 151 of file mzintegrationparams.h.
Referenced by MzIntegrationParams(), createBins(), getBinningType(), isValid(), operator=(), reset(), setBinningType(), and toString().
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Definition at line 153 of file mzintegrationparams.h.
Referenced by createArbitraryBins(), createDataBasedBins(), getDecimalPlaces(), operator=(), setDecimalPlaces(), and toString().
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Definition at line 149 of file mzintegrationparams.h.
Referenced by createArbitraryBins(), getGreatestMz(), hasValidMzRange(), isValid(), operator=(), reset(), setGreatestMz(), toString(), and updateGreatestMz().
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Definition at line 160 of file mzintegrationparams.h.
Referenced by getMzShift(), operator=(), reset(), setMzShift(), and toString().
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Definition at line 161 of file mzintegrationparams.h.
Referenced by isRemoveZeroValDataPoints(), operator=(), reset(), setRemoveZeroValDataPoints(), and toString().
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Definition at line 145 of file mzintegrationparams.h.
Referenced by createArbitraryBins(), createDataBasedBins(), getSmallestMz(), hasValidMzRange(), isValid(), operator=(), reset(), setSmallestMz(), toString(), and updateSmallestMz().
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Definition at line 157 of file mzintegrationparams.h.
Referenced by MzIntegrationParams(), createArbitraryBins(), getPrecision(), isValid(), operator=(), reset(), setPrecision(), and toString().