libpappsomspp
Library for mass spectrometry
pappso Namespace Reference

tries to keep as much as possible monoisotopes, removing any possible C13 peaks More...

Classes

class  Aa
 
class  AaBase
 
class  AaModification
 
class  AtomNumberInterface
 
class  BaseColorMapPlotWidget
 
struct  BasePlotContext
 
class  BasePlotWidget
 
class  BaseTracePlotWidget
 
struct  ColorMapPlotConfig
 
class  DaltonPrecision
 
struct  DataPoint
 
class  DriftSpecMassSpecColorMapPlotWidget
 
class  DriftSpecTracePlotWidget
 
class  Enzyme
 
class  EnzymeProductInterface
 
class  ExceptionNotFound
 
class  ExceptionNotImplemented
 
class  ExceptionNotPossible
 
class  ExceptionOutOfRange
 
class  FastaFileIndexer
 
class  FastaFileIndexerInterface
 
class  FastaHandlerInterface
 
class  FastaOutputStream
 
class  FastaReader
 
class  FastaWriterInterface
 
class  FilterComplementIonEnhancer
 try to detect complementary ions and assign maximum intensity of both elements More...
 
class  FilterFloorY
 apply std::floor (round to lowest integer) to all Y values More...
 
class  FilterGreatestY
 keep N datapoints form the greatest intensities to the lowest More...
 
class  FilterGreatestYperWindow
 keep N datapoints form the greatest intensities to the lowest within a mass range in dalton More...
 
class  FilterHighPass
 remove datapoints below a given Y value (intensity) More...
 
class  FilterHighPassPercentage
 remove datapoints below a given intensity percentage (ratio) of the maximum intensity More...
 
class  FilterInterface
 generic interface to apply a filter on a trace More...
 
class  FilterLocalMaximum
 finds all local maxima, i.e. any point that has a greater y value than both of its neighboring points and only keep those points More...
 
class  FilterLowPass
 remove datapoints higher than a given Y value (intensity) More...
 
class  FilterMorphoAntiSpike
 anti spike filter set to zero alone values inside the window More...
 
class  FilterMorphoBackground
 compute background of a trace compute background noise on a trace More...
 
class  FilterMorphoMax
 transform the trace into its maximum over a window More...
 
class  FilterMorphoMaxMin
 transform the trace with the maximum of the minimum equivalent of the erode filter for pictures More...
 
class  FilterMorphoMean
 mean filter apply mean of y values inside the window : this results in a kind of smoothing More...
 
class  FilterMorphoMedian
 median filter apply median of y values inside the window More...
 
class  FilterMorphoMin
 transform the trace into its minimum over a window More...
 
class  FilterMorphoMinMax
 transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures More...
 
class  FilterMorphoSum
 test purpose More...
 
class  FilterMorphoWindowBase
 base class that apply a signal treatment based on a window More...
 
class  FilterOboPsiModSink
 
class  FilterOboPsiModTermAccession
 
class  FilterOboPsiModTermDiffMono
 
class  FilterOboPsiModTermLabel
 
class  FilterOboPsiModTermName
 
class  FilterPseudoCentroid
 
class  FilterRemoveC13
 
class  FilterResampleKeepGreater
 
class  FilterResampleKeepSmaller
 
class  FilterResampleKeepXRange
 
class  FilterResampleRemoveXRange
 
class  FilterRescaleY
 rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored More...
 
class  FilterRoundY
 apply std::round (round to nearest integer) to all Y values More...
 
class  FilterSavitzkyGolay
 uses Savitsky-Golay filter on trace More...
 
class  FilterScaleFactorY
 rescales Y values given a tranformation factor More...
 
class  FilterSuite
 apply a suite of filters from a vector More...
 
class  FilterTandemDeisotope
 Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests: More...
 
class  FilterTriangle
 
class  GrpExperiment
 
class  GrpGroup
 
class  GrpGroupingMonitor
 
class  GrpGroupingMonitorInterface
 
class  GrpMapPeptideToGroup
 
class  GrpMapPeptideToSubGroupSet
 
class  GrpPeptide
 
class  GrpPeptideSet
 
class  GrpProtein
 
class  GrpSubGroup
 
class  GrpSubGroupSet
 
class  Ion
 
class  IonIsotopeRatioScore
 
class  LinearRegression
 
class  MapTrace
 
class  MassDataCombinerInterface
 
struct  MassSpecTracePlotContext
 
class  MassSpecTracePlotWidget
 
class  MassSpectrum
 Class to represent a mass spectrum. More...
 
class  MassSpectrumCombiner
 
class  MassSpectrumCombinerFactory
 
class  MassSpectrumFilterGreatestItensities
 
class  MassSpectrumFilterInterface
 generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface, but some filter are only relevant if they are used on MassSpectrum using this interface means the filter can only be applied on MassSpectrum and not on Trace More...
 
class  MassSpectrumFilterResampleKeepMzRange
 
class  MassSpectrumFilterResampleRemoveMzRange
 
class  MassSpectrumId
 
class  MassSpectrumMinusCombiner
 
class  MassSpectrumPlusCombiner
 
class  MassSpectrumWidget
 
class  MgfOutput
 
class  MorpheusScore
 
class  MsFileAccessor
 
class  MsFileReader
 
class  MsRunAlignment
 
class  MsRunDataSetTree
 
class  MsRunDataSetTreeNode
 
class  MsRunDataSetTreeNodeVisitorInterface
 
class  MsRunId
 MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL) More...
 
class  MsRunReader
 base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More...
 
class  MsRunReaderScanNumberMultiMap
 provides a multimap to find quickly spectrum index from scan number More...
 
class  MsRunRetentionTime
 
struct  MsRunRetentionTimeSeamarkPoint
 
class  MsRunSimpleStatistics
 example of interface to count MS levels of all spectrum in an MSrun More...
 
class  MsRunSlice
 
class  MsRunXicExtractor
 
class  MsRunXicExtractorDisk
 
class  MsRunXicExtractorDiskBuffer
 
class  MsRunXicExtractorFactory
 factory to build different kinds of XIC extractors More...
 
class  MsRunXicExtractorInterface
 
class  MzPrecision
 
class  MzRange
 
class  MzxmlOutput
 
class  OboPsiMod
 
class  OboPsiModHandlerInterface
 
class  OboPsiModTerm
 
class  PappsoException
 
class  PeakIonIsotopeMatch
 
class  PeakIonMatch
 
class  Peptide
 
class  PeptideBuilder
 builds a peptide shared pointer from peptide string and adds fixed modifications More...
 
class  PeptideFixedModificationBuilder
 
class  PeptideFragment
 
class  PeptideFragmentIon
 
class  PeptideFragmentIonListBase
 
class  PeptideInterface
 
class  PeptideIsotopeSpectrumMatch
 
class  PeptideMethioninRemove
 potential remove Nter Methionin More...
 
class  PeptideModificatorBase
 
class  PeptideModificatorInterface
 
class  PeptideModificatorPipeline
 
class  PeptideModificatorTee
 
class  PeptideNaturalIsotope
 
class  PeptideNaturalIsotopeAverage
 
class  PeptideNaturalIsotopeList
 
class  PeptideRawFragmentMasses
 
class  PeptideSemiEnzyme
 cut a regular peptide obtained with an enzyme at any position from Nter or Cter More...
 
class  PeptideSinkInterface
 
class  PeptideSizeFilter
 filter peptide string by size More...
 
class  PeptideSpectrumMatch
 
class  PeptideSpSinkInterface
 
class  PeptideStrParser
 
class  PeptideVariableModificationBuilder
 Modify a peptide shared pointer with a variable modification on one AA. More...
 
class  PeptideVariableModificationReplacement
 
class  PpmPrecision
 
class  PrecisionBase
 
class  PrecisionFactory
 
class  PrecisionWidget
 
class  Protein
 
class  PwizMsFileReader
 
class  PwizMsRunReader
 
class  QCPSpectrum
 
class  QCPXic
 
class  QualifiedMassSpectrum
 Class representing a fully specified mass spectrum. More...
 
class  QualifiedXic
 
class  ResPrecision
 
struct  RtPoint
 
struct  SavGolParams
 Parameters for the Savitzky-Golay filter. More...
 
struct  SimplePeakIonMatch
 
class  SpectrumCollectionHandlerInterface
 interface to collect spectrums from the MsRunReader class More...
 
class  TandemWrapperRun
 
class  TicXicChromDriftSpecColorMapPlotWidget
 
class  TicXicChromMassSpecColorMapPlotWidget
 
class  TicXicChromTracePlotWidget
 
class  TimsBinDec
 
class  TimsData
 
class  TimsDirectXicExtractor
 
class  TimsFrame
 
class  TimsFrameBase
 
class  TimsMs2CentroidFilter
 
class  TimsMsFileReader
 
class  TimsMsRunReader
 
class  TimsMsRunReaderMs2
 
class  TimsXicExtractorInterface
 
struct  TimsXicStructure
 structure needed to extract XIC from Tims data More...
 
class  Trace
 A simple container of DataPoint instances. More...
 
