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 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 More... | |
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 & | minYDataPoint () const |
const DataPoint & | maxYDataPoint () 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 | sortX () |
void | sortY () |
void | unique () |
std::size_t | removeZeroYDataPoints () |
virtual Trace & | filter (const FilterInterface &filter) final |
apply a filter on this trace More... | |
QString | toString () const |
std::vector< DataPoint >::const_iterator | dataPointCstIteratorWithX (pappso_double value) const |
find datapoint with exactly x value More... | |
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 488 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 515 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 614 of file trace.cpp.
Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram(), and initialize().
DataPoint pappso::Trace::containsX | ( | pappso_double | value, |
PrecisionPtr | precision_p = nullptr |
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) | const |
Definition at line 766 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 741 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 753 of file trace.cpp.
References dataPointCstIteratorWithX().
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protected |
Definition at line 729 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 1059 of file trace.cpp.
References filter().
Referenced by pappso::MsRunRetentionTime< T >::align(), filter(), pappso::FilterSuiteString::filter(), pappso::FilterSuite::filter(), 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 std::map< pappso_double, pappso_double > & | map | ) |
Definition at line 587 of file trace.cpp.
size_t pappso::Trace::initialize | ( | const std::vector< pappso_double > & | xVector, |
const std::vector< pappso_double > & | yVector | ||
) |
Definition at line 554 of file trace.cpp.
References sortX().
Referenced by Trace().
size_t pappso::Trace::initialize | ( | const Trace & | other | ) |
TraceCstSPtr pappso::Trace::makeTraceCstSPtr | ( | ) | const |
TraceSPtr pappso::Trace::makeTraceSPtr | ( | ) | const |
pappso_double pappso::Trace::maxY | ( | ) | const |
Definition at line 930 of file trace.cpp.
References maxYDataPoint(), and pappso::DataPoint::y.
pappso_double pappso::Trace::maxY | ( | double | mzStart, |
double | mzEnd | ||
) | const |
Definition at line 969 of file trace.cpp.
References pappso::findFirstEqualOrGreaterX(), and pappso::findFirstGreaterX().
const DataPoint & pappso::Trace::maxYDataPoint | ( | ) | const |
Definition at line 904 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by pappso::flooredLocalMaxima(), pappso::MassSpectrum::maxIntensityDataPoint(), and maxY().
pappso_double pappso::Trace::minY | ( | ) | const |
Definition at line 923 of file trace.cpp.
References minYDataPoint(), and pappso::DataPoint::y.
const DataPoint & pappso::Trace::minYDataPoint | ( | ) | const |
Definition at line 885 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 1015 of file trace.cpp.
References pappso::Utils::almostEqual().
void pappso::Trace::sortX | ( | ) |
Definition at line 987 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), Trace(), pappso::MsRunRetentionTime< T >::align(), pappso::TimsFrame::cumulateScanToTrace(), pappso::FilterChargeDeconvolution::filter(), pappso::FilterComplementIonEnhancer::filter(), pappso::FilterMzExclusion::filter(), pappso::FilterGreatestYperWindow::filter(), pappso::FilterRemoveC13::filter(), pappso::FilterTriangle::filter(), pappso::MsRunRetentionTime< T >::getCommonDeltaRt(), pappso::TimsFrameBase::getTraceFromCumulatedScans(), pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid(), initialize(), pappso::Xic::sortByRetentionTime(), and pappso::MassSpectrum::sortMz().
void pappso::Trace::sortY | ( | ) |
Definition at line 995 of file trace.cpp.
References pappso::a, and pappso::b.
Referenced by pappso::FilterChargeDeconvolution::filter(), and pappso::FilterMzExclusion::filter().
pappso_double pappso::Trace::sumY | ( | ) | const |
Definition at line 937 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 959 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 682 of file trace.cpp.
QString pappso::Trace::toString | ( | ) | const |
Definition at line 1042 of file trace.cpp.
Referenced by pappso::FilterSuiteString::filter(), and pappso::FilterSuiteString::toString().
void pappso::Trace::unique | ( | ) |
Definition at line 1003 of file trace.cpp.
References pappso::a, pappso::b, and pappso::last.
Referenced by pappso::MsRunRetentionTime< T >::getCommonDeltaRt().
std::vector< pappso_double > pappso::Trace::xValues | ( | ) | const |
Definition at line 654 of file trace.cpp.
Referenced by pappso::BaseTracePlotWidget::addTrace().
std::vector< pappso_double > pappso::Trace::yValues | ( | ) | const |
Definition at line 668 of file trace.cpp.
Referenced by pappso::BaseTracePlotWidget::addTrace(), and pappso::MsRunRetentionTime< T >::align().
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friend |
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friend |