libpappsomspp
Library for mass spectrometry
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A simple container of DataPoint instances. More...
#include <trace.h>
Public Member Functions | |
Trace () | |
Trace (const QString &text) | |
Trace (const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector) | |
Trace (const std::vector< std::pair< pappso_double, pappso_double > > &dataPoints) | |
Trace (const std::vector< DataPoint > &dataPoints) | |
Trace (const std::vector< DataPoint > &&dataPoints) | |
Trace (const MapTrace &map_trace) | |
Trace (const Trace &other) | |
Trace (const Trace &&other) | |
virtual | ~Trace () |
size_t | initialize (const std::vector< pappso_double > &xVector, const std::vector< pappso_double > &yVector) |
size_t | initialize (const QString &x_text, const QString &y_text) |
size_t | initialize (const QString &space_sep_text) |
size_t | initialize (const Trace &other) |
size_t | initialize (const std::map< pappso_double, pappso_double > &map) |
virtual Trace & | operator= (const Trace &x) |
virtual Trace & | operator= (Trace &&x) |
TraceSPtr | makeTraceSPtr () const |
TraceCstSPtr | makeTraceCstSPtr () const |
size_t | append (const DataPoint &data_point) |
appends a datapoint and return new size | |
std::vector< pappso_double > | xValues () const |
std::vector< pappso_double > | yValues () const |
std::map< pappso_double, pappso_double > | toMap () const |
DataPoint | containsX (pappso_double value, PrecisionPtr precision_p=nullptr) const |
const DataPoint & | minXDataPoint () const |
const DataPoint & | maxXDataPoint () const |
const DataPoint & | minYDataPoint () const |
const DataPoint & | maxYDataPoint () const |
pappso_double | minX () const |
pappso_double | maxX () const |
pappso_double | minY () const |
pappso_double | maxY () const |
pappso_double | maxY (double mzStart, double mzEnd) const |
pappso_double | sumY () const |
pappso_double | sumY (double mzStart, double mzEnd) const |
void | sort (SortType sort_type, SortOrder sort_order=SortOrder::ascending) |
void | sortX (SortOrder sort_order=SortOrder::ascending) |
void | sortY (SortOrder sort_order=SortOrder::ascending) |
void | unique () |
std::size_t | removeZeroYDataPoints () |
virtual Trace & | filter (const FilterInterface &filter) final |
apply a filter on this trace | |
QString | toString () const |
QByteArray | xAsBase64Encoded () const |
QByteArray | yAsBase64Encoded () const |
std::vector< DataPoint >::const_iterator | dataPointCstIteratorWithX (pappso_double value) const |
find datapoint with exactly x value | |
Protected Member Functions | |
std::size_t | dataPointIndexWithX (pappso_double value) const |
std::vector< DataPoint >::iterator | dataPointIteratorWithX (pappso_double value) |
Friends | |
class | TraceCombiner |
class | TraceMinusCombiner |
class | TracePlusCombiner |
class | MassSpectrumCombinerInterface |
pappso::Trace::Trace | ( | const QString & | text | ) |
Definition at line 449 of file trace.cpp.
References initialize().
pappso::Trace::Trace | ( | const std::vector< pappso_double > & | xVector, |
const std::vector< pappso_double > & | yVector | ||
) |
Definition at line 455 of file trace.cpp.
References initialize().
pappso::Trace::Trace | ( | const std::vector< std::pair< pappso_double, pappso_double > > & | dataPoints | ) |
Definition at line 522 of file trace.cpp.
References sortX().
pappso::Trace::Trace | ( | const std::vector< DataPoint > & | dataPoints | ) |
pappso::Trace::Trace | ( | const std::vector< DataPoint > && | dataPoints | ) |
Definition at line 549 of file trace.cpp.
References sortX().
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explicit |
pappso::Trace::Trace | ( | const Trace & | other | ) |
pappso::Trace::Trace | ( | const Trace && | other | ) |
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virtual |
size_t pappso::Trace::append | ( | const DataPoint & | data_point | ) |
appends a datapoint and return new size
Definition at line 648 of file trace.cpp.
Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram(), initialize(), initialize(), and pappso::MapTrace::toString().
DataPoint pappso::Trace::containsX | ( | pappso_double | value, |
PrecisionPtr | precision_p = nullptr |
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) | const |
Definition at line 800 of file trace.cpp.
References pappso::PrecisionBase::delta(), and pappso::DataPoint::x.
std::vector< DataPoint >::const_iterator pappso::Trace::dataPointCstIteratorWithX | ( | pappso_double | value | ) | const |
find datapoint with exactly x value
Definition at line 775 of file trace.cpp.
References pappso::DataPoint::x.
Referenced by dataPointIndexWithX().
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protected |
Return a reference to the DataPoint instance that has its y member equal to value
.
Definition at line 787 of file trace.cpp.
References dataPointCstIteratorWithX().
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protected |
Definition at line 763 of file trace.cpp.
References pappso::DataPoint::x.
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finalvirtual |
apply a filter on this trace
filter | to process the signal |
Definition at line 1210 of file trace.cpp.
References filter().
Referenced by pappso::MsRunRetentionTime< T >::align(), filter(), pappso::FilterSuiteString::filter(), pappso::FilterSuite::filter(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), and pappso::MassSpectrum::massSpectrumFilter().
size_t pappso::Trace::initialize | ( | const QString & | space_sep_text | ) |
Definition at line 463 of file trace.cpp.
size_t pappso::Trace::initialize | ( | const QString & | x_text, |
const QString & | y_text | ||
) |
Definition at line 495 of file trace.cpp.