class  TraceCombiner
 
class  TraceDetectionInterface
 
class  TraceDetectionMoulon
 
class  TraceDetectionSinkInterface
 
class  TraceDetectionZivy
 
class  TraceMinusCombiner
 
class  TracePeak
 
class  TracePlusCombiner
 
class  Utils
 
class  Xic
 
class  XicPeptideFragmentIon
 
class  XicPeptideFragmentIonNaturalIsotope
 
class  XicPeptideInterface
 
class  XicWidget
 
class  XtandemHyperscore
 
class  XtandemHyperscoreBis
 
class  XtandemInputSaxHandler
 
class  XtandemOutputSaxHandler
 
class  XtandemPresetSaxHandler
 
class  XtandemSpectrumProcess
 
class  XyMsFileReader
 
class  XyMsRunReader
 

Typedefs

typedef std::shared_ptr< const PeptidePeptideSp
 
typedef std::unique_ptr< const AaModificationAaModificationUp
 
typedef const AaModificationAaModificationP
 
typedef std::shared_ptr< FastaFileIndexerFastaFileIndexerSPtr
 
typedef std::shared_ptr< GrpGroupGrpGroupSp
 
typedef std::shared_ptr< const GrpGroupGrpGroupSpConst
 
typedef std::shared_ptr< const GrpPeptideGrpPeptideSpConst
 
typedef std::shared_ptr< GrpPeptideGrpPeptideSp
 
typedef std::shared_ptr< const GrpProteinGrpProteinSpConst
 
typedef std::shared_ptr< GrpProteinGrpProteinSp
 
typedef std::shared_ptr< const GrpSubGroupGrpSubGroupSpConst
 
typedef std::shared_ptr< GrpSubGroupGrpSubGroupSp
 
typedef std::shared_ptr< MassSpectrumMassSpectrumSPtr
 
typedef std::shared_ptr< const MassSpectrumMassSpectrumCstSPtr
 
typedef std::shared_ptr< QualifiedMassSpectrumQualifiedMassSpectrumSPtr
 
typedef std::shared_ptr< const QualifiedMassSpectrumQualifiedMassSpectrumCstSPtr
 
typedef std::shared_ptr< TimsMsRunReaderMs2TimsMsRunReaderMs2SPtr
 
typedef std::shared_ptr< MsRunDataSetTreeMsRunDataSetTreeSPtr
 
typedef std::shared_ptr< const MsRunDataSetTreeMsRunDataSetTreeCstSPtr
 
typedef std::shared_ptr< MsRunDataSetTreeNodeMsRunDataSetTreeNodeSPtr
 
typedef std::shared_ptr< const MsRunDataSetTreeNodeMsRunDataSetTreeNodeCstSPtr
 
typedef std::shared_ptr< const MsRunIdMsRunIdCstSPtr
 
typedef std::shared_ptr< MsRunReaderMsRunReaderSPtr
 
typedef std::shared_ptr< const MsRunReaderMsRunReaderCstSPtr
 
typedef std::shared_ptr< PeptideNoConstPeptideSp
 
typedef std::shared_ptr< const PeptideFragmentPeptideFragmentSp
 
typedef std::shared_ptr< const PeptideFragmentIonPeptideFragmentIonSp
 
typedef std::shared_ptr< const PeptideFragmentIonListBasePeptideFragmentIonListBaseSp
 
typedef std::shared_ptr< const PeptideInterfacePeptideInterfaceSp
 
typedef std::shared_ptr< const PeptideNaturalIsotopePeptideNaturalIsotopeSp
 
typedef std::shared_ptr< const PeptideNaturalIsotopeAveragePeptideNaturalIsotopeAverageSp
 
typedef std::shared_ptr< const PeptideNaturalIsotopeListPeptideNaturalIsotopeListSp
 
typedef const PrecisionBasePrecisionPtr
 
typedef std::shared_ptr< const MassSpectrumCombinerMassSpectrumCombinerCstSPtr
 
typedef std::shared_ptr< MassSpectrumCombinerMassSpectrumCombinerSPtr
 
typedef std::shared_ptr< const MassSpectrumMinusCombinerMassSpectrumMinusCombinerCstSPtr
 
typedef std::shared_ptr< MassSpectrumMinusCombinerMassSpectrumMinusCombinerSPtr
 
typedef std::shared_ptr< const MassSpectrumPlusCombinerMassSpectrumPlusCombinerCstSPtr
 
typedef std::shared_ptr< MassSpectrumPlusCombinerMassSpectrumPlusCombinerSPtr
 
typedef std::shared_ptr< const TraceCombinerTraceCombinerCstSPtr
 
typedef std::shared_ptr< TraceCombinerTraceCombinerSPtr
 
typedef std::shared_ptr< const TraceMinusCombinerTraceMinusCombinerCstSPtr
 
typedef std::shared_ptr< TraceMinusCombinerTraceMinusCombinerSPtr
 
typedef std::shared_ptr< const TracePlusCombinerTracePlusCombinerCstSPtr
 
typedef std::shared_ptr< TracePlusCombinerTracePlusCombinerSPtr
 
typedef std::shared_ptr< TraceDetectionInterfaceTraceDetectionInterfaceSPtr
 
typedef std::shared_ptr< const TraceDetectionInterfaceTraceDetectionInterfaceCstSPtr
 
typedef std::shared_ptr< const TracePeakTracePeakCstSPtr
 
typedef std::shared_ptr< FilterInterfaceFilterInterfaceSPtr
 
typedef std::shared_ptr< const FilterInterfaceFilterInterfaceCstSPtr
 
typedef std::shared_ptr< const ProteinProteinSp
 shared pointer on a Protein object More...
 
typedef std::shared_ptr< const PeakIonIsotopeMatchPeakIonIsotopeMatchCstSPtr
 
typedef std::shared_ptr< const DataPointDataPointCstSPtr
 
typedef std::shared_ptr< MapTraceMapTraceSPtr
 
typedef std::shared_ptr< const MapTraceMapTraceCstSPtr
 
typedef std::shared_ptr< TraceTraceSPtr
 
typedef std::shared_ptr< const TraceTraceCstSPtr
 
typedef QString PeptideStr
 A type definition for PeptideStr. More...
 
typedef double pappso_double
 A type definition for doubles. More...
 
typedef float pappso_float
 
typedef unsigned int uint
 
typedef std::shared_ptr< TimsFrameTimsFrameSPtr
 
typedef std::shared_ptr< const TimsFrameTimsFrameCstSPtr
 
typedef std::shared_ptr< TimsFrameBaseTimsFrameBaseSPtr
 
typedef std::shared_ptr< const TimsFrameBaseTimsFrameBaseCstSPtr
 
typedef std::shared_ptr< BaseColorMapPlotWidgetBaseColorMapPlotWidgetSPtr
 
typedef std::shared_ptr< const BaseColorMapPlotWidgetBaseColorMapPlotWidgetCstSPtr
 
typedef std::shared_ptr< BasePlotWidgetBasePlotWidgetSPtr
 
typedef std::shared_ptr< const BasePlotWidgetBasePlotWidgetCstSPtr
 
typedef std::shared_ptr< BaseTracePlotWidgetBaseTracePlotWidgetSPtr
 
typedef std::shared_ptr< const BaseTracePlotWidgetBaseTracePlotWidgetCstSPtr
 
typedef std::vector< std::pair< XicCstSPtr, TracePeakCstSPtr > > XicXicPeakPairList
 
typedef std::shared_ptr< XicQualifiedXicSp
 
typedef std::shared_ptr< const XicXicCstSPtr
 
typedef std::shared_ptr< XicXicSPtr
 
typedef std::shared_ptr< MsRunXicExtractorInterfaceMsRunXicExtractorInterfaceSp
 
typedef std::shared_ptr< const MsRunSliceMsRunSliceSPtr
 

Enumerations

enum  QualifiedMassSpectrumParameter {
  QualifiedMassSpectrumParameter::OneOverK0, QualifiedMassSpectrumParameter::OneOverK0begin, QualifiedMassSpectrumParameter::OneOverK0end, QualifiedMassSpectrumParameter::IsolationMz,
  QualifiedMassSpectrumParameter::IsolationWidth, QualifiedMassSpectrumParameter::CollisionEnergy, QualifiedMassSpectrumParameter::BrukerPrecursorIndex, QualifiedMassSpectrumParameter::last
}
 
enum  FileReaderType { FileReaderType::pwiz, FileReaderType::xy, FileReaderType::tims, FileReaderType::tims_ms2 }
 
enum  PeptideDirection : std::int8_t { PeptideDirection::Nter = 0, PeptideDirection::Cter = 1 }
 
enum  PeptideIonNter {
  PeptideIonNter::b, PeptideIonNter::bstar, PeptideIonNter::bo, PeptideIonNter::a,
  PeptideIonNter::astar, PeptideIonNter::ao, PeptideIonNter::bp, PeptideIonNter::c
}
 
enum  PeptideIonCter {
  PeptideIonCter::y, PeptideIonCter::ystar, PeptideIonCter::yo, PeptideIonCter::z,
  PeptideIonCter::yp, PeptideIonCter::x
}
 
enum  AtomIsotope {
  AtomIsotope::C, AtomIsotope::H, AtomIsotope::O, AtomIsotope::N,
  AtomIsotope::S
}
 
enum  RawFragmentationMode : std::int8_t { RawFragmentationMode::full = 0, RawFragmentationMode::proline_effect = 1 }
 
enum  PrecisionUnit {
  PrecisionUnit::none, PrecisionUnit::dalton, PrecisionUnit::ppm, PrecisionUnit::res,
  PrecisionUnit::mz, PrecisionUnit::last
}
 
enum  AtomIsotopeSurvey : std::int8_t {
  AtomIsotopeSurvey::C, AtomIsotopeSurvey::H, AtomIsotopeSurvey::O, AtomIsotopeSurvey::N,
  AtomIsotopeSurvey::S, AtomIsotopeSurvey::last
}
 
enum  Isotope {
  Isotope::C13, Isotope::H2, Isotope::O17, Isotope::O18,
  Isotope::N15, Isotope::S33, Isotope::S34, Isotope::S36
}
 
enum  MzFormat : std::int8_t {
  MzFormat::unknown = 0, MzFormat::mzML = 1, MzFormat::mzXML = 2, MzFormat::MGF = 3,
  MzFormat::SQLite3 = 4, MzFormat::xy = 5, MzFormat::mz5 = 6, MzFormat::msn = 7,
  MzFormat::abSciexWiff = 8, MzFormat::abSciexT2D = 9, MzFormat::agilentMassHunter = 10, MzFormat::thermoRaw = 11,
  MzFormat::watersRaw = 12, MzFormat::brukerFid = 13, MzFormat::brukerYep = 14, MzFormat::brukerBaf = 15,
  MzFormat::brukerTims = 16, MzFormat::last = 17
}
 
