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 |
bool | m_applySavGolFilter = false |
pappso::SavGolParams | m_savGolParams |
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 85 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 | ||
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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(), pappso::SavGolParams::initialize(), m_savGolParams, and mp_precision.
pappso::MzIntegrationParams::MzIntegrationParams | ( | const pappso::SavGolParams & | savGolParams | ) |
Definition at line 113 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), m_binningType, mp_precision, pappso::NONE, and setSavGolParams().
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Definition at line 122 of file mzintegrationparams.cpp.
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Definition at line 451 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 391 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 420 of file mzintegrationparams.cpp.
References pappso::ARBITRARY, createArbitraryBins(), createDataBasedBins(), pappso::DATA_BASED, m_binningType, and pappso::NONE.
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Definition at line 606 of file mzintegrationparams.cpp.
References m_decimalPlaces, m_smallestMz, and pappso::MassSpectrum::sortMz().
Referenced by createBins().
BinningType pappso::MzIntegrationParams::getBinningType | ( | ) | const |
Definition at line 203 of file mzintegrationparams.cpp.
References m_binningType.
int pappso::MzIntegrationParams::getDecimalPlaces | ( | ) | const |
Definition at line 216 of file mzintegrationparams.cpp.
References m_decimalPlaces.
pappso::pappso_double pappso::MzIntegrationParams::getGreatestMz | ( | ) | const |
Definition at line 191 of file mzintegrationparams.cpp.
References m_greatestMz.
double pappso::MzIntegrationParams::getMzShift | ( | ) | const |
Definition at line 273 of file mzintegrationparams.cpp.
References m_mzShift.
pappso::PrecisionPtr pappso::MzIntegrationParams::getPrecision | ( | ) | const |
Definition at line 231 of file mzintegrationparams.cpp.
References mp_precision.
pappso::SavGolParams pappso::MzIntegrationParams::getSavGolParams | ( | ) | const |
Definition at line 317 of file mzintegrationparams.cpp.
References m_savGolParams.
pappso::pappso_double pappso::MzIntegrationParams::getSmallestMz | ( | ) | const |
Definition at line 170 of file mzintegrationparams.cpp.
References m_smallestMz.
bool pappso::MzIntegrationParams::hasValidMzRange | ( | ) | const |
bool pappso::MzIntegrationParams::isApplyMzShift | ( | ) | const |
Definition at line 245 of file mzintegrationparams.cpp.
References m_applyMzShift.
bool pappso::MzIntegrationParams::isApplySavGolFilter | ( | ) | const |
Definition at line 287 of file mzintegrationparams.cpp.
References m_applySavGolFilter.
bool pappso::MzIntegrationParams::isRemoveZeroValDataPoints | ( | ) | const |
Definition at line 259 of file mzintegrationparams.cpp.
References m_removeZeroValDataPoints.
bool pappso::MzIntegrationParams::isValid | ( | ) | const |
Definition at line 349 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 128 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getPpmInstance(), m_applyMzShift, m_applySavGolFilter, m_binningType, m_decimalPlaces, m_greatestMz, m_mzShift, m_removeZeroValDataPoints, m_savGolParams, m_smallestMz, mp_precision, and setSavGolParams().
void pappso::MzIntegrationParams::reset | ( | ) |
Reset the instance to default values.
Definition at line 325 of file mzintegrationparams.cpp.
References pappso::SavGolParams::convolveWithNr, pappso::PrecisionFactory::getPpmInstance(), pappso::SavGolParams::lD, pappso::SavGolParams::m, m_applyMzShift, m_applySavGolFilter, m_binningType, m_greatestMz, m_mzShift, m_removeZeroValDataPoints, m_savGolParams, m_smallestMz, mp_precision, pappso::SavGolParams::nL, pappso::NONE, and pappso::SavGolParams::nR.
void pappso::MzIntegrationParams::setApplyMzShift | ( | bool | applyMzShift | ) |
Definition at line 238 of file mzintegrationparams.cpp.
References m_applyMzShift.
void pappso::MzIntegrationParams::setApplySavGolFilter | ( | bool | applySavGolFilter | ) |
Definition at line 280 of file mzintegrationparams.cpp.
References m_applySavGolFilter.
void pappso::MzIntegrationParams::setBinningType | ( | BinningType | binningType | ) |
Definition at line 197 of file mzintegrationparams.cpp.
References m_binningType.
void pappso::MzIntegrationParams::setDecimalPlaces | ( | int | decimal_places | ) |
Definition at line 209 of file mzintegrationparams.cpp.
References m_decimalPlaces.
void pappso::MzIntegrationParams::setGreatestMz | ( | pappso::pappso_double | value | ) |
Definition at line 177 of file mzintegrationparams.cpp.
