libpappsomspp
Library for mass spectrometry
pappso Namespace Reference

tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge More...

Classes

class  Aa
 
class  AaBase
 
class  AaModification
 
class  AtomNumberInterface
 
class  ExceptionInterrupted
 
class  ExceptionNotFound
 
class  ExceptionNotImplemented
 
class  ExceptionNotPossible
 
class  ExceptionNotRecognized
 excetion to use when an item type is not recognized More...
 
class  ExceptionOutOfRange
 
class  FastaFileIndexerInterface
 
class  FastaFileIndexer
 
class  FastaHandlerInterface
 
class  FastaOutputStream
 
class  FastaReader
 
class  FastaWriterInterface
 
class  GrpExperiment
 
class  GrpGroup
 
class  GrpGroupingMonitorInterface
 
class  GrpGroupingMonitor
 
class  GrpMapPeptideToGroup
 
class  GrpMapPeptideToSubGroupSet
 
class  GrpPeptide
 
class  GrpPeptideSet
 
class  GrpProtein
 
class  GrpSubGroup
 
class  GrpSubGroupSet
 
class  MassSpectrum
 Class to represent a mass spectrum. More...
 
class  MassSpectrumId
 
struct  PrecursorIonData
 
class  QualifiedMassSpectrum
 Class representing a fully specified mass spectrum. More...
 
class  MsFileAccessor
 
class  MsFileReader
 
class  MzFormatEnumStr
 static functions to convert mz file formats More...
 
class  PwizMsFileReader
 
class  TimsMsFileReader
 
class  XyMsFileReader
 
class  MsRunAlignment
 
struct  MsRunRetentionTimeSeamarkPoint
 
class  MsRunRetentionTime
 
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  SpectrumCollectionHandlerInterface
 interface to collect spectrums from the MsRunReader class More...
 
class  MsRunSimpleStatistics
 example of interface to count MS levels of all spectrum in an MSrun More...
 
class  MsRunReaderScanNumberMultiMap
 provides a multimap to find quickly spectrum index from scan number More...
 
class  MsRunReaderRetentionTimeLine
 collect retention times along MS run More...
 
class  MsRunReaderTicChromatogram
 calculate a TIC chromatogram More...
 
class  MsRunReader
 base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More...
 
class  MgfOutput
 
class  MzxmlOutput
 
class  PwizMsRunReader
 
class  TimsFramesMsRunReader
 
class  TimsMsRunReader
 
class  TimsMsRunReaderMs2
 
class  TimsMsRunReaderMs2Selected
 
struct  XicCoord
 coordinates of the XIC to extract and the resulting XIC after extraction More...
 
struct  XicCoordTims
 coordinates of the XIC to extract and the resulting XIC after extraction More...
 
class  XyMsRunReader
 
class  MzRange
 
class  FilterOboPsiModSink
 
class  FilterOboPsiModTermAccession
 
class  FilterOboPsiModTermDiffMono
 
class  FilterOboPsiModTermLabel
 
class  FilterOboPsiModTermName
 
class  OboPsiMod
 
class  OboPsiModHandlerInterface
 
class  OboPsiModTerm
 
class  PappsoException
 
class  Ion
 
class  Peptide
 
class  PeptideFragment
 
class  PeptideFragmentIon
 
class  PeptideFragmentIonListBase
 
class  PeptideInterface
 
class  PeptideNaturalIsotope
 
class  PeptideNaturalIsotopeAverage
 
class  PeptideNaturalIsotopeList
 
struct  SimplePeakIonMatch
 
class  PeptideRawFragmentMasses
 
class  PeptideStrParser
 
class  PrecisionBase
 
class  DaltonPrecision
 
class  PpmPrecision
 
class  ResPrecision
 
class  PrecisionFactory
 
class  MassDataCombinerInterface
 
class  MassSpectrumCombiner
 
class  MassSpectrumMinusCombiner
 
class  MassSpectrumPlusCombiner
 
class  MzIntegrationParams
 The MzIntegrationParams class provides the parameters definining how m/z ! More...
 
class  SelectionPolygon
 
struct  SelectionPolygonSpec
 
class  TraceCombiner
 
class  TraceMinusCombiner
 
class  TracePlusCombiner
 
class  TraceDetectionSinkInterface
 
class  TraceDetectionInterface
 
class  TraceDetectionMoulon
 
class  TraceDetectionZivy
 
class  TracePeak
 
class  TracePeakList
 
class  FilterCeilingAmplitudePercentage
 Redefines the ceiling intensity of the Trace. More...
 
class  FilterChargeDeconvolution
 
class  FilterComplementIonEnhancer
 try to detect complementary ions and assign maximum intensity of both elements More...
 
class  FilterMzExclusion
 
class  FilterFloorAmplitudePercentage
 Redefines the floor intensity of the Trace. More...
 
class  FilterInterface
 generic interface to apply a filter on a trace More...
 
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  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  FilterLowIntensitySignalRemoval
 Redefines the floor intensity of the Trace. More...
 
class  FilterMorphoWindowBase
 base class that apply a signal treatment based on a window More...
 
class  FilterMorphoSum
 test purpose More...
 
class  FilterMorphoMax
 transform the trace into its maximum over a 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  FilterMorphoMaxMin
 transform the trace with the maximum of the minimum equivalent of the erode filter for pictures More...
 
class  FilterMorphoAntiSpike
 anti spike filter set to zero alone values inside the window More...
 
class  FilterMorphoMedian
 median filter apply median of y values inside the window More...
 
class  FilterMorphoMean
 mean filter apply mean of y values inside the window : this results in a kind of smoothing More...
 
class  FilterMorphoBackground
 compute background of a trace compute background noise on a trace More...
 
class  FilterNameInterface
 Interface that allows to build filter objects from strings. More...
 
class  FilterLowPass
 remove datapoints higher than a given Y value (intensity) 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  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  MassSpectrumFilterGreatestItensities
 
class  FilterFloorY
 apply std::floor (round to lowest integer) to all Y values More...
 
class  FilterRoundY
 apply std::round (round to nearest integer) to all Y values More...
 
class  FilterRescaleY
 rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored More...
 
class  FilterScaleFactorY
 rescales Y values given a tranformation factor More...
 
class  FilterRemoveY
 removes a value to all Y values More...
 
class  FilterQuantileBasedRemoveY
 removes a value found by quantile to all Y values More...
 
class  FilterRemoveC13
 
class  FilterResampleKeepSmaller
 
class  FilterResampleKeepGreater
 
class  FilterResampleRemoveXRange
 
class  FilterResampleKeepXRange
 
class  FilterResampleKeepPointInPolygon
 
class  MassSpectrumFilterResampleRemoveMzRange
 
class  MassSpectrumFilterResampleKeepMzRange
 
class  FilterSuite
 apply a suite of filters from a vector More...
 
class  FilterSuiteString
 
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
 
struct  SavGolParams
 Parameters for the Savitzky-Golay filter. More...
 
class  FilterSavitzkyGolay
 uses Savitsky-Golay filter on trace More...
 