enum  AminoAcidChar : char {
  AminoAcidChar::alanine = 'A', AminoAcidChar::cysteine = 'C', AminoAcidChar::aspartic_acid = 'D', AminoAcidChar::glutamic_acid = 'E',
  AminoAcidChar::phenylalanine = 'F', AminoAcidChar::glycine = 'G', AminoAcidChar::histidine = 'H', AminoAcidChar::isoleucine = 'I',
  AminoAcidChar::lysine = 'K', AminoAcidChar::leucine = 'L', AminoAcidChar::methionine = 'M', AminoAcidChar::asparagine = 'N',
  AminoAcidChar::proline = 'P', AminoAcidChar::glutamine = 'Q', AminoAcidChar::arginine = 'R', AminoAcidChar::serine = 'S',
  AminoAcidChar::threonine = 'T', AminoAcidChar::valine = 'V', AminoAcidChar::tryptophan = 'W', AminoAcidChar::tyrosine = 'Y',
  AminoAcidChar::selenocysteine = 'U', AminoAcidChar::pyrrolysine = 'O'
}
 
enum  DataCompression : std::int8_t { DataCompression::unset = -1, DataCompression::none = 0, DataCompression::zlib = 1 }
 
enum  DataKind : std::int8_t { DataKind::unset = -1, DataKind::rt = 0, DataKind::dt = 1, DataKind::mz = 2 }
 
enum  XicExtractMethod : std::int8_t { XicExtractMethod::sum = 1, XicExtractMethod::max = 2 }
 
enum  PeptideIon : std::int8_t {
  PeptideIon::b = 0, PeptideIon::bstar = 1, PeptideIon::bo = 2, PeptideIon::a = 3,
  PeptideIon::astar = 4, PeptideIon::ao = 5, PeptideIon::bp = 6, PeptideIon::c = 7,
  PeptideIon::y = 8, PeptideIon::ystar = 9, PeptideIon::yo = 10, PeptideIon::z = 11,
  PeptideIon::yp = 12, PeptideIon::x = 13
}
 PeptideIon enum defines all types of ions (Nter or Cter) More...
 
enum  PlotAxis { PlotAxis::none = 0x000, PlotAxis::x_axis = 1 << 1, PlotAxis::y_axis = 1 << 2, PlotAxis::both = (x_axis | y_axis) }
 
enum  RangeType { RangeType::outermost = 1, RangeType::innermost = 2 }
 

Functions

bool operator== (Aa const &l, Aa const &r)
 
bool operator< (Aa const &l, Aa const &r)
 
QDataStream & operator<< (QDataStream &outstream, const MassSpectrum &massSpectrum)
 
QDataStream & operator>> (QDataStream &instream, MassSpectrum &massSpectrum)
 
bool peptideIonIsNter (PeptideIon ion_type)
 tells if an ion is Nter More...
 
PeptideDirection getPeptideIonDirection (PeptideIon ion_type)
 get the direction of a peptide ion More...
 
uint64_t Combinations (unsigned int n, unsigned int k)
 
pappso_double isotopem_ratio (pappso_double abundance, unsigned int total, unsigned int heavy)
 
pappso_double isotopem_ratio_cache (Isotope isotope, unsigned int total, unsigned int heavy)
 
std::vector< PeptideNaturalIsotopeAverageSpgetByIntensityRatioByIsotopeNumber (const PeptideInterfaceSp &peptide, unsigned int charge, PrecisionPtr precision, unsigned int isotopeNumber, pappso_double minimumIntensity)
 
unsigned int factorial (unsigned int n)
 
QDataStream & operator<< (QDataStream &out, const DataPoint &dataPoint)
 
QDataStream & operator>> (QDataStream &in, DataPoint &dataPoint)
 
QDataStream & operator<< (QDataStream &out, const Trace &trace)
 
QDataStream & operator>> (QDataStream &out, Trace &trace)
 
std::vector< DataPoint >::iterator findFirstEqualOrGreaterX (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
 find the first element in which X is equal or greater than the value searched important : it implies that Trace is sorted by X More...
 
std::vector< DataPoint >::const_iterator findFirstEqualOrGreaterX (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, const double &value)
 
std::vector< DataPoint >::iterator findFirstGreaterX (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
 find the first element in which X is greater than the value searched important : it implies that Trace is sorted by X More...
 
std::vector< DataPoint >::const_iterator findFirstGreaterX (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, const double &value)
 
std::vector< DataPoint >::iterator findDifferentYvalue (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &y_value)
 find the first element in which Y is different of value More...
 
std::vector< DataPoint >::const_iterator findDifferentYvalue (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, const double &y_value)
 
std::vector< DataPoint >::const_iterator minYDataPoint (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
 
std::vector< DataPoint >::iterator minYDataPoint (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end)
 find the element with the smallest Y value (intensity) More...
 
std::vector< DataPoint >::const_iterator maxYDataPoint (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
 
std::vector< DataPoint >::iterator maxYDataPoint (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end)
 find the element with the greatest Y value (intensity) More...
 
std::vector< DataPoint >::const_iterator moveLowerYRigthDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin)
 Move right to the lower value. More...
 
std::vector< DataPoint >::const_iterator moveLowerYLeftDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin)
 Move left to the lower value. More...
 
double sumYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
 calculate the sum of y value of a trace More...
 
double meanYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
 calculate the mean of y value of a trace More...
 
double medianYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
 calculate the median of y value of a trace More...
 
double areaTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
 calculate the area of a trace More...
 
Trace flooredLocalMaxima (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double y_floor)
 
const pappso_double MHPLUS (1.007276466879)
 
const pappso_double MPROTON (1.007276466879)
 
const pappso_double MPROTIUM (1.007825032241)
 
const pappso_double ONEMILLION (1000000)
 
const pappso_double MASSOXYGEN (15.99491461956)
 
const pappso_double MASSCARBON (12)
 
const pappso_double MASSH2O ((MPROTIUM *2)+MASSOXYGEN)
 
const pappso_double MASSNITROGEN (14.0030740048)
 
const pappso_double MASSNH3 ((MPROTIUM *3)+MASSNITROGEN)
 
const pappso_double MASSCO (MASSCARBON+MASSOXYGEN)
 
const pappso_double MASSPHOSPHORUS (30.973761998)
 
const pappso_double MASSSULFUR (31.97207100)
 
const pappso_double MASSPHOSPHORYLATEDR (MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
 
const pappso_double MASSSELENIUM (79.916520)
 
const pappso_double DIFFC12C13 (1.0033548378)
 
const pappso_double DIFFS32S33 (32.97145876 - MASSSULFUR)
 
const pappso_double DIFFS32S34 (33.96786690 - MASSSULFUR)
 
const pappso_double DIFFS32S36 (35.96708076 - MASSSULFUR)
 
const pappso_double DIFFH1H2 (2.0141017778 - MPROTIUM)
 
const pappso_double DIFFO16O18 (17.9991610 - MASSOXYGEN)
 
const pappso_double DIFFO16O17 (16.99913150 - MASSOXYGEN)
 
const pappso_double DIFFN14N15 (15.0001088982 - MASSNITROGEN)
 
const pappso_double ABUNDANCEH2 (0.00015574)
 
const pappso_double ABUNDANCEN15 (0.003663)
 
const pappso_double ABUNDANCEO17 (0.000372)
 
const pappso_double ABUNDANCEO18 (0.0020004)
 
const pappso_double ABUNDANCEC13 (0.011078)
 
const pappso_double ABUNDANCEC12 (0.988922)
 
const pappso_double ABUNDANCES33 (0.00750)
 
const pappso_double ABUNDANCES34 (0.04215)
 
const pappso_double ABUNDANCES36 (0.00020)
 
QDataStream & operator>> (QDataStream &instream, MsRunSlice &slice)
 

Variables

class PMSPP_LIB_DECL MsRunReader
 
uint64_t combinations_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioC13_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioN15_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioS36_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioS34_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioS33_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioO17_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioO18_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 
pappso_double ratioH2_cache [CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}
 

Detailed Description

tries to keep as much as possible monoisotopes, removing any possible C13 peaks

first sort peaks by decreasing intensities, then keep most intense ones and avoid any peaks in possible C13 windows after

Todo:
write docs
Todo:
write docs
Todo:
write docs
Todo:
write docs

Typedef Documentation

◆ AaModificationP

Definition at line 73 of file aamodification.h.

◆ AaModificationUp

typedef std::unique_ptr<const AaModification> pappso::AaModificationUp

Definition at line 72 of file aamodification.h.

◆ BaseColorMapPlotWidgetCstSPtr

Definition at line 59 of file basecolormapplotwidget.h.

◆ BaseColorMapPlotWidgetSPtr

Definition at line 57 of file basecolormapplotwidget.h.

◆ BasePlotWidgetCstSPtr

typedef std::shared_ptr<const BasePlotWidget> pappso::BasePlotWidgetCstSPtr

Definition at line 133 of file baseplotwidget.h.

◆ BasePlotWidgetSPtr

typedef std::shared_ptr<BasePlotWidget> pappso::BasePlotWidgetSPtr

Definition at line 132 of file baseplotwidget.h.

◆ BaseTracePlotWidgetCstSPtr

Definition at line 57 of file basetraceplotwidget.h.

◆ BaseTracePlotWidgetSPtr

Definition at line 56 of file basetraceplotwidget.h.

◆ DataPointCstSPtr

typedef std::shared_ptr<const DataPoint> pappso::DataPointCstSPtr

Definition at line 17 of file datapoint.h.

◆ FastaFileIndexerSPtr

Definition at line 67 of file fastafileindexer.h.

◆ FilterInterfaceCstSPtr

typedef std::shared_ptr<const FilterInterface> pappso::FilterInterfaceCstSPtr

Definition at line 64 of file filterinterface.h.

◆ FilterInterfaceSPtr

typedef std::shared_ptr<FilterInterface> pappso::FilterInterfaceSPtr

Definition at line 63 of file filterinterface.h.