References m_greatestMz.
void pappso::MzIntegrationParams::setMzShift | ( | double | value | ) |
Definition at line 266 of file mzintegrationparams.cpp.
References m_mzShift.
void pappso::MzIntegrationParams::setPrecision | ( | pappso::PrecisionPtr | precisionPtr | ) |
Definition at line 222 of file mzintegrationparams.cpp.
References pappso::PrecisionFactory::getDaltonInstance(), and mp_precision.
void pappso::MzIntegrationParams::setRemoveZeroValDataPoints | ( | bool | removeOrNot = true | ) |
Definition at line 252 of file mzintegrationparams.cpp.
References m_removeZeroValDataPoints.
void pappso::MzIntegrationParams::setSavGolParams | ( | const pappso::SavGolParams & | params | ) |
Definition at line 306 of file mzintegrationparams.cpp.
References pappso::SavGolParams::convolveWithNr, pappso::SavGolParams::lD, pappso::SavGolParams::m, m_savGolParams, pappso::SavGolParams::nL, and pappso::SavGolParams::nR.
void pappso::MzIntegrationParams::setSavGolParams | ( | int | nL = 15 , |
int | nR = 15 , |
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int | m = 4 , |
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int | lD = 0 , |
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bool | convolveWithNr = false |
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Definition at line 294 of file mzintegrationparams.cpp.
References pappso::SavGolParams::convolveWithNr, pappso::SavGolParams::lD, pappso::SavGolParams::m, m_savGolParams, pappso::SavGolParams::nL, and pappso::SavGolParams::nR.
Referenced by MzIntegrationParams(), and operator=().
void pappso::MzIntegrationParams::setSmallestMz | ( | pappso::pappso_double | value | ) |
Definition at line 156 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 721 of file mzintegrationparams.cpp.
References pappso::ARBITRARY, pappso::binningTypeMap, pappso::SavGolParams::convolveWithNr, pappso::PrecisionBase::getNominal(), pappso::SavGolParams::lD, pappso::SavGolParams::m, m_applyMzShift, m_applySavGolFilter, m_binningType, m_decimalPlaces, m_greatestMz, m_mzShift, m_removeZeroValDataPoints, m_savGolParams, m_smallestMz, mp_precision, pappso::SavGolParams::nL, pappso::SavGolParams::nR, and pappso::PrecisionBase::toString().
void pappso::MzIntegrationParams::updateGreatestMz | ( | pappso::pappso_double | value | ) |
Definition at line 184 of file mzintegrationparams.cpp.
References m_greatestMz.
void pappso::MzIntegrationParams::updateSmallestMz | ( | pappso::pappso_double | value | ) |
Definition at line 163 of file mzintegrationparams.cpp.
References m_smallestMz.
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Definition at line 172 of file mzintegrationparams.h.
Referenced by isApplyMzShift(), operator=(), reset(), setApplyMzShift(), and toString().
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Definition at line 176 of file mzintegrationparams.h.
Referenced by isApplySavGolFilter(), operator=(), reset(), setApplySavGolFilter(), and toString().
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Definition at line 164 of file mzintegrationparams.h.
Referenced by MzIntegrationParams(), createBins(), getBinningType(), isValid(), operator=(), reset(), setBinningType(), and toString().
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Definition at line 166 of file mzintegrationparams.h.
Referenced by createArbitraryBins(), createDataBasedBins(), getDecimalPlaces(), operator=(), setDecimalPlaces(), and toString().
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Definition at line 162 of file mzintegrationparams.h.
Referenced by createArbitraryBins(), getGreatestMz(), hasValidMzRange(), isValid(), operator=(), reset(), setGreatestMz(), toString(), and updateGreatestMz().
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Definition at line 173 of file mzintegrationparams.h.
Referenced by getMzShift(), operator=(), reset(), setMzShift(), and toString().
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Definition at line 174 of file mzintegrationparams.h.
Referenced by isRemoveZeroValDataPoints(), operator=(), reset(), setRemoveZeroValDataPoints(), and toString().
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Definition at line 177 of file mzintegrationparams.h.
Referenced by MzIntegrationParams(), getSavGolParams(), operator=(), reset(), setSavGolParams(), and toString().
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Definition at line 158 of file mzintegrationparams.h.
Referenced by createArbitraryBins(), createDataBasedBins(), getSmallestMz(), hasValidMzRange(), isValid(), operator=(), reset(), setSmallestMz(), toString(), and updateSmallestMz().
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Definition at line 170 of file mzintegrationparams.h.
Referenced by MzIntegrationParams(), createArbitraryBins(), getPrecision(), isValid(), operator=(), reset(), setPrecision(), and toString().