class  XtandemError
 
class  TandemWrapperRun
 
class  WrapTandemInput
 
class  WrapTandemResults
 
class  XtandemPresetReader
 
class  UiMonitorInterface
 
class  UiMonitorText
 
class  UiMonitorTextPercent
 
class  UiMonitorVoid
 
class  XmlStreamReaderInterface
 convenient xml reader helper More...
 
class  Enzyme
 
class  EnzymeProductInterface
 
class  PeptideModificatorInterface
 
class  PeptideSinkInterface
 
class  PeptideSpSinkInterface
 
class  PeptideBuilder
 builds a peptide shared pointer from peptide string and adds fixed modifications More...
 
class  PeptideFixedModificationBuilder
 
class  PeptideMethioninRemove
 potential remove Nter Methionin More...
 
class  PeptideModificatorBase
 
class  PeptideModificatorPipeline
 
class  PeptideModificatorTee
 
class  PeptideSemiEnzyme
 cut a regular peptide obtained with an enzyme at any position from Nter or Cter More...
 
class  PeptideSizeFilter
 filter peptide string by size More...
 
class  PeptideVariableModificationBuilder
 Modify a peptide shared pointer with a variable modification on one AA. More...
 
class  PeptideVariableModificationReplacement
 
class  Protein
 
class  DeepProtEnumStr
 
class  IonIsotopeRatioScore
 
class  PsmFeatures
 
class  MorpheusScore
 
class  PeakIonIsotopeMatch
 
class  PeakIonMatch
 
class  PeptideIsotopeSpectrumMatch
 
class  PeptideSpectrumMatch
 
class  XtandemHyperscore
 
class  XtandemHyperscoreBis
 
class  XtandemSpectrumProcess
 
struct  DataPoint
 
class  LinearRegression
 
class  MapTrace
 
class  Trace
 A simple container of DataPoint instances. More...
 
class  Utils
 
class  MzCalibrationInterface
 
class  MzCalibrationModel1
 
class  MzCalibrationModel1Cached
 
class  MzCalibrationStore
 
class  TimsBinDec
 
struct  FrameIdDescr
 
class  TimsData
 
class  TimsFrame
 
class  TimsFrameBase
 
class  TimsFrameRawDataChunck
 
struct  TimsFrameRecord
 
class  TimsFrameType1
 
class  TimsMs2CentroidFilter
 
class  TimsDirectXicExtractor
 
class  TimsXicExtractorInterface
 
class  HttpButton
 
class  MassSpectrumWidget
 
class  QCPSpectrum
 
class  OboChooserWidget
 
class  OboListModel
 
class  OboListProxyModel
 
class  OboListWidget
 
class  OboTermForm
 
class  BaseColorMapPlotWidget
 
class  BasePlotContext
 
class  BasePlotWidget
 
class  BaseTracePlotWidget
 
struct  ColorMapPlotConfig
 
class  DriftSpecMassSpecColorMapPlotWidget
 
class  DriftSpecTracePlotWidget
 
class  MassSpecTracePlotContext
 
class  MassSpecTracePlotWidget
 
class  TicXicChromDriftSpecColorMapPlotWidget
 
class  TicXicChromMassSpecColorMapPlotWidget
 
class  TicXicChromTracePlotWidget
 
class  PrecisionWidget
 
class  SwitchWidget
 
class  QCPXic
 
class  XicWidget
 
class  QualifiedXic
 
class  Xic
 
class  XicPeptideFragmentIon
 
class  XicPeptideFragmentIonNaturalIsotope
 
class  XicPeptideInterface
 
class  MsRunXicExtractorFactory
 factory to build different kinds of XIC extractors More...
 
class  MsRunXicExtractorInterface
 
class  MsRunSlice
 
class  MsRunXicExtractor
 
class  MsRunXicExtractorDisk
 
class  MsRunXicExtractorDiskBuffer
 

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< XicCoordXicCoordSPtr
 
typedef std::shared_ptr< XicCoordTimsXicCoordTimsSPtr
 
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< FilterCeilingAmplitudePercentageFilterCeilingAmplitudePercentageSPtr
 
typedef std::shared_ptr< const FilterCeilingAmplitudePercentageFilterCeilingAmplitudePercentageCstSPtr
 
typedef std::shared_ptr< FilterFloorAmplitudePercentageFilterFloorAmplitudePercentageSPtr
 
typedef std::shared_ptr< const FilterFloorAmplitudePercentageFilterFloorAmplitudePercentageCstSPtr
 
typedef std::shared_ptr< FilterInterfaceFilterInterfaceSPtr
 
typedef std::shared_ptr< const FilterInterfaceFilterInterfaceCstSPtr
 
typedef std::shared_ptr< FilterLowIntensitySignalRemovalFilterLowIntensitySignalRemovalSPtr
 
typedef std::shared_ptr< const FilterLowIntensitySignalRemovalFilterLowIntensitySignalRemovalCstSPtr
 
typedef std::shared_ptr< FilterNameInterfaceFilterNameInterfaceSPtr
 
typedef std::shared_ptr< const FilterNameInterfaceFilterNameInterfaceCstSPtr
 
using SelectionPolygonSpecVector = std::vector< SelectionPolygonSpec >
 
typedef std::shared_ptr< FilterSuiteStringFilterSuiteStringSPtr
 
typedef std::shared_ptr< FilterSavitzkyGolayFilterSavitzkyGolaySPtr
 
typedef std::shared_ptr< const FilterSavitzkyGolayFilterSavitzkyGolayCstSPtr
 
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< MzCalibrationInterfaceMzCalibrationInterfaceSPtr
 
typedef std::shared_ptr< TimsDataTimsDataSp
 shared pointer on a TimsData object More...
 
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 class  QualifiedMassSpectrumParameter {
  OneOverK0 , OneOverK0begin , OneOverK0end , IsolationMz ,
  IsolationWidth , CollisionEnergy , BrukerPrecursorIndex , last
}
 
enum class  FileReaderType {
  pwiz , xy , tims , tims_frames ,
  tims_ms2
}
 
enum class  PeptideDirection : std::int8_t { Nter = 0 , Cter = 1 }
 
enum class  PeptideIonNter {
  b , bstar , bo , a ,
  astar , ao , bp , c
}
 
enum class  PeptideIonCter {
  y , ystar , yo , z ,
  yp , x
}
 
enum class  AtomIsotope {
  C , H , O , N ,
  S
}
 
enum class  RawFragmentationMode : std::int8_t { full = 0 , proline_effect = 1 }
 
enum class  BinningType { NONE = 0 , DATA_BASED , ARBITRARY , LAST }
 Type of binning when performing integrations to a mass spectrum. More...
 