◆ GrpGroupSp

typedef std::shared_ptr<GrpGroup> pappso::GrpGroupSp

Definition at line 60 of file grpgroup.h.

◆ GrpGroupSpConst

typedef std::shared_ptr<const GrpGroup> pappso::GrpGroupSpConst

Definition at line 61 of file grpgroup.h.

◆ GrpPeptideSp

typedef std::shared_ptr<GrpPeptide> pappso::GrpPeptideSp

Definition at line 61 of file grppeptide.h.

◆ GrpPeptideSpConst

typedef std::shared_ptr<const GrpPeptide> pappso::GrpPeptideSpConst

Definition at line 60 of file grppeptide.h.

◆ GrpProteinSp

typedef std::shared_ptr<GrpProtein> pappso::GrpProteinSp

Definition at line 58 of file grpprotein.h.

◆ GrpProteinSpConst

typedef std::shared_ptr<const GrpProtein> pappso::GrpProteinSpConst

Definition at line 57 of file grpprotein.h.

◆ GrpSubGroupSp

typedef std::shared_ptr<GrpSubGroup> pappso::GrpSubGroupSp

Definition at line 60 of file grpsubgroup.h.

◆ GrpSubGroupSpConst

typedef std::shared_ptr<const GrpSubGroup> pappso::GrpSubGroupSpConst

Definition at line 59 of file grpsubgroup.h.

◆ MapTraceCstSPtr

typedef std::shared_ptr<const MapTrace> pappso::MapTraceCstSPtr

Definition at line 26 of file maptrace.h.

◆ MapTraceSPtr

typedef std::shared_ptr<MapTrace> pappso::MapTraceSPtr

Definition at line 25 of file maptrace.h.

◆ MassSpectrumCombinerCstSPtr

Definition at line 25 of file massspectrumcombiner.h.

◆ MassSpectrumCombinerSPtr

Definition at line 26 of file massspectrumcombiner.h.

◆ MassSpectrumCstSPtr

typedef std::shared_ptr<const MassSpectrum> pappso::MassSpectrumCstSPtr

Definition at line 76 of file massspectrum.h.

◆ MassSpectrumMinusCombinerCstSPtr

Definition at line 20 of file massspectrumminuscombiner.h.

◆ MassSpectrumMinusCombinerSPtr

◆ MassSpectrumPlusCombinerCstSPtr

Definition at line 19 of file massspectrumpluscombiner.h.

◆ MassSpectrumPlusCombinerSPtr

◆ MassSpectrumSPtr

typedef std::shared_ptr<MassSpectrum> pappso::MassSpectrumSPtr

Definition at line 75 of file massspectrum.h.

◆ MsRunDataSetTreeCstSPtr

typedef std::shared_ptr<const MsRunDataSetTree> pappso::MsRunDataSetTreeCstSPtr

Definition at line 28 of file msrundatasettree.h.

◆ MsRunDataSetTreeNodeCstSPtr

Definition at line 30 of file msrundatasettreenode.h.

◆ MsRunDataSetTreeNodeSPtr

Definition at line 29 of file msrundatasettreenode.h.

◆ MsRunDataSetTreeSPtr

Definition at line 27 of file msrundatasettree.h.

◆ MsRunIdCstSPtr

typedef std::shared_ptr<const MsRunId> pappso::MsRunIdCstSPtr

Definition at line 66 of file msrunid.h.

◆ MsRunReaderCstSPtr

typedef std::shared_ptr<const MsRunReader> pappso::MsRunReaderCstSPtr

Definition at line 173 of file msrunreader.h.

◆ MsRunReaderSPtr

typedef std::shared_ptr<MsRunReader> pappso::MsRunReaderSPtr

Definition at line 172 of file msrunreader.h.

◆ MsRunSliceSPtr

typedef std::shared_ptr<const MsRunSlice> pappso::MsRunSliceSPtr

Definition at line 61 of file msrunslice.h.

◆ MsRunXicExtractorInterfaceSp

◆ NoConstPeptideSp

typedef std::shared_ptr<Peptide> pappso::NoConstPeptideSp

Definition at line 111 of file peptide.h.

◆ pappso_double

typedef double pappso::pappso_double

A type definition for doubles.

Definition at line 69 of file types.h.

◆ pappso_float

typedef float pappso::pappso_float

Definition at line 74 of file types.h.

◆ PeakIonIsotopeMatchCstSPtr

Definition at line 34 of file peakionisotopematch.h.

◆ PeptideFragmentIonListBaseSp

Definition at line 64 of file peptidefragmentionlistbase.h.

◆ PeptideFragmentIonSp

typedef std::shared_ptr<const PeptideFragmentIon> pappso::PeptideFragmentIonSp

Definition at line 67 of file peptidefragmention.h.

◆ PeptideFragmentSp

typedef std::shared_ptr<const PeptideFragment> pappso::PeptideFragmentSp

Definition at line 66 of file peptidefragment.h.

◆ PeptideInterfaceSp

typedef std::shared_ptr<const PeptideInterface> pappso::PeptideInterfaceSp

Definition at line 60 of file peptideinterface.h.

◆ PeptideNaturalIsotopeAverageSp

◆ PeptideNaturalIsotopeListSp

Definition at line 66 of file peptidenaturalisotopelist.h.

◆ PeptideNaturalIsotopeSp

Definition at line 64 of file peptidenaturalisotope.h.

◆ PeptideSp

typedef std::shared_ptr< const Peptide > pappso::PeptideSp

Definition at line 69 of file aamodification.h.

◆ PeptideStr

typedef QString pappso::PeptideStr

A type definition for PeptideStr.

Definition at line 64 of file types.h.

◆ PrecisionPtr

Definition at line 143 of file precision.h.

◆ ProteinSp

typedef std::shared_ptr<const Protein> pappso::ProteinSp

shared pointer on a Protein object

Definition at line 68 of file protein.h.

◆ QualifiedMassSpectrumCstSPtr

Definition at line 63 of file qualifiedmassspectrum.h.

◆ QualifiedMassSpectrumSPtr

Definition at line 61 of file qualifiedmassspectrum.h.

◆ QualifiedXicSp

typedef std::shared_ptr<Xic> pappso::QualifiedXicSp

Definition at line 42 of file qualifiedxic.h.

◆ TimsFrameBaseCstSPtr

typedef std::shared_ptr<const TimsFrameBase> pappso::TimsFrameBaseCstSPtr

Definition at line 58 of file timsframebase.h.

◆ TimsFrameBaseSPtr

typedef std::shared_ptr<TimsFrameBase> pappso::TimsFrameBaseSPtr

Definition at line 57 of file timsframebase.h.

◆ TimsFrameCstSPtr

typedef std::shared_ptr<const TimsFrame> pappso::TimsFrameCstSPtr

Definition at line 60 of file timsframe.h.

◆ TimsFrameSPtr

typedef std::shared_ptr<TimsFrame> pappso::TimsFrameSPtr

Definition at line 59 of file timsframe.h.

◆ TimsMsRunReaderMs2SPtr

Definition at line 18 of file msfileaccessor.h.

◆ TraceCombinerCstSPtr

typedef std::shared_ptr<const TraceCombiner> pappso::TraceCombinerCstSPtr

Definition at line 23 of file tracecombiner.h.

◆ TraceCombinerSPtr

typedef std::shared_ptr<TraceCombiner> pappso::TraceCombinerSPtr

Definition at line 24 of file tracecombiner.h.

◆ TraceCstSPtr

typedef std::shared_ptr<const Trace> pappso::TraceCstSPtr

Definition at line 120 of file trace.h.

◆ TraceDetectionInterfaceCstSPtr

Definition at line 56 of file tracedetectioninterface.h.

◆ TraceDetectionInterfaceSPtr

Definition at line 54 of file tracedetectioninterface.h.

◆ TraceMinusCombinerCstSPtr

typedef std::shared_ptr<const TraceMinusCombiner> pappso::TraceMinusCombinerCstSPtr

Definition at line 22 of file traceminuscombiner.h.

◆ TraceMinusCombinerSPtr

Definition at line 23 of file traceminuscombiner.h.

◆ TracePeakCstSPtr

typedef std::shared_ptr<const TracePeak> pappso::TracePeakCstSPtr

Definition at line 56 of file tracepeak.h.

◆ TracePlusCombinerCstSPtr

typedef std::shared_ptr<const TracePlusCombiner> pappso::TracePlusCombinerCstSPtr

Definition at line 22 of file tracepluscombiner.h.

◆ TracePlusCombinerSPtr

Definition at line 23 of file tracepluscombiner.h.

◆ TraceSPtr

typedef std::shared_ptr<Trace> pappso::TraceSPtr

Definition at line 119 of file trace.h.

◆ uint

typedef unsigned int pappso::uint

Definition at line 76 of file types.h.

◆ XicCstSPtr

typedef std::shared_ptr<const Xic> pappso::XicCstSPtr

Definition at line 59 of file xic.h.

◆ XicSPtr

typedef std::shared_ptr<Xic> pappso::XicSPtr

Definition at line 60 of file xic.h.

◆ XicXicPeakPairList

typedef std::vector<std::pair<XicCstSPtr, TracePeakCstSPtr> > pappso::XicXicPeakPairList

Definition at line 65 of file xicwidget.h.

Enumeration Type Documentation

◆ AminoAcidChar

enum pappso::AminoAcidChar : char
strong
Enumerator
alanine 
cysteine 
aspartic_acid 
glutamic_acid 
phenylalanine 
glycine 
histidine 
isoleucine 
lysine 
leucine 
methionine 
asparagine 
proline 
glutamine 
arginine 
serine 
threonine 
valine 
tryptophan 
tyrosine 
selenocysteine 
pyrrolysine 

Definition at line 153 of file types.h.

162  : std::int8_t
163 {
164  unset = -1, ///< not net
165  none = 0, ///< no compression
166  zlib = 1, ///< zlib compresssion
167 };
168 
169 
170 enum class DataKind : std::int8_t
171 {
172  unset = -1, ///< not set
173  rt = 0, ///< Retention time
174  dt = 1, ///< Drift time
175  mz = 2, ///< m/z
176 };
177 

◆ AtomIsotope

enum pappso::AtomIsotope
strong
Enumerator

Definition at line 69 of file peptidenaturalisotope.cpp.