References append().
size_t pappso::Trace::initialize | ( | const std::map< pappso_double, pappso_double > & | map | ) |
Definition at line 621 of file trace.cpp.
size_t pappso::Trace::initialize | ( | const std::vector< pappso_double > & | xVector, |
const std::vector< pappso_double > & | yVector | ||
) |
Definition at line 588 of file trace.cpp.
References sortX().
size_t pappso::Trace::initialize | ( | const Trace & | other | ) |
TraceCstSPtr pappso::Trace::makeTraceCstSPtr | ( | ) | const |
TraceSPtr pappso::Trace::makeTraceSPtr | ( | ) | const |
pappso_double pappso::Trace::maxX | ( | ) | const |
Definition at line 1002 of file trace.cpp.
References maxXDataPoint(), and pappso::DataPoint::x.
const DataPoint & pappso::Trace::maxXDataPoint | ( | ) | const |
Definition at line 938 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by maxX().
pappso_double pappso::Trace::maxY | ( | ) | const |
Definition at line 1016 of file trace.cpp.
References maxYDataPoint(), and pappso::DataPoint::y.
Referenced by pappso::QCPSpectrum::setSpectrumP().
pappso_double pappso::Trace::maxY | ( | double | mzStart, |
double | mzEnd | ||
) | const |
Definition at line 1055 of file trace.cpp.
References pappso::findFirstEqualOrGreaterX(), and pappso::findFirstGreaterX().
const DataPoint & pappso::Trace::maxYDataPoint | ( | ) | const |
Definition at line 976 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by pappso::QCPXic::addXicP(), pappso::flooredLocalMaxima(), pappso::MassSpectrum::maxIntensityDataPoint(), and maxY().
pappso_double pappso::Trace::minX | ( | ) | const |
Definition at line 995 of file trace.cpp.
References minXDataPoint(), and pappso::DataPoint::x.
const DataPoint & pappso::Trace::minXDataPoint | ( | ) | const |
Definition at line 919 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by minX().
pappso_double pappso::Trace::minY | ( | ) | const |
Definition at line 1009 of file trace.cpp.
References minYDataPoint(), and pappso::DataPoint::y.
const DataPoint & pappso::Trace::minYDataPoint | ( | ) | const |
Definition at line 957 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by pappso::MassSpectrum::minIntensityDataPoint(), and minY().
std::size_t pappso::Trace::removeZeroYDataPoints | ( | ) |
Definition at line 1126 of file trace.cpp.
References pappso::Utils::almostEqual().
void pappso::Trace::sort | ( | SortType | sort_type, |
SortOrder | sort_order = SortOrder::ascending |
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) |
void pappso::Trace::sortX | ( | SortOrder | sort_order = SortOrder::ascending | ) |
Definition at line 1086 of file trace.cpp.
References pappso::a, pappso::ascending, and pappso::b.
Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), Trace(), Trace(), Trace(), pappso::MsRunRetentionTime< T >::align(), pappso::TimsFrame::cumulateScansToTrace(), pappso::FilterChargeDeconvolution::filter(), pappso::FilterComplementIonEnhancer::filter(), pappso::FilterMzExclusion::filter(), pappso::FilterGreatestYperWindow::filter(), pappso::FilterPeakDelta::filter(), pappso::FilterRemoveC13::filter(), pappso::FilterTriangle::filter(), pappso::MsRunRetentionTime< T >::getCommonDeltaRt(), pappso::PsmFeatures::getIonIsotopeLinearRegression(), pappso::TimsFrameBase::getTraceFromCumulatedScans(), pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid(), initialize(), sort(), pappso::Xic::sortByRetentionTime(), and pappso::MassSpectrum::sortMz().
void pappso::Trace::sortY | ( | SortOrder | sort_order = SortOrder::ascending | ) |
Definition at line 1100 of file trace.cpp.
References pappso::a, pappso::ascending, and pappso::b.
Referenced by pappso::FilterChargeDeconvolution::filter(), pappso::FilterMzExclusion::filter(), and sort().
pappso_double pappso::Trace::sumY | ( | ) | const |
Definition at line 1023 of file trace.cpp.
References pappso::sum, and pappso::DataPoint::y.
Referenced by pappso::PsmFeatures::setPeptideSpectrumCharge(), pappso::MassSpectrum::tic(), and pappso::MassSpectrum::totalIonCurrent().
pappso_double pappso::Trace::sumY | ( | double | mzStart, |
double | mzEnd | ||
) | const |
Definition at line 1045 of file trace.cpp.
References pappso::findFirstEqualOrGreaterX(), pappso::findFirstGreaterX(), and pappso::sumYTrace().
std::map< pappso_double, pappso_double > pappso::Trace::toMap | ( | ) | const |
Definition at line 716 of file trace.cpp.
QString pappso::Trace::toString | ( | ) | const |
Definition at line 1153 of file trace.cpp.
Referenced by pappso::FilterSuiteString::filter(), and pappso::FilterSuiteString::toString().
void pappso::Trace::unique | ( | ) |
Definition at line 1114 of file trace.cpp.
References pappso::a, pappso::b, and pappso::last.
Referenced by pappso::MsRunRetentionTime< T >::getCommonDeltaRt().
QByteArray pappso::Trace::xAsBase64Encoded | ( | ) | const |
Definition at line 1168 of file trace.cpp.
std::vector< pappso_double > pappso::Trace::xValues | ( | ) | const |
Definition at line 688 of file trace.cpp.
Referenced by pappso::BaseTracePlotWidget::addTrace().
QByteArray pappso::Trace::yAsBase64Encoded | ( | ) | const |
Definition at line 1189 of file trace.cpp.
std::vector< pappso_double > pappso::Trace::yValues | ( | ) | const |
Definition at line 702 of file trace.cpp.
Referenced by pappso::BaseTracePlotWidget::addTrace(), and pappso::MsRunRetentionTime< T >::align().
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