enum class  PointSpecs {
  TOP_LEFT_POINT = 0 , TOP_RIGHT_POINT = 1 , BOTTOM_RIGHT_POINT = 2 , BOTTOM_LEFT_POINT = 3 ,
  ENUM_LAST = 4
}
 
enum class  DataDimension { NOT_SET = 0 , HORIZONTAL , VERTICAL }
 
enum class  PolygonType {
  NOT_SET = 0x0000 , TOP_LINE = 1 << 0 , BOTTOM_LINE = 1 << 1 , HORIZONTAL_LINES = (TOP_LINE | BOTTOM_LINE) ,
  RIGHT_LINE = 1 << 2 , LEFT_LINE = 1 << 3 , VERTICAL_LINES = (RIGHT_LINE | LEFT_LINE) , FULL_POLYGON = (HORIZONTAL_LINES | VERTICAL_LINES)
}
 
enum class  DeepProtMatchType : std::uint8_t {
  uncategorized = 0 , ZeroMassDelta = 1 , ZeroMassDeltaMissedCleavage , ZeroMassDeltaSemiTryptic ,
  DeltaPosition = 4 , NoDeltaPosition = 5 , last = 6
}
 definition of different class of PSMs used by DeepProt More...
 
enum class  DeepProtPeptideCandidateStatus : std::uint8_t {
  unmodified = 0 , ZeroMassDelta = 1 , CterRemoval = 2 , NterRemoval = 3 ,
  MissedCleavage = 4 , DeltaPosition = 5 , NoDeltaPosition = 6 , last = 7
}
 definition of different status for potential peptide candidates on the same spectrum More...
 
enum class  PrecisionUnit {
  none , dalton , ppm , res ,
  mz , last
}
 
enum class  AtomIsotopeSurvey : std::int8_t {
  C , H , O , N ,
  S , last
}
 
enum class  Isotope {
  C13 , H2 , O17 , O18 ,
  N15 , S33 , S34 , S36
}
 
enum class  MzFormat : std::int8_t {
  unknown = 0 , mzML = 1 , mzXML = 2 , MGF = 3 ,
  SQLite3 = 4 , xy = 5 , mz5 = 6 , msn = 7 ,
  abSciexWiff = 8 , abSciexT2D = 9 , agilentMassHunter = 10 , thermoRaw = 11 ,
  watersRaw = 12 , brukerFid = 13 , brukerYep = 14 , brukerBaf = 15 ,
  brukerTims = 16 , last = 17
}
 
enum class  AminoAcidChar : char {
  alanine = 'A' , cysteine = 'C' , aspartic_acid = 'D' , glutamic_acid = 'E' ,
  phenylalanine = 'F' , glycine = 'G' , histidine = 'H' , isoleucine = 'I' ,
  lysine = 'K' , leucine = 'L' , methionine = 'M' , asparagine = 'N' ,
  proline = 'P' , glutamine = 'Q' , arginine = 'R' , serine = 'S' ,
  threonine = 'T' , valine = 'V' , tryptophan = 'W' , tyrosine = 'Y' ,
  selenocysteine = 'U' , pyrrolysine = 'O'
}
 
enum class  DataCompression : std::int8_t { unset = -1 , none = 0 , zlib = 1 }
 
enum class  DataKind : std::int8_t { unset = -1 , rt = 0 , dt = 1 , mz = 2 }
 
enum class  Axis : std::int8_t { unset = 0x000 , x = 1 << 0 , y = 1 << 1 , z = 1 << 2 }
 
enum class  AxisScale : std::int8_t { unset = 0 , orig = 1 , log10 = 2 }
 
enum class  XicExtractMethod : std::int8_t { sum = 1 , max = 2 }
 
enum class  PeptideIon : std::int8_t {
  b = 0 , bstar = 1 , bo = 2 , a = 3 ,
  astar = 4 , ao = 5 , bp = 6 , c = 7 ,
  y = 8 , ystar = 9 , yo = 10 , z = 11 ,
  yp = 12 , x = 13
}
 PeptideIon enum defines all types of ions (Nter or Cter) More...
 
enum class  DragDirections {
  NOT_SET = 0x0000 , LEFT_TO_RIGHT = 1 << 0 , RIGHT_TO_LEFT = 1 << 1 , TOP_TO_BOTTOM = 1 << 2 ,
  BOTTOM_TO_TOP = 1 << 3
}
 
enum class  RangeType { outermost = 1 , innermost = 2 }
 
enum class  MsRunXicExtractorFactoryType : std::int8_t { nose = 0 , direct = 1 , disk = 2 , diskbuffer }
 

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 peptideIonTypeIsComplement (PeptideIon ion_type_ref, PeptideIon ion_type)
 tells if an ion type is the complement ion of the other More...
 
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)
 
PMSPP_LIB_DECL std::vector< TracePeak >::iterator findBestTracePeakGivenRtList (std::vector< TracePeak >::iterator begin, std::vector< TracePeak >::iterator end, const std::vector< double > &rt_list, std::size_t &nb_peaks)
 find the best peak matching a list of retention times More...
 
PMSPP_LIB_DECL std::vector< TracePeak >::iterator findTracePeakGivenRt (std::vector< TracePeak >::iterator begin, std::vector< TracePeak >::iterator end, double rt)
 find the peak matching a retention time More...
 
std::vector< PeakIonIsotopeMatch >::iterator findComplementIonType (std::vector< PeakIonIsotopeMatch >::iterator begin, std::vector< PeakIonIsotopeMatch >::iterator end, const PeakIonIsotopeMatch &peak_ion, std::size_t peptide_size)
 find the first element containing the complementary ion complementary ion of y1 is b(n-1) for instance More...
 
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 quantileYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double quantile)
 calculate the quantile 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 (31.9720711741)
 
const pappso_double MASSPHOSPHORYLATEDR (MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
 
const pappso_double MASSSELENIUM (79.916520)
 
const pappso_double DIFFC12C13 (1.0033548378)
 
const pappso_double DIFFS32S33 (32.9714589101 - MASSSULFUR)
 
const pappso_double DIFFS32S34 (33.9678670300 - MASSSULFUR)
 
const pappso_double DIFFS32S36 (35.9670812000 - 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 (0.00011570983569203332000374651045149221317842602729797363281250)
 
const pappso_double ABUNDANCEN15 (0.00364198543205827118818262988497735932469367980957031250000000)
 
const pappso_double ABUNDANCEO17 (0.00038099847600609595965615028489992255344986915588378906250000)
 
const pappso_double ABUNDANCEO18 (0.00205139179443282221315669744399201590567827224731445312500000)
 
const pappso_double ABUNDANCEC13 (0.01078805814953308406245469086570665240287780761718750000000000)
 
const pappso_double ABUNDANCEC12 (0.98921194185046687152862432412803173065185546875000000000000000)
 
const pappso_double ABUNDANCES33 (0.00751939844812414937003097747947322204709053039550781250000000)
 
const pappso_double ABUNDANCES34 (0.04252059835213182203972337447339668869972229003906250000000000)
 
const pappso_double ABUNDANCES36 (0.00010999120070394368536836893213148869108408689498901367187500)
 
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}
 
std::map< BinningType, QString > binningTypeMap
 Map relating the BinningType to a textual representation. More...
 

Detailed Description

tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge

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

Typedef Documentation

◆ AaModificationP

Definition at line 52 of file aamodification.h.