70 {
71  C,
72  H,
73  O,
74  N,
75  S
76 };

◆ AtomIsotopeSurvey

enum pappso::AtomIsotopeSurvey : std::int8_t
strong
Enumerator
last 

Definition at line 96 of file types.h.

106  : std::int8_t

◆ DataCompression

enum pappso::DataCompression : std::int8_t
strong
Enumerator
unset 

not net

none 

no compression

zlib 

zlib compresssion

Definition at line 183 of file types.h.

333  : std::int8_t

◆ DataKind

enum pappso::DataKind : std::int8_t
strong
Enumerator
unset 

not set

rt 

Retention time.

dt 

Drift time.

mz 

m/z

Definition at line 191 of file types.h.

193  ://en.wikipedia.org/wiki/Proton (One Proton alone)
194  1.007276466879
195  */
196 const pappso_double MHPLUS(1.007276466879);
197 const pappso_double MPROTON(1.007276466879);

◆ FileReaderType

Enumerator
pwiz 
xy 
tims 
tims_ms2 

Definition at line 20 of file msfileaccessor.h.

21 {
22  pwiz,
23  xy,
24  tims,
25  tims_ms2,
26 };

◆ Isotope

enum pappso::Isotope
strong
Enumerator
C13 
H2 
O17 
O18 
N15 
S33 
S34 
S36 

Definition at line 111 of file types.h.

132  : char

◆ MzFormat

enum pappso::MzFormat : std::int8_t
strong
Enumerator
unknown 

unknown format

mzML 

mzML

mzXML 

mzXML

MGF 

Mascot format.

SQLite3 

SQLite3 format.

xy 

(x,y) format

mz5 
msn 
abSciexWiff 
abSciexT2D 
agilentMassHunter 
thermoRaw 
watersRaw 
brukerFid 
brukerYep 
brukerBaf 
brukerTims 
last 

Definition at line 127 of file types.h.

132  : char
133 {
134  alanine = 'A',
135  cysteine = 'C',
136  aspartic_acid = 'D',
137  glutamic_acid = 'E',
138  phenylalanine = 'F',
139  glycine = 'G',
140  histidine = 'H',
141  isoleucine = 'I',
142  lysine = 'K',
143  leucine = 'L',
144  methionine = 'M',
145  asparagine = 'N',
146  proline = 'P',
147  glutamine = 'Q',

◆ PeptideDirection

enum pappso::PeptideDirection : std::int8_t
strong
Enumerator
Nter 
Cter 

Definition at line 66 of file peptide.h.

78 {

◆ PeptideIon

enum pappso::PeptideIon : std::int8_t
strong

PeptideIon enum defines all types of ions (Nter or Cter)

Enumerator

Nter acylium ions.

bstar 

Nter acylium ions + NH3 loss.

bo 

Nter acylium ions + H2O loss.

Nter aldimine ions.

astar 

Nter aldimine ions + NH3 loss.

ao 

Nter aldimine ions + H2O loss.

bp 

Nter amino ions.

Cter amino ions.

ystar 

Cter amino ions + NH3 loss.

yo 

Cter amino ions + H2O loss.

Cter carbocations.

yp 

Cter acylium ions.

Definition at line 354 of file types.h.

◆ PeptideIonCter

Enumerator
ystar 
yo 
yp 

Definition at line 98 of file peptide.h.

104  {
105  return (l.m_aaVec < r.m_aaVec);
106  }

◆ PeptideIonNter

Enumerator
bstar 
bo 
astar 
ao 
bp 

Definition at line 85 of file peptide.h.

92  : public PeptideInterface
93 {
94  protected:
95  std::vector<Aa> m_aaVec;

◆ PlotAxis

enum pappso::PlotAxis
strong
Enumerator
none 
x_axis 
y_axis 
both 

Definition at line 53 of file baseplotwidget.h.

54 {
55  none = 0x000,
56  x_axis = 1 << 1,
57  y_axis = 1 << 2,
58  both = (x_axis | y_axis)
59 };

◆ PrecisionUnit

enum pappso::PrecisionUnit
strong
Enumerator
none 
dalton 
ppm 
res 
mz 
last 

Definition at line 83 of file types.h.

91 {

◆ QualifiedMassSpectrumParameter

Enumerator
OneOverK0 

1/kO of a simple scan

OneOverK0begin 

1/kO of first acquisition for composite pasef MS/MS spectrum

OneOverK0end 

1/k0 of last acquisition for composite pasef MS/MS spectrum

IsolationMz 

isolation window

IsolationWidth 

isolation window width

CollisionEnergy 

Bruker's Tims tof collision energy.

BrukerPrecursorIndex 

Bruker's Tims tof precursor index.

last 

Definition at line 65 of file qualifiedmassspectrum.h.

68 {
69  public:
70  QualifiedMassSpectrum();
71  QualifiedMassSpectrum(const MassSpectrumId &id);
72  QualifiedMassSpectrum(MassSpectrumSPtr mass_spectrum_SPtr);
73  QualifiedMassSpectrum(const QualifiedMassSpectrum &other);
74  ~QualifiedMassSpectrum();
75 
76  QualifiedMassSpectrum &operator=(const QualifiedMassSpectrum &other);
77 

◆ RangeType

enum pappso::RangeType
strong
Enumerator
outermost 
innermost 

Definition at line 62 of file baseplotwidget.h.

63 {
64  outermost = 1,
65  innermost = 2,
66 };

◆ RawFragmentationMode

enum pappso::RawFragmentationMode : std::int8_t
strong
Enumerator
full 
proline_effect 

Definition at line 63 of file peptiderawfragmentmasses.h.

◆ XicExtractMethod

enum pappso::XicExtractMethod : std::int8_t
strong
Enumerator
sum 

sum of intensities

max 

maximum of intensities

Definition at line 203 of file types.h.

204  : 1.007825032241
205  */
206 const pappso_double MPROTIUM(1.007825032241);
207 

Function Documentation

◆ ABUNDANCEC12()

const pappso_double pappso::ABUNDANCEC12 ( 0.  988922)

References a, b, bo, and bstar.

◆ ABUNDANCEC13()

const pappso_double pappso::ABUNDANCEC13 ( 0.  011078)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEH2()

const pappso_double pappso::ABUNDANCEH2 ( 0.  00015574)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEN15()

const pappso_double pappso::ABUNDANCEN15 ( 0.  003663)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEO17()

const pappso_double pappso::ABUNDANCEO17 ( 0.  000372)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEO18()

const pappso_double pappso::ABUNDANCEO18 ( 0.  0020004)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES33()

const pappso_double pappso::ABUNDANCES33 ( 0.  00750)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES34()

const pappso_double pappso::ABUNDANCES34 ( 0.  04215)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES36()

const pappso_double pappso::ABUNDANCES36 ( 0.  00020)

Referenced by isotopem_ratio_cache().

◆ areaTrace()

PMSPP_LIB_DECL double pappso::areaTrace ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end 
)

calculate the area of a trace

Definition at line 231 of file trace.cpp.

233 {
234 
235  if(begin == end)
236  return 0;
237  auto previous = begin;
238  auto next = begin + 1;
239  double area = 0;
240  while(next != end)
241  {
242  area += ((next->x - previous->x) * (previous->y + next->y)) / (double)2;
243  previous++;
244  next++;
245  }
246  return area;
247 }

◆ Combinations()

uint64_t pappso::Combinations ( unsigned int  n,
unsigned int  k 
)

Definition at line 47 of file peptidenaturalisotope.cpp.

48 {
49  if(k > n)
50  return 0;
51 
52  uint64_t r = 1;
53  if((n < CACHE_ARRAY_SIZE) && (combinations_cache[n][k] != 0))
54  {
55  return combinations_cache[n][k];
56  }
57  for(unsigned int d = 1; d <= k; ++d)
58  {
59  r *= n--;
60  r /= d;
61  }
62  if(n < CACHE_ARRAY_SIZE)
63  {
64  combinations_cache[n][k] = r;
65  }
66  return r;
67 }

References CACHE_ARRAY_SIZE, and combinations_cache.

Referenced by isotopem_ratio().

◆ DIFFC12C13()

◆ DIFFH1H2()

const pappso_double pappso::DIFFH1H2 ( 2.0141017778 -  MPROTIUM)

◆ DIFFN14N15()

const pappso_double pappso::DIFFN14N15 ( 15.0001088982 -  MASSNITROGEN)

◆ DIFFO16O17()

const pappso_double pappso::DIFFO16O17 ( 16.99913150 -  MASSOXYGEN)

◆ DIFFO16O18()

const pappso_double pappso::DIFFO16O18 ( 17.9991610 -  MASSOXYGEN)

◆ DIFFS32S33()

const pappso_double pappso::DIFFS32S33 ( 32.97145876 -  MASSSULFUR)

◆ DIFFS32S34()

const pappso_double pappso::DIFFS32S34 ( 33.96786690 -  MASSSULFUR)

◆ DIFFS32S36()

const pappso_double pappso::DIFFS32S36 ( 35.96708076 -  MASSSULFUR)

◆ factorial()

unsigned int pappso::factorial ( unsigned int  n)

Definition at line 64 of file xtandemhyperscore.cpp.

64  {
65  current_max_charge--;
66  }
67  }*/
68  unsigned int max_charge = parent_charge;
69  if(parent_charge > 1)
70  {

Referenced by pappso::XtandemHyperscoreBis::computeXtandemHyperscore().

◆ findDifferentYvalue() [1/2]

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::findDifferentYvalue ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end,
const double &  y_value 
)

Definition at line 101 of file trace.cpp.

104 {
105  return std::find_if(begin, end, [y_value](const DataPoint &to_compare) {
106  if(to_compare.y != y_value)
107  {
108  return true;
109  }
110  return false;
111  });
112 }

References pappso::DataPoint::y.

◆ findDifferentYvalue() [2/2]

PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::findDifferentYvalue ( std::vector< DataPoint >::iterator  begin,
std::vector< DataPoint >::iterator  end,
const double &  y_value 
)

find the first element in which Y is different of value

Definition at line 87 of file trace.cpp.

90 {
91  return std::find_if(begin, end, [y_value](const DataPoint &to_compare) {
92  if(to_compare.y != y_value)
93  {
94  return true;
95  }
96  return false;
97  });
98 }

References pappso::DataPoint::y.

Referenced by pappso::FilterMorphoAntiSpike::filter().

◆ findFirstEqualOrGreaterX() [1/2]

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::findFirstEqualOrGreaterX ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end,
const double &  value 
)

Definition at line 44 of file trace.cpp.

47 {
48  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
49  if(to_compare.x < value)
50  {
51  return false;
52  }
53  return true;
54  });
55 }

References pappso::DataPoint::x.

◆ findFirstEqualOrGreaterX() [2/2]

PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::findFirstEqualOrGreaterX ( std::vector< DataPoint >::iterator  begin,
std::vector< DataPoint >::iterator  end,
const double &  value 
)

find the first element in which X is equal or greater than the value searched important : it implies that Trace is sorted by X

Definition at line 30 of file trace.cpp.

33 {
34  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
35  if(to_compare.x < value)
36  {
37  return false;
38  }
39  return true;
40  });
41 }

References pappso::DataPoint::x.

Referenced by pappso::FilterResampleKeepSmaller::filter(), pappso::FilterResampleRemoveXRange::filter(), pappso::FilterResampleKeepXRange::filter(), pappso::Trace::maxY(), and pappso::Trace::sumY().

◆ findFirstGreaterX() [1/2]

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::findFirstGreaterX ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end,
const double &  value 
)

Definition at line 72 of file trace.cpp.

75 {
76  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
77  if(to_compare.x > value)
78  {
79  return true;
80  }
81  return false;
82  });
83 }

References pappso::DataPoint::x.

◆ findFirstGreaterX() [2/2]

PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::findFirstGreaterX ( std::vector< DataPoint >::iterator  begin,
std::vector< DataPoint >::iterator  end,
const double &  value 
)

find the first element in which X is greater than the value searched important : it implies that Trace is sorted by X

Definition at line 58 of file trace.cpp.

61 {
62  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
63  if(to_compare.x > value)
64  {
65  return true;
66  }
67  return false;
68  });
69 }

References pappso::DataPoint::x.

Referenced by pappso::FilterResampleKeepGreater::filter(), pappso::FilterResampleRemoveXRange::filter(), pappso::FilterResampleKeepXRange::filter(), pappso::Trace::maxY(), and pappso::Trace::sumY().

◆ flooredLocalMaxima()

PMSPP_LIB_DECL Trace pappso::flooredLocalMaxima ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end,
double  y_floor 
)

Definition at line 251 of file trace.cpp.

254 {
255  Trace local_maxima_trace;
256 
257  Trace single_peak_trace;
258 
259  DataPoint previous_data_point;
260 
261  for(auto iter = begin; iter != end; ++iter)
262  {
263  DataPoint iterated_data_point(iter->x, iter->y);
264 
265  // qDebug().noquote() << "Current data point:"
266  //<< iterated_data_point.toString();
267 
268  if(iterated_data_point.y < y_floor)
269  {
270  // qDebug() << "under the floor";
271 
272  if(single_peak_trace.size())
273  {
274  // qDebug() << "There was a single peak trace cooking";
275 
276  local_maxima_trace.push_back(single_peak_trace.maxYDataPoint());
277 
278  // qDebug().noquote() << "pushed back local maximum point:"
279  //<< local_maxima_trace.back().toString();
280 
281  // Clean and set the context.
282  single_peak_trace.clear();
283 
284  previous_data_point = iterated_data_point;
285 
286  continue;
287  }
288  else
289  {
290  // qDebug() << "no single peak trace cooking";
291 
292  previous_data_point = iterated_data_point;
293 
294  continue;
295  }
296  }
297  else
298  {
299  // qDebug() << "over the floor";
300 
301  // The iterated value is greater than the y_floor value, so we need to
302  // handle it.
303 
304  if(iterated_data_point.y == previous_data_point.y)
305  {
306  // We are in a flat region, no need to change anything to the
307  // context, just skip the point.
308  continue;
309  }
310  else if(iterated_data_point.y > previous_data_point.y)
311  {
312  // qDebug().noquote() << "ascending in a peak";
313 
314  // The previously iterated y value was smaller than the presently
315  // iterated one, so we are ascending in a peak.
316 
317  // All we need to do is set the context.
318 
319  single_peak_trace.push_back(iterated_data_point);
320 
321  // qDebug().noquote() << "pushed back normal point:"
322  //<< single_peak_trace.back().toString();
323 
324  previous_data_point = iterated_data_point;
325 
326  continue;
327  }
328  else
329  {
330  // qDebug().noquote() << "started descending in a peak";
331 
332  // No, the currently iterated y value is less than the previously
333  // iterated value.
334 
335  single_peak_trace.push_back(iterated_data_point);
336 
337  // qDebug().noquote() << "pushed back normal point:"
338  //<< single_peak_trace.back().toString();
339 
340  previous_data_point = iterated_data_point;
341 
342  continue;
343  }
344  }
345  }
346  // End of
347  // for(auto iter = begin; iter != end; ++iter)
348 
349  // Attention, we might arrive here with a peak being created, we need to get
350  // its maximum if that peak is non-empty;
351 
352  if(single_peak_trace.size())
353  {
354 
355  local_maxima_trace.push_back(single_peak_trace.maxYDataPoint());
356 
357  // qDebug().noquote()
358  //<< "was cooking a peak: pushed back local maximum point:"
359  //<< local_maxima_trace.back().toString();
360  }
361 
362  return local_maxima_trace;
363 }

References pappso::Trace::maxYDataPoint(), and pappso::DataPoint::y.

◆ getByIntensityRatioByIsotopeNumber()

std::vector<PeptideNaturalIsotopeAverageSp> pappso::getByIntensityRatioByIsotopeNumber ( const PeptideInterfaceSp peptide,
unsigned int  charge,
PrecisionPtr  precision,
unsigned int  isotopeNumber,
pappso_double  minimumIntensity 
)

/brief get a sorted (by expected intensity) vector of natural isotope average by isotope number

Definition at line 372 of file peptidenaturalisotopelist.cpp.

375  {
376  }
377  else
378  {
379  if(std::find(previousIsotopeRank.begin(),
380  previousIsotopeRank.end(),
381  isotopeAverage.getIsotopeRank()) ==
382  previousIsotopeRank.end())
383  { // not Found
384  previousIsotopeRank.push_back(isotopeAverage.getIsotopeRank());
385  v_isotopeAverageList.push_back(
386  isotopeAverage.makePeptideNaturalIsotopeAverageSp());
387  }
388  }
389  }
390  if(v_isotopeAverageList.size() == 0)
391  return v_isotopeAverageListResult;
392 
393  // qDebug() << "getByIntensityRatioByIsotopeNumber comp";
394  std::sort(v_isotopeAverageList.begin(),
395  v_isotopeAverageList.end(),
396  [](const PeptideNaturalIsotopeAverageSp &m,
398  return (m.get()->getIntensityRatio() >
399  n.get()->getIntensityRatio());
400  });
401 
402  cumulativeRatio = 0;
403  auto it = v_isotopeAverageList.begin();
404  v_isotopeAverageListResult.clear();
405  // qDebug() << "getByIntensityRatioByIsotopeNumber cumul";
406  while((it != v_isotopeAverageList.end()) &&
407  (cumulativeRatio < minimumIntensity))
408  {
409  cumulativeRatio += it->get()->getIntensityRatio();
410  v_isotopeAverageListResult.push_back(*it);
411  it++;
412  }
413 
414  // qDebug() << "getByIntensityRatioByIsotopeNumber end";
415 
416  return v_isotopeAverageListResult;
417 }
418 
419 
420 /** /brief get a sorted (by expected intensity) vector of natural isotope
421  * average
422  *
423  * */
424 std::vector<PeptideNaturalIsotopeAverageSp>
425 PeptideNaturalIsotopeList::getByIntensityRatio(
426  unsigned int charge,
427  PrecisionPtr precision,
428  pappso_double minimumIntensityRatio) const
429 {
430 
431  // qDebug() << "PeptideNaturalIsotopeList::getByIntensityRatio begin";
432  std::vector<PeptideNaturalIsotopeAverageSp>
433  peptide_natural_isotope_average_list;
434 
435  std::map<unsigned int, pappso::pappso_double> map_isotope_number =
436  getIntensityRatioPerIsotopeNumber();
437  std::vector<std::pair<unsigned int, pappso::pappso_double>>
438  sorted_number_ratio;

◆ getPeptideIonDirection()

PeptideDirection pappso::getPeptideIonDirection ( PeptideIon  ion_type)

get the direction of a peptide ion

Parameters
ion_typethe ion to test
Returns
the peptide direction

Definition at line 75 of file peptide.cpp.

79  {
80  m_aaVec.push_back(Aa(it->toLatin1()));
81  it++;
82  }

References pappso::Peptide::m_aaVec.

Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon().

◆ isotopem_ratio()

pappso_double pappso::isotopem_ratio ( pappso_double  abundance,
unsigned int  total,
unsigned int  heavy 
)

Definition at line 79 of file peptidenaturalisotope.cpp.

80 {
81  return (pow(abundance, heavy) * pow((double)1 - abundance, (total - heavy)) *
82  (double)Combinations(total, heavy));
83 }

References Combinations().

Referenced by isotopem_ratio_cache().

◆ isotopem_ratio_cache()

pappso_double pappso::isotopem_ratio_cache ( Isotope  isotope,
unsigned int  total,
unsigned int  heavy 
)

Definition at line 95 of file peptidenaturalisotope.cpp.