◆ AaModificationUp

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

Definition at line 51 of file aamodification.h.

◆ BaseColorMapPlotWidgetCstSPtr

Definition at line 61 of file basecolormapplotwidget.h.

◆ BaseColorMapPlotWidgetSPtr

Definition at line 59 of file basecolormapplotwidget.h.

◆ BasePlotWidgetCstSPtr

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

Definition at line 64 of file baseplotwidget.h.

◆ BasePlotWidgetSPtr

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

Definition at line 63 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 18 of file datapoint.h.

◆ FastaFileIndexerSPtr

Definition at line 49 of file fastafileindexer.h.

◆ FilterCeilingAmplitudePercentageCstSPtr

◆ FilterCeilingAmplitudePercentageSPtr

◆ FilterFloorAmplitudePercentageCstSPtr

◆ FilterFloorAmplitudePercentageSPtr

◆ FilterInterfaceCstSPtr

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

Definition at line 47 of file filterinterface.h.

◆ FilterInterfaceSPtr

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

Definition at line 46 of file filterinterface.h.

◆ FilterLowIntensitySignalRemovalCstSPtr

◆ FilterLowIntensitySignalRemovalSPtr

◆ FilterNameInterfaceCstSPtr

Definition at line 60 of file filternameinterface.h.

◆ FilterNameInterfaceSPtr

Definition at line 59 of file filternameinterface.h.

◆ FilterSavitzkyGolayCstSPtr

Definition at line 122 of file savgolfilter.h.

◆ FilterSavitzkyGolaySPtr

Definition at line 121 of file savgolfilter.h.

◆ FilterSuiteStringSPtr

Definition at line 77 of file filtersuitestring.h.

◆ GrpGroupSp

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

Definition at line 39 of file grpgroup.h.

◆ GrpGroupSpConst

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

Definition at line 40 of file grpgroup.h.

◆ GrpPeptideSp

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

Definition at line 40 of file grppeptide.h.

◆ GrpPeptideSpConst

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

Definition at line 39 of file grppeptide.h.

◆ GrpProteinSp

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

Definition at line 37 of file grpprotein.h.

◆ GrpProteinSpConst

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

Definition at line 36 of file grpprotein.h.

◆ GrpSubGroupSp

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

Definition at line 39 of file grpsubgroup.h.

◆ GrpSubGroupSpConst

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

Definition at line 38 of file grpsubgroup.h.

◆ MapTraceCstSPtr

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

Definition at line 27 of file maptrace.h.

◆ MapTraceSPtr

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

Definition at line 26 of file maptrace.h.

◆ MassSpectrumCombinerCstSPtr

Definition at line 24 of file massspectrumcombiner.h.

◆ MassSpectrumCombinerSPtr

Definition at line 25 of file massspectrumcombiner.h.

◆ MassSpectrumCstSPtr

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

Definition at line 55 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 54 of file massspectrum.h.

◆ MsRunDataSetTreeCstSPtr

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

Definition at line 26 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 25 of file msrundatasettree.h.

◆ MsRunIdCstSPtr

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

Definition at line 45 of file msrunid.h.

◆ MsRunReaderCstSPtr

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

Definition at line 186 of file msrunreader.h.

◆ MsRunReaderSPtr

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

Definition at line 185 of file msrunreader.h.

◆ MsRunSliceSPtr

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

Definition at line 40 of file msrunslice.h.

◆ MsRunXicExtractorInterfaceSp

◆ MzCalibrationInterfaceSPtr

Definition at line 38 of file mzcalibrationinterface.h.

◆ NoConstPeptideSp

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

Definition at line 97 of file peptide.h.

◆ pappso_double

typedef double pappso::pappso_double

A type definition for doubles.

Definition at line 49 of file types.h.

◆ pappso_float

typedef float pappso::pappso_float

Definition at line 54 of file types.h.

◆ PeakIonIsotopeMatchCstSPtr

Definition at line 34 of file peakionisotopematch.h.

◆ PeptideFragmentIonListBaseSp

Definition at line 43 of file peptidefragmentionlistbase.h.

◆ PeptideFragmentIonSp

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

Definition at line 46 of file peptidefragmention.h.

◆ PeptideFragmentSp

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

Definition at line 45 of file peptidefragment.h.

◆ PeptideInterfaceSp

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

Definition at line 39 of file peptideinterface.h.

◆ PeptideNaturalIsotopeAverageSp

◆ PeptideNaturalIsotopeListSp

Definition at line 45 of file peptidenaturalisotopelist.h.

◆ PeptideNaturalIsotopeSp

Definition at line 43 of file peptidenaturalisotope.h.

◆ PeptideSp

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

Definition at line 48 of file aamodification.h.

◆ PeptideStr

typedef QString pappso::PeptideStr

A type definition for PeptideStr.

Definition at line 44 of file types.h.

◆ PrecisionPtr

Definition at line 122 of file precision.h.

◆ ProteinSp

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

shared pointer on a Protein object

Definition at line 47 of file protein.h.

◆ QualifiedMassSpectrumCstSPtr

Definition at line 45 of file qualifiedmassspectrum.h.

◆ QualifiedMassSpectrumSPtr

Definition at line 43 of file qualifiedmassspectrum.h.

◆ QualifiedXicSp

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

Definition at line 42 of file qualifiedxic.h.

◆ SelectionPolygonSpecVector

Definition at line 103 of file filterresample.h.

◆ TimsDataSp

typedef std::shared_ptr<TimsData> pappso::TimsDataSp

shared pointer on a TimsData object

Definition at line 50 of file timsdata.h.

◆ TimsFrameBaseCstSPtr

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

Definition at line 41 of file timsframebase.h.

◆ TimsFrameBaseSPtr

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

Definition at line 40 of file timsframebase.h.

◆ TimsFrameCstSPtr

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

Definition at line 42 of file timsframe.h.

◆ TimsFrameSPtr

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

Definition at line 41 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 136 of file trace.h.

◆ TraceDetectionInterfaceCstSPtr

Definition at line 35 of file tracedetectioninterface.h.

◆ TraceDetectionInterfaceSPtr

Definition at line 33 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 35 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 135 of file trace.h.

◆ uint

typedef unsigned int pappso::uint

Definition at line 56 of file types.h.

◆ XicCoordSPtr

typedef std::shared_ptr<XicCoord> pappso::XicCoordSPtr

Definition at line 43 of file xiccoord.h.

◆ XicCoordTimsSPtr

typedef std::shared_ptr<XicCoordTims> pappso::XicCoordTimsSPtr

Definition at line 40 of file xiccoordtims.h.

◆ XicCstSPtr

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

Definition at line 38 of file xic.h.

◆ XicSPtr

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

Definition at line 39 of file xic.h.

◆ XicXicPeakPairList

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

Definition at line 45 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 133 of file types.h.

◆ AtomIsotope

enum pappso::AtomIsotope
strong
Enumerator

Definition at line 69 of file peptidenaturalisotope.cpp.

◆ AtomIsotopeSurvey

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

Definition at line 76 of file types.h.

77 {
78  C,
79  H,
80  O,
81  N,
82  S,
83  last
84 };

◆ Axis

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

Definition at line 180 of file types.h.

181 {
182  unset = 0x000,
183  x = 1 << 0,
184  y = 1 << 1,
185  z = 1 << 2,
186 };

◆ AxisScale

enum pappso::AxisScale : std::int8_t
strong
Enumerator
unset 
orig 
log10 

Definition at line 189 of file types.h.

190 {
191  unset = 0,
192  orig = 1,
193  log10 = 2,
194 };

◆ BinningType

enum pappso::BinningType
strong

Type of binning when performing integrations to a mass spectrum.

Enumerator
NONE 

< no binning

DATA_BASED 

binning based on mass spectral data

ARBITRARY 

binning based on arbitrary bin size value

LAST 

Definition at line 47 of file mzintegrationparams.h.

48 {
49  //! < no binning
50  NONE = 0,
51 
52  //! binning based on mass spectral data
53  DATA_BASED,
54 
55  //! binning based on arbitrary bin size value
56  ARBITRARY,
57 
58  LAST,
59 };
@ DATA_BASED
binning based on mass spectral data
@ ARBITRARY
binning based on arbitrary bin size value
@ NONE
< no binning

◆ DataCompression

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

not net

none 

no compression

zlib 

zlib compresssion

Definition at line 163 of file types.h.

164 {
165  unset = -1, ///< not net
166  none = 0, ///< no compression
167  zlib = 1, ///< zlib compresssion
168 };
@ zlib
zlib compresssion

◆ DataDimension

enum pappso::DataDimension
strong
Enumerator
NOT_SET 
HORIZONTAL 
VERTICAL 

Definition at line 34 of file selectionpolygon.h.

◆ DataKind

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

not set

rt 

Retention time.

dt 

Drift time.

mz 

m/z

Definition at line 171 of file types.h.

172 {
173  unset = -1, ///< not set
174  rt = 0, ///< Retention time
175  dt = 1, ///< Drift time
176  mz = 2, ///< m/z
177 };
@ dt
Drift time.
@ rt
Retention time.

◆ DeepProtMatchType

enum pappso::DeepProtMatchType : std::uint8_t
strong

definition of different class of PSMs used by DeepProt

Enumerator
uncategorized 

precursor mass was not compared

ZeroMassDelta 

peptide candidate is in precursor mz range

ZeroMassDeltaMissedCleavage 

peptide candidate with missed cleavage is in precursor mz range

ZeroMassDeltaSemiTryptic 

semi tryptic peptide candidate is in precursor mz range

DeltaPosition 

spectrum shifter on peptide candidate has detected a position for the mass delta

NoDeltaPosition 

spectrum shifter on peptide candidate has not detected a position for the mass delta

last 

Definition at line 41 of file deepprotenum.h.

42 {
43  uncategorized = 0, ///< precursor mass was not compared
44  ZeroMassDelta = 1, ///< peptide candidate is in precursor mz range
46  2, ///< peptide candidate with missed cleavage is in precursor mz range
48  3, ///< semi tryptic peptide candidate is in precursor mz range
49  DeltaPosition = 4, ///< spectrum shifter on peptide candidate has detected a
50  ///< position for the mass delta
51  NoDeltaPosition = 5, ///< spectrum shifter on peptide candidate has not
52  ///< detected a position for the mass delta
53  last = 6
54 };
@ ZeroMassDeltaMissedCleavage
peptide candidate with missed cleavage is in precursor mz range
@ uncategorized
precursor mass was not compared
@ ZeroMassDelta
peptide candidate is in precursor mz range
@ ZeroMassDeltaSemiTryptic
semi tryptic peptide candidate is in precursor mz range

◆ DeepProtPeptideCandidateStatus

enum pappso::DeepProtPeptideCandidateStatus : std::uint8_t
strong

definition of different status for potential peptide candidates on the same spectrum

Enumerator
unmodified 

precursor mass was not compared

ZeroMassDelta 
CterRemoval 
NterRemoval 
MissedCleavage 
DeltaPosition 
NoDeltaPosition 
last 

Definition at line 60 of file deepprotenum.h.

61 {
62  unmodified = 0, ///< precursor mass was not compared
63  ZeroMassDelta = 1,
64  CterRemoval = 2,
65  NterRemoval = 3,
66  MissedCleavage = 4,
67  DeltaPosition = 5,
68  NoDeltaPosition = 6,
69  last = 7
70 };
@ unmodified
precursor mass was not compared

◆ DragDirections

Enumerator
NOT_SET 
LEFT_TO_RIGHT 
RIGHT_TO_LEFT 
TOP_TO_BOTTOM 
BOTTOM_TO_TOP 

Definition at line 25 of file baseplotcontext.h.

26 {
27  NOT_SET = 0x0000,
28  LEFT_TO_RIGHT = 1 << 0,
29  RIGHT_TO_LEFT = 1 << 1,
30  TOP_TO_BOTTOM = 1 << 2,
31  BOTTOM_TO_TOP = 1 << 3
32 };

◆ FileReaderType

Enumerator
pwiz 
xy 
tims 
tims_frames 
tims_ms2 

Definition at line 20 of file msfileaccessor.h.

◆ Isotope

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

Definition at line 91 of file types.h.

◆ MsRunXicExtractorFactoryType

enum pappso::MsRunXicExtractorFactoryType : std::int8_t
strong
Enumerator
nose 

default factory

direct 

build a simple XIC extractor that directly uses Proeowizard library to read and extract XICs building the xic extractor is fast, but extracting each XIC is slow

disk 

build Xic extractor that first read the whole MsRun, put it on disk and extract XICs more quickly This needs some space on disk to store slices (1 dalton each) building the XIC extractor is slow extracting XIC from slices is a very quick operation

diskbuffer 

build Xic extractor that first read the whole MsRun, put it on disk using a write cache and extract XICs more quickly This needs some space on disk to store slices (1 dalton each) building the XIC extractor is slower than buildMsRunXicExtractorPwizSp, but faster than buildMsRunXicExtractorDiskSp extracting XIC from slices is a very quick operation

Definition at line 45 of file msrunxicextractorfactory.h.

46 {
47  nose = 0, ///< default factory
48  direct = 1, ///< build a simple XIC extractor that directly uses Proeowizard
49  ///< library to read and extract XICs building the xic extractor
50  ///< is fast, but extracting each XIC is slow
51  disk = 2, ///< build Xic extractor that first read the whole MsRun, put it on
52  ///< disk and extract XICs more quickly This needs some space on
53  ///< disk to store slices (1 dalton each) building the XIC extractor
54  ///< is slow extracting XIC from slices is a very quick operation
55  diskbuffer =
56  3, ///< build Xic extractor that first read the whole MsRun, put it on disk
57  ///< using a write cache and extract XICs more quickly This needs some
58  ///< space on disk to store slices (1 dalton each) building the XIC
59  ///< extractor is slower than buildMsRunXicExtractorPwizSp, but faster
60  ///< than buildMsRunXicExtractorDiskSp extracting XIC from slices is a
61  ///< very quick operation
62 };

◆ 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 107 of file types.h.

108 {
109  unknown = 0, ///< unknown format
110  mzML = 1, ///< mzML
111  mzXML = 2, ///< mzXML
112  MGF = 3, ///< Mascot format
113  SQLite3 = 4, ///< SQLite3 format
114  xy = 5, ///< (x,y) format
115  mz5 = 6, //< MZ5 format
116  msn = 7, //< MS_MS2 format
117  abSciexWiff = 8,
118  abSciexT2D = 9,
119  agilentMassHunter = 10,
120  thermoRaw = 11,
121  watersRaw = 12,
122  brukerFid = 13,
123  brukerYep = 14,
124  brukerBaf = 15,
125  brukerTims = 16,
126  last = 17
127 };
@ unknown
unknown format
@ SQLite3
SQLite3 format.
@ MGF
Mascot format.

◆ PeptideDirection

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

Definition at line 45 of file peptide.h.

46 {
47  Nter = 0,
48  Cter = 1
49 };

◆ 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 385 of file types.h.

386 {
387  b = 0, ///< Nter acylium ions
388  bstar = 1, ///< Nter acylium ions + NH3 loss
389  bo = 2, ///< Nter acylium ions + H2O loss
390  a = 3, ///< Nter aldimine ions
391  astar = 4, ///< Nter aldimine ions + NH3 loss
392  ao = 5, ///< Nter aldimine ions + H2O loss
393  bp = 6,
394  c = 7, ///< Nter amino ions
395  y = 8, ///< Cter amino ions
396  ystar = 9, ///< Cter amino ions + NH3 loss
397  yo = 10, ///< Cter amino ions + H2O loss
398  z = 11, ///< Cter carbocations
399  yp = 12,
400  x = 13 ///< Cter acylium ions
401 };

◆ PeptideIonCter

Enumerator
ystar 
yo 
yp 

Definition at line 84 of file peptide.h.

85 {
86  y,
87  ystar,
88  yo,
89  z,
90  yp,
91  x
92 };

◆ PeptideIonNter

Enumerator
bstar 
bo 
astar 
ao 
bp 

Definition at line 71 of file peptide.h.

72 {
73  b,
74  bstar,
75  bo,
76  a,
77  astar,
78  ao,
79  bp,
80  c
81 };

◆ PointSpecs

enum pappso::PointSpecs
strong
Enumerator
TOP_LEFT_POINT 
TOP_RIGHT_POINT 
BOTTOM_RIGHT_POINT 
BOTTOM_LEFT_POINT 
ENUM_LAST 

Definition at line 23 of file selectionpolygon.h.

24 {
25  // Starting top left and then clockwise
26  TOP_LEFT_POINT = 0,
27  TOP_RIGHT_POINT = 1,
30  ENUM_LAST = 4,
31 };

◆ PolygonType

enum pappso::PolygonType
strong
Enumerator
NOT_SET 
TOP_LINE 
BOTTOM_LINE 
HORIZONTAL_LINES 
RIGHT_LINE 
LEFT_LINE 
VERTICAL_LINES 
FULL_POLYGON 

Definition at line 42 of file selectionpolygon.h.

43 {
44  NOT_SET = 0x0000,
45 
46  TOP_LINE = 1 << 0,
47  BOTTOM_LINE = 1 << 1,
48 
50 
51  RIGHT_LINE = 1 << 2,
52  LEFT_LINE = 1 << 3,
53 
54  VERTICAL_LINES = (RIGHT_LINE | LEFT_LINE),
55 
57 };

◆ PrecisionUnit

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

Definition at line 63 of file types.h.

64 {
65  none,
66  dalton,
67  ppm,
68  res,
69  mz,
70  last
71 };

◆ 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 47 of file qualifiedmassspectrum.h.

48 {
49 
50  OneOverK0, ///< 1/kO of a simple scan
51  OneOverK0begin, ///< 1/kO of first acquisition for composite pasef MS/MS
52  ///< spectrum
53  OneOverK0end, ///< 1/k0 of last acquisition for composite pasef MS/MS spectrum
54  IsolationMz, ///< isolation window
55  IsolationWidth, ///< isolation window width
56  CollisionEnergy, ///< Bruker's Tims tof collision energy
57  BrukerPrecursorIndex, ///< Bruker's Tims tof precursor index
58  last
59 };
@ CollisionEnergy
Bruker's Tims tof collision energy.
@ OneOverK0end
1/k0 of last acquisition for composite pasef MS/MS spectrum
@ IsolationWidth
isolation window width
@ BrukerPrecursorIndex
Bruker's Tims tof precursor index.

◆ RangeType

enum pappso::RangeType
strong
Enumerator
outermost 
innermost 

Definition at line 55 of file baseplotwidget.h.

56 {
57  outermost = 1,
58  innermost = 2,
59 };

◆ RawFragmentationMode

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

Definition at line 42 of file peptiderawfragmentmasses.h.

◆ XicExtractMethod

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

sum of intensities

max 

maximum of intensities

Definition at line 200 of file types.h.

201 {
202  sum = 1, ///< sum of intensities
203  max = 2 ///< maximum of intensities
204 };
@ sum
sum of intensities
@ max
maximum of intensities

Function Documentation

◆ ABUNDANCEC12()

const pappso_double pappso::ABUNDANCEC12 ( 0.  98921194185046687152862432412803173065185546875000000000000000)

◆ ABUNDANCEC13()

const pappso_double pappso::ABUNDANCEC13 ( 0.  01078805814953308406245469086570665240287780761718750000000000)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEH2()

const pappso_double pappso::ABUNDANCEH2 ( 0.  00011570983569203332000374651045149221317842602729797363281250)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEN15()

const pappso_double pappso::ABUNDANCEN15 ( 0.  00364198543205827118818262988497735932469367980957031250000000)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEO17()

const pappso_double pappso::ABUNDANCEO17 ( 0.  00038099847600609595965615028489992255344986915588378906250000)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEO18()

const pappso_double pappso::ABUNDANCEO18 ( 0.  00205139179443282221315669744399201590567827224731445312500000)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES33()

const pappso_double pappso::ABUNDANCES33 ( 0.  00751939844812414937003097747947322204709053039550781250000000)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES34()

const pappso_double pappso::ABUNDANCES34 ( 0.  04252059835213182203972337447339668869972229003906250000000000)

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES36()

const pappso_double pappso::ABUNDANCES36 ( 0.  00010999120070394368536836893213148869108408689498901367187500)

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 309 of file trace.cpp.

311 {
312 
313  if(begin == end)
314  return 0;
315  auto previous = begin;
316  auto next = begin + 1;
317  double area = 0;
318  while(next != end)
319  {
320  area += ((next->x - previous->x) * (previous->y + next->y)) / (double)2;
321  previous++;
322  next++;
323  }
324  return area;
325 }

Referenced by pappso::TracePeak::TracePeak().

◆ 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 }
uint64_t combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
#define CACHE_ARRAY_SIZE

References CACHE_ARRAY_SIZE, and combinations_cache.

Referenced by isotopem_ratio().

◆ DIFFC12C13()

◆ DIFFH1H2()

◆ DIFFN14N15()

◆ DIFFO16O17()

◆ DIFFO16O18()

◆ DIFFS32S33()

◆ DIFFS32S34()

◆ DIFFS32S36()

◆ factorial()

unsigned int pappso::factorial ( unsigned int  n)

Definition at line 43 of file xtandemhyperscore.cpp.

44 {
45  unsigned int retval = 1;
46  for(int i = n; i > 1; --i)
47  retval *= i;
48  return retval;
49 }

Referenced by pappso::XtandemHyperscore::XtandemHyperscore(), and pappso::XtandemHyperscoreBis::computeXtandemHyperscore().

◆ findBestTracePeakGivenRtList()

std::vector< TracePeak >::iterator pappso::findBestTracePeakGivenRtList ( std::vector< TracePeak >::iterator  begin,
std::vector< TracePeak >::iterator  end,
const std::vector< double > &  rt_list,
std::size_t &  nb_peaks 
)

find the best peak matching a list of retention times

Parameters
beginbegin iterator
endend iterator
rt_listretention time list in seconds
nb_peaksretrieve the number of detected peaks concerned by the retention times
Returns
iterator on the best peak (bigger area) concerned by the retention times

Definition at line 55 of file tracepeaklist.cpp.

59 {
60  // get peak containing rt ahead :
61  auto itend = std::partition(begin, end, [rt_list](const TracePeak &a) {
62  for(double rt : rt_list)
63  {
64  if(a.containsRt(rt))
65  {
66  return true;
67  };
68  }
69  return false;
70  });
71  nb_peaks = std::distance(begin, itend);
72  if(nb_peaks == 0)
73  return end;
74  return std::max_element(
75  begin, itend, [](const TracePeak &a, const TracePeak &b) {
76  return a.getArea() < b.getArea();
77  });
78 }

References a, b, and rt.

◆ findComplementIonType()

PMSPP_LIB_DECL std::vector< PeakIonIsotopeMatch >::iterator pappso::findComplementIonType ( std::vector< PeakIonIsotopeMatch >::iterator  begin,
std::vector< PeakIonIsotopeMatch >::iterator  end,
const PeakIonIsotopeMatch peak_ion,
std::size_t  peptide_size 
)

find the first element containing the complementary ion complementary ion of y1 is b(n-1) for instance

Definition at line 30 of file peakionisotopematch.cpp.

34 {
35 
36  return std::find_if(
37  begin,
38  end,
39  [peak_ion, peptide_size](const PeakIonIsotopeMatch &to_compare) {
40  if(to_compare.getCharge() == peak_ion.getCharge())
41  {
42  if((to_compare.getPeptideFragmentIonSp().get()->size() +
43  peak_ion.getPeptideFragmentIonSp().get()->size()) == peptide_size)
44  {
45  if(peptideIonTypeIsComplement(to_compare.getPeptideIonType(),
46  peak_ion.getPeptideIonType()))
47  {
48  if(to_compare.getPeptideNaturalIsotopeAverageSp()
49  .get()
50  ->getIsotopeNumber() ==
51  peak_ion.getPeptideNaturalIsotopeAverageSp()
52  .get()
53  ->getIsotopeNumber())
54  {
55  return true;
56  }
57  }
58  }
59  }
60 
61  return false;
62  });
63 }

References pappso::PeakIonMatch::getCharge().

Referenced by pappso::PsmFeatures::findComplementIonPairs().

◆ 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 141 of file trace.cpp.

144 {
145  return std::find_if(begin, end, [y_value](const DataPoint &to_compare) {
146 
147  if(to_compare.y != y_value)
148  {
149  return true;
150  }
151 
152  return false;
153  });
154 }

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 125 of file trace.cpp.

128 {
129  return std::find_if(begin, end, [y_value](const DataPoint &to_compare) {
130 
131  if(to_compare.y != y_value)
132  {
133  return true;
134  }
135 
136  return false;
137  });
138 }

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 83 of file trace.cpp.

86 {
87  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
88  if(to_compare.x < value)
89  {
90  return false;
91  }
92  return true;
93  });
94 }

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 69 of file trace.cpp.

72 {
73  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
74  if(to_compare.x < value)
75  {
76  return false;
77  }
78  return true;
79  });
80 }

References pappso::DataPoint::x.

Referenced by pappso::TraceDetectionZivy::detect(), 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 111 of file trace.cpp.

114 {
115  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
116  if(to_compare.x > value)
117  {
118  return true;
119  }
120  return false;
121  });
122 }

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 97 of file trace.cpp.

100 {
101  return std::find_if(begin, end, [value](const DataPoint &to_compare) {
102  if(to_compare.x > value)
103  {
104  return true;
105  }
106  return false;
107  });
108 }

References pappso::DataPoint::x.

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

◆ findTracePeakGivenRt()

std::vector< TracePeak >::iterator pappso::findTracePeakGivenRt ( std::vector< TracePeak >::iterator  begin,
std::vector< TracePeak >::iterator  end,
double  rt 
)

find the peak matching a retention time

Parameters
beginbegin iterator
endend iterator
rtretention time in seconds
Returns
iterator on the peak concerned by the retention time

Definition at line 81 of file tracepeaklist.cpp.

84 {
85  return find_if(
86  begin, end, [rt](const TracePeak &a) { return a.containsRt(rt); });
87 }

References a, and rt.

◆ 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 329 of file trace.cpp.

332 {
333  Trace local_maxima_trace;
334 
335  Trace single_peak_trace;
336 
337  DataPoint previous_data_point;
338 
339  for(auto iter = begin; iter != end; ++iter)
340  {
341  DataPoint iterated_data_point(iter->x, iter->y);
342 
343  // qDebug().noquote() << "Current data point:"
344  //<< iterated_data_point.toString();
345 
346  if(iterated_data_point.y < y_floor)
347  {
348  // qDebug() << "under the floor";
349 
350  if(single_peak_trace.size())
351  {
352  // qDebug() << "There was a single peak trace cooking";
353 
354  local_maxima_trace.push_back(single_peak_trace.maxYDataPoint());
355 
356  // qDebug().noquote() << "pushed back local maximum point:"
357  //<< local_maxima_trace.back().toString();
358 
359  // Clean and set the context.
360  single_peak_trace.clear();
361 
362  previous_data_point = iterated_data_point;
363 
364  continue;
365  }
366  else
367  {
368  // qDebug() << "no single peak trace cooking";
369 
370  previous_data_point = iterated_data_point;
371 
372  continue;
373  }
374  }
375  else
376  {
377  // qDebug() << "over the floor";
378 
379  // The iterated value is greater than the y_floor value, so we need to
380  // handle it.
381 
382  if(iterated_data_point.y == previous_data_point.y)
383  {
384  // We are in a flat region, no need to change anything to the
385  // context, just skip the point.
386  continue;
387  }
388  else if(iterated_data_point.y > previous_data_point.y)
389  {
390  // qDebug().noquote() << "ascending in a peak";
391 
392  // The previously iterated y value was smaller than the presently
393  // iterated one, so we are ascending in a peak.
394 
395  // All we need to do is set the context.
396 
397  single_peak_trace.push_back(iterated_data_point);
398 
399  // qDebug().noquote() << "pushed back normal point:"
400  //<< single_peak_trace.back().toString();
401 
402  previous_data_point = iterated_data_point;
403 
404  continue;
405  }
406  else
407  {
408  // qDebug().noquote() << "started descending in a peak";
409 
410  // No, the currently iterated y value is less than the previously
411  // iterated value.
412 
413  single_peak_trace.push_back(iterated_data_point);
414 
415  // qDebug().noquote() << "pushed back normal point:"
416  //<< single_peak_trace.back().toString();
417 
418  previous_data_point = iterated_data_point;
419 
420  continue;
421  }
422  }
423  }
424  // End of
425  // for(auto iter = begin; iter != end; ++iter)
426 
427  // Attention, we might arrive here with a peak being created, we need to get
428  // its maximum if that peak is non-empty;
429 
430  if(single_peak_trace.size())
431  {
432 
433  local_maxima_trace.push_back(single_peak_trace.maxYDataPoint());
434 
435  // qDebug().noquote()
436  //<< "was cooking a peak: pushed back local maximum point:"
437  //<< local_maxima_trace.back().toString();
438  }
439 
440  return local_maxima_trace;
441 }

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 351 of file peptidenaturalisotopelist.cpp.

356 {
357 
358  // qDebug() << "getByIntensityRatioByIsotopeNumber begin";
359  unsigned int askedIsotopeRank;
360  unsigned int maxAskedIsotopeRank = 10;
361  pappso_double cumulativeRatio = 0;
362  std::vector<PeptideNaturalIsotopeAverageSp> v_isotopeAverageList;
363  std::vector<PeptideNaturalIsotopeAverageSp> v_isotopeAverageListResult;
364 
365  std::vector<unsigned int> previousIsotopeRank;
366  bool isEmpty = false;
367  for(askedIsotopeRank = 1;
368  (askedIsotopeRank < maxAskedIsotopeRank) && (!isEmpty);
369  askedIsotopeRank++)
370  {
371  PeptideNaturalIsotopeAverage isotopeAverage(
372  peptide, askedIsotopeRank, isotopeNumber, charge, precision);
373  isEmpty = isotopeAverage.isEmpty();
374  if(isEmpty)
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 }
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp

References pappso::PeptideNaturalIsotopeAverage::getIsotopeRank(), pappso::PeptideNaturalIsotopeAverage::isEmpty(), and pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp().

◆ getPeptideIonDirection()

PMSPP_LIB_DECL 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 70 of file peptide.cpp.

71 {
72  if(peptideIonIsNter(ion_type))
73  {
74  return PeptideDirection::Nter;
75  }
76  return PeptideDirection::Cter;
77 }
bool peptideIonIsNter(PeptideIon ion_type)
tells if an ion is Nter
Definition: peptide.cpp:60

References Cter, Nter, and peptideIonIsNter().

Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon(), and pappso::PeptideFragmentIon::getPeptideIonDirection().

◆ 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 }
uint64_t Combinations(unsigned int n, unsigned int k)

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 }
pappso_double ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCES36(0.00010999120070394368536836893213148869108408689498901367187500)
pappso_double ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCEN15(0.00364198543205827118818262988497735932469367980957031250000000)
pappso_double ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
pappso_double isotopem_ratio(pappso_double abundance, unsigned int total, unsigned int heavy)
pappso_double ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCEC13(0.01078805814953308406245469086570665240287780761718750000000000)
const pappso_double ABUNDANCEO17(0.00038099847600609595965615028489992255344986915588378906250000)
const pappso_double ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250)
pappso_double ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCES34(0.04252059835213182203972337447339668869972229003906250000000000)
pappso_double ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCEO18(0.00205139179443282221315669744399201590567827224731445312500000)
const pappso_double ABUNDANCES33(0.00751939844812414937003097747947322204709053039550781250000000)
pappso_double ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
pappso_double ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]

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

◆ 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()

◆ 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.  9720711741)

◆ 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 
)

◆ 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 191 of file trace.cpp.

193 {
194  return std::max_element(
195  begin, end, [](const DataPoint &a, const DataPoint &b) {
196  return a.y < b.y;
197  });
198 }

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 253 of file trace.cpp.

255 {
256  pappso_double nb_element = distance(begin, end);
257  if(nb_element == 0)
258  throw ExceptionOutOfRange(
259  QObject::tr("unable to compute mean on a trace of size 0"));
260  return (sumYTrace(begin, end, 0) / nb_element);
261 }
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:244

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 291 of file trace.cpp.

293 {
294  std::size_t nb_element = distance(begin, end);
295  if(nb_element == 0)
296  throw ExceptionOutOfRange(
297  QObject::tr("unable to compute median on a trace of size 0"));
298 
299  std::vector<DataPoint> data(begin, end);
300  std::nth_element(
301  data.begin(),
302  data.begin() + data.size() / 2,
303  data.end(),
304  [](const DataPoint &a, const DataPoint &b) { return a.y < b.y; });
305  return data[data.size() / 2].y;
306 }

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 158 of file trace.cpp.

160 {
161  return std::min_element(
162  begin, end, [](const DataPoint &a, const DataPoint &b) {
163  return a.y < b.y;
164  });
165 }

References a, and b.

Referenced by pappso::FilterCeilingAmplitudePercentage::filter(), pappso::FilterFloorAmplitudePercentage::filter(), 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 169 of file trace.cpp.

171 {
172  return std::min_element(
173  begin, end, [](const DataPoint &a, const DataPoint &b) {
174  return a.y < b.y;
175  });
176 }

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 223 of file trace.cpp.

225 {
226  if(begin == trace.begin())
227  return begin;
228  auto it = begin - 1;
229  auto result = begin;
230 
231  // As long as prev datapoint has y value less or equal to next,
232  // move along up the container. That is, continue moving if
233  // direction is downhill to the beginning of the container (its front).
234  while((it != trace.begin()) && (it->y <= result->y))
235  {
236  it--;
237  result--;
238  }
239  return result;
240 }

Referenced by pappso::TraceDetectionZivy::detect().

◆ 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 205 of file trace.cpp.

207 {
208  if(begin == trace.end())
209  return begin;
210  auto it = begin + 1;
211  auto result = begin;
212  // Move along as long as next point's y value is less
213  // or equal to prev point's y value (FR, check).
214  while((it != trace.end()) && (it->y <= result->y))
215  {
216  it++;
217  result++;
218  }
219  return result;
220 }

Referenced by pappso::TraceDetectionZivy::detect().

◆ MPROTIUM()