96 {
97  pappso_double abundance = 1;
98  switch(isotope)
99  {
100  case Isotope::H2:
101  abundance = ABUNDANCEH2;
102  if(total < CACHE_ARRAY_SIZE)
103  {
104  if(ratioH2_cache[total][heavy] == 0)
105  {
106  ratioH2_cache[total][heavy] =
107  isotopem_ratio(abundance, total, heavy);
108  }
109  return ratioH2_cache[total][heavy];
110  }
111  break;
112  case Isotope::C13:
113  abundance = ABUNDANCEC13;
114  if(total < CACHE_ARRAY_SIZE)
115  {
116  if(ratioC13_cache[total][heavy] == 0)
117  {
118  ratioC13_cache[total][heavy] =
119  isotopem_ratio(abundance, total, heavy);
120  }
121  return ratioC13_cache[total][heavy];
122  }
123  break;
124  case Isotope::N15:
125  abundance = ABUNDANCEN15;
126  if(total < CACHE_ARRAY_SIZE)
127  {
128  if(ratioN15_cache[total][heavy] == 0)
129  {
130  ratioN15_cache[total][heavy] =
131  isotopem_ratio(abundance, total, heavy);
132  }
133  return ratioN15_cache[total][heavy];
134  }
135  break;
136  case Isotope::O18:
137  abundance = ABUNDANCEO18;
138  if(total < CACHE_ARRAY_SIZE)
139  {
140  if(ratioO18_cache[total][heavy] == 0)
141  {
142  ratioO18_cache[total][heavy] =
143  isotopem_ratio(abundance, total, heavy);
144  }
145  return ratioO18_cache[total][heavy];
146  }
147  break;
148  case Isotope::O17:
149  abundance = ABUNDANCEO17;
150  if(total < CACHE_ARRAY_SIZE)
151  {
152  if(ratioO17_cache[total][heavy] == 0)
153  {
154  ratioO17_cache[total][heavy] =
155  isotopem_ratio(abundance, total, heavy);
156  }
157  return ratioO17_cache[total][heavy];
158  }
159  break;
160  case Isotope::S33:
161  abundance = ABUNDANCES33;
162  if(total < CACHE_ARRAY_SIZE)
163  {
164  if(ratioS33_cache[total][heavy] == 0)
165  {
166  ratioS33_cache[total][heavy] =
167  isotopem_ratio(abundance, total, heavy);
168  }
169  return ratioS33_cache[total][heavy];
170  }
171  break;
172  case Isotope::S34:
173  abundance = ABUNDANCES34;
174  if(total < CACHE_ARRAY_SIZE)
175  {
176  if(ratioS34_cache[total][heavy] == 0)
177  {
178  ratioS34_cache[total][heavy] =
179  isotopem_ratio(abundance, total, heavy);
180  }
181  return ratioS34_cache[total][heavy];
182  }
183  break;
184  case Isotope::S36:
185  abundance = ABUNDANCES36;
186  if(total < CACHE_ARRAY_SIZE)
187  {
188  if(ratioS36_cache[total][heavy] == 0)
189  {
190  ratioS36_cache[total][heavy] =
191  isotopem_ratio(abundance, total, heavy);
192  }
193  return ratioS36_cache[total][heavy];
194  }
195  break;
196  }
197  return isotopem_ratio(abundance, total, heavy);
198 }

References ABUNDANCEC13(), ABUNDANCEH2(), ABUNDANCEN15(), ABUNDANCEO17(), ABUNDANCEO18(), ABUNDANCES33(), ABUNDANCES34(), ABUNDANCES36(), CACHE_ARRAY_SIZE, isotopem_ratio(), ratioC13_cache, ratioH2_cache, ratioN15_cache, ratioO17_cache, ratioO18_cache, ratioS33_cache, ratioS34_cache, and ratioS36_cache.

Referenced by pappso::PeptideNaturalIsotope::getIntensityRatio(), and pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ MASSCARBON()

const pappso_double pappso::MASSCARBON ( 12  )

◆ MASSCO()

const pappso_double pappso::MASSCO ( MASSCARBON MASSOXYGEN)

◆ MASSH2O()

const pappso_double pappso::MASSH2O ( (MPROTIUM *2)+  MASSOXYGEN)

◆ MASSNH3()

const pappso_double pappso::MASSNH3 ( (MPROTIUM *3)+  MASSNITROGEN)

◆ MASSNITROGEN()

const pappso_double pappso::MASSNITROGEN ( 14.  0030740048)

◆ MASSOXYGEN()

const pappso_double pappso::MASSOXYGEN ( 15.  99491461956)

◆ MASSPHOSPHORUS()

const pappso_double pappso::MASSPHOSPHORUS ( 30.  973761998)

◆ MASSPHOSPHORYLATEDR()

const pappso_double pappso::MASSPHOSPHORYLATEDR ( MPROTIUM+(MASSOXYGEN *3)+  MASSPHOSPHORUS)

◆ MASSSELENIUM()

const pappso_double pappso::MASSSELENIUM ( 79.  916520)

◆ MASSSULFUR()

const pappso_double pappso::MASSSULFUR ( 31.  97207100)

◆ maxYDataPoint() [1/2]

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::maxYDataPoint ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end 
)

Definition at line 138 of file trace.cpp.

140 {
141  return std::max_element(
142  begin, end, [](const DataPoint &a, const DataPoint &b) {
143  return a.y < b.y;
144  });
145 }

References a, and b.

Referenced by pappso::FilterTriangle::filter(), pappso::FilterLocalMaximum::filter(), pappso::FilterHighPassPercentage::filter(), pappso::FilterRescaleY::filter(), pappso::LinearRegression::getNrmsd(), pappso::FilterMorphoMax::getWindowValue(), and pappso::MsRunXicExtractor::getXicCstSPtr().

◆ maxYDataPoint() [2/2]

PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::maxYDataPoint ( std::vector< DataPoint >::iterator  begin,
std::vector< DataPoint >::iterator  end 
)

find the element with the greatest Y value (intensity)

Definition at line 149 of file trace.cpp.

151 {
152  return std::max_element(
153  begin, end, [](const DataPoint &a, const DataPoint &b) {
154  return a.y < b.y;
155  });
156 }

References a, and b.

◆ meanYTrace()

PMSPP_LIB_DECL double pappso::meanYTrace ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end 
)

calculate the mean of y value of a trace

Definition at line 202 of file trace.cpp.

204 {
205  pappso_double nb_element = distance(begin, end);
206  if(nb_element == 0)
207  throw ExceptionOutOfRange(
208  QObject::tr("unable to compute mean on a trace of size 0"));
209  return (sumYTrace(begin, end, 0) / nb_element);
210 }

References sumYTrace().

Referenced by pappso::LinearRegression::getCoefficientOfDetermination(), and pappso::FilterMorphoMean::getWindowValue().

◆ medianYTrace()

PMSPP_LIB_DECL double pappso::medianYTrace ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end 
)

calculate the median of y value of a trace

Definition at line 213 of file trace.cpp.

215 {
216  pappso_double nb_element = distance(begin, end);
217  if(nb_element == 0)
218  throw ExceptionOutOfRange(
219  QObject::tr("unable to compute median on a trace of size 0"));
220 
221  std::vector<DataPoint> data(begin, end);
222  std::nth_element(
223  data.begin(),
224  data.begin() + data.size() / 2,
225  data.end(),
226  [](const DataPoint &a, const DataPoint &b) { return a.y < b.y; });
227  return data[data.size() / 2].y;
228 }

References a, and b.

Referenced by pappso::FilterMorphoMedian::getWindowValue().

◆ MHPLUS()

◆ minYDataPoint() [1/2]

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::minYDataPoint ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end 
)

Definition at line 116 of file trace.cpp.

118 {
119  return std::min_element(
120  begin, end, [](const DataPoint &a, const DataPoint &b) {
121  return a.y < b.y;
122  });
123 }

References a, and b.

Referenced by pappso::FilterGreatestYperWindow::filter(), pappso::LinearRegression::getNrmsd(), and pappso::FilterMorphoMin::getWindowValue().

◆ minYDataPoint() [2/2]

PMSPP_LIB_DECL std::vector< DataPoint >::iterator pappso::minYDataPoint ( std::vector< DataPoint >::iterator  begin,
std::vector< DataPoint >::iterator  end 
)

find the element with the smallest Y value (intensity)

Definition at line 127 of file trace.cpp.

129 {
130  return std::min_element(
131  begin, end, [](const DataPoint &a, const DataPoint &b) {
132  return a.y < b.y;
133  });
134 }

References a, and b.

◆ moveLowerYLeftDataPoint()

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::moveLowerYLeftDataPoint ( const Trace trace,
std::vector< DataPoint >::const_iterator  begin 
)

Move left to the lower value.

Definition at line 176 of file trace.cpp.

178 {
179  if(begin == trace.begin())
180  return begin;
181  auto it = begin - 1;
182  auto result = begin;
183  while((it != trace.begin()) && (it->y <= result->y))
184  {
185  it--;
186  result--;
187  }
188  return result;
189 }

◆ moveLowerYRigthDataPoint()

PMSPP_LIB_DECL std::vector< DataPoint >::const_iterator pappso::moveLowerYRigthDataPoint ( const Trace trace,
std::vector< DataPoint >::const_iterator  begin 
)

Move right to the lower value.

Definition at line 160 of file trace.cpp.

162 {
163  if(begin == trace.end())
164  return begin;
165  auto it = begin + 1;
166  auto result = begin;
167  while((it != trace.end()) && (it->y <= result->y))
168  {
169  it++;
170  result++;
171  }
172  return result;
173 }

◆ MPROTIUM()

const pappso_double pappso::MPROTIUM ( 1.  007825032241)

◆ MPROTON()

◆ ONEMILLION()

const pappso_double pappso::ONEMILLION ( 1000000  )

◆ operator<()

bool pappso::operator< ( Aa const &  l,
Aa const &  r 
)

Definition at line 305 of file aa.cpp.

◆ operator<<() [1/3]

QDataStream & pappso::operator<< ( QDataStream &  out,
const DataPoint dataPoint 
)

Definition at line 130 of file datapoint.cpp.

132 {
133  out << dataPoint.x;
134  out << dataPoint.y;
135 
136  return out;
137 }

References pappso::DataPoint::x, and pappso::DataPoint::y.

◆ operator<<() [2/3]

QDataStream & pappso::operator<< ( QDataStream &  out,
const Trace trace 
)

◆ operator<<() [3/3]

QDataStream & pappso::operator<< ( QDataStream &  outstream,
const MassSpectrum massSpectrum 
)

Definition at line 358 of file massspectrum.cpp.

359  {
360  instream >> vector_size;
361  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
362  << " vector_size=" << vector_size;
363 
364  for(quint32 i = 0; i < vector_size; i++)
365  {
366 
367  if(instream.status() != QDataStream::Ok)
368  {
369  throw PappsoException(

◆ operator==()

bool pappso::operator== ( Aa const &  l,
Aa const &  r 
)

Definition at line 300 of file aa.cpp.

◆ operator>>() [1/4]

QDataStream & pappso::operator>> ( QDataStream &  in,
DataPoint dataPoint 
)

Definition at line 141 of file datapoint.cpp.

142 {
143 
144  if(in.atEnd())
145  {
146  throw PappsoException(
147  QString("error in QDataStream unserialize operator>> of massSpectrum "
148  "dataPoint:\nread datastream failed status=%1")
149  .arg(in.status()));
150  }
151  in >> dataPoint.x;
152  in >> dataPoint.y;
153 
154  return in;
155 }

References pappso::DataPoint::x, and pappso::DataPoint::y.

◆ operator>>() [2/4]

QDataStream & pappso::operator>> ( QDataStream &  instream,
MassSpectrum massSpectrum 
)

Definition at line 373 of file massspectrum.cpp.

382  {
383  throw PappsoException(
384  QString(
385  "error in QDataStream unserialize operator>> of massSpectrum "
386  ":\nread datastream failed status=%1")
387  .arg(instream.status()));
388  }
389  }
390 
391  return instream;
392 }
393 
394 
395 MassSpectrum &
396 MassSpectrum::massSpectrumFilter(const MassSpectrumFilterInterface &filter)
397 {
398  return filter.filter(*this);
399 }
400 
401 } // namespace pappso

◆ operator>>() [3/4]

QDataStream & pappso::operator>> ( QDataStream &  instream,
MsRunSlice slice 
)

Definition at line 177 of file msrunslice.cpp.

178  {
179  instream >> spectrum;
180  }
181  catch(PappsoException &error)
182  {
183  throw PappsoException(
184  QString("error in QDataStream unserialize operator>> of "
185  "MsRunSlice %2 on %3:\n%1")
186  .arg(error.qwhat())
187  .arg(spectrum_position)
188  .arg(vector_size));
189  }
190  slice.setSpectrum(spectrum_position, spectrum);
191 
192  if(instream.status() != QDataStream::Ok)
193  {
194  throw PappsoException(
195  QString("error in QDataStream unserialize operator>> of "
196  "MsRunSlice :\nread datastream failed status=%1")
197  .arg(instream.status()));
198  }
199  }
200  }
201 
202  if(slice.size() != vector_size)
203  {
204  throw PappsoException(
205  QString("error in QDataStream unserialize operator>> of MsRunSlice "
206  "slice.size() != vector_size :\n %1 %2:")
207  .arg(slice.size())
208  .arg(vector_size));
209  }
210 
211  return instream;
212 }
213 
214 
215 } // namespace pappso

◆ operator>>() [4/4]

QDataStream & pappso::operator>> ( QDataStream &  out,
Trace trace 
)

◆ peptideIonIsNter()

bool pappso::peptideIonIsNter ( PeptideIon  ion_type)

tells if an ion is Nter

Parameters
ion_typethe ion to test

Definition at line 65 of file peptide.cpp.

68  {
69  // first amino acid is the Nter one
70  // by default, it is obtained by hydrolytic cleavage in normal water
71  // and it is loaded with one Hydrogen
72  Aa nter_aa(it->toLatin1());

Referenced by pappso::XtandemHyperscoreBis::getXtandemPredictedIonIntensityFactor(), and pappso::PeptideRawFragmentMasses::pushBackIonMasses().

◆ sumYTrace()

PMSPP_LIB_DECL double pappso::sumYTrace ( std::vector< DataPoint >::const_iterator  begin,
std::vector< DataPoint >::const_iterator  end,
double  init 
)

calculate the sum of y value of a trace

Definition at line 193 of file trace.cpp.

196 {
197  return std::accumulate(
198  begin, end, init, [](double a, const DataPoint &b) { return a + b.y; });
199 }

References a, and b.

Referenced by pappso::FilterMorphoSum::getWindowValue(), pappso::LinearRegression::LinearRegression(), meanYTrace(), and pappso::Trace::sumY().

Variable Documentation

◆ combinations_cache

uint64_t pappso::combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 44 of file peptidenaturalisotope.cpp.

Referenced by Combinations().

◆ MsRunReader

Definition at line 223 of file msrunreader.h.

◆ ratioC13_cache

pappso_double pappso::ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 85 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioH2_cache

pappso_double pappso::ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 92 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioN15_cache

pappso_double pappso::ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 86 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioO17_cache

pappso_double pappso::ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 90 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioO18_cache

pappso_double pappso::ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 91 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioS33_cache

pappso_double pappso::ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 89 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioS34_cache

pappso_double pappso::ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 88 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

◆ ratioS36_cache

pappso_double pappso::ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE] = {0}

Definition at line 87 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

pappso::ratioH2_cache
pappso_double ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:92
pappso::AminoAcidChar::glycine
@ glycine
pappso::DataCompression::zlib
@ zlib
zlib compresssion
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:69
pappso::ratioS34_cache
pappso_double ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:88
pappso::ratioO17_cache
pappso_double ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:90
pappso::MHPLUS
const pappso_double MHPLUS(1.007276466879)
pappso::AminoAcidChar::glutamine
@ glutamine
pappso::ABUNDANCEO17
const pappso_double ABUNDANCEO17(0.000372)
pappso::AminoAcidChar::alanine
@ alanine
pappso::ABUNDANCES36
const pappso_double ABUNDANCES36(0.00020)
pappso::FileReaderType::xy
@ xy
pappso::AminoAcidChar::lysine
@ lysine
pappso::ABUNDANCES33
const pappso_double ABUNDANCES33(0.00750)
pappso::AminoAcidChar::proline
@ proline
pappso::ABUNDANCEH2
const pappso_double ABUNDANCEH2(0.00015574)
pappso::FileReaderType::tims
@ tims
pappso::RangeType::innermost
@ innermost
pappso::DataKind
DataKind
Definition: types.h:192
pappso::FileReaderType::pwiz
@ pwiz
pappso::ratioC13_cache
pappso_double ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:85
pappso::ABUNDANCEN15
const pappso_double ABUNDANCEN15(0.003663)
pappso::PeptideIonNter::a
@ a
pappso::AminoAcidChar::aspartic_acid
@ aspartic_acid
pappso::DataKind::rt
@ rt
Retention time.
pappso::Combinations
uint64_t Combinations(unsigned int n, unsigned int k)
Definition: peptidenaturalisotope.cpp:47
pappso::AminoAcidChar::glutamic_acid
@ glutamic_acid
pappso::PrecisionUnit::none
@ none
pappso::MPROTON
const pappso_double MPROTON(1.007276466879)
pappso::AminoAcidChar::isoleucine
@ isoleucine
pappso::AminoAcidChar::methionine
@ methionine
pappso::isotopem_ratio
pappso_double isotopem_ratio(pappso_double abundance, unsigned int total, unsigned int heavy)
Definition: peptidenaturalisotope.cpp:79
pappso::DataCompression::unset
@ unset
not net
pappso::sumYTrace
double sumYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
calculate the sum of y value of a trace
Definition: trace.cpp:193
pappso::AminoAcidChar::leucine
@ leucine
pappso::AminoAcidChar::asparagine
@ asparagine
pappso::AtomIsotope::C
@ C
pappso::AtomIsotope::N
@ N
pappso::AtomIsotope::H
@ H
pappso::AminoAcidChar::phenylalanine
@ phenylalanine
pappso::AminoAcidChar::histidine
@ histidine
pappso::PlotAxis::both
@ both
pappso::combinations_cache
uint64_t combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:44
pappso::FileReaderType::tims_ms2
@ tims_ms2
pappso::RangeType::outermost
@ outermost
pappso::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition: precision.h:143
CACHE_ARRAY_SIZE
#define CACHE_ARRAY_SIZE
Definition: peptidenaturalisotope.cpp:42
pappso::AtomIsotope::O
@ O
pappso::ABUNDANCES34
const pappso_double ABUNDANCES34(0.04215)
pappso::ABUNDANCEC13
const pappso_double ABUNDANCEC13(0.011078)
pappso::ratioS36_cache
pappso_double ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:87
pappso::PeptideIonNter::b
@ b
pappso::ratioN15_cache
pappso_double ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:86
pappso::PrecisionUnit::mz
@ mz
pappso::AtomIsotope::S
@ S
pappso::DataKind::dt
@ dt
Drift time.
pappso::AminoAcidChar::cysteine
@ cysteine
pappso::PlotAxis::y_axis
@ y_axis
pappso::MPROTIUM
const pappso_double MPROTIUM(1.007825032241)
pappso::PlotAxis::x_axis
@ x_axis
pappso::ABUNDANCEO18
const pappso_double ABUNDANCEO18(0.0020004)
pappso::ratioO18_cache
pappso_double ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:91
pappso::PeptideNaturalIsotopeAverageSp
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp
Definition: peptidenaturalisotopeaverage.h:58
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:75
pappso::ratioS33_cache
pappso_double ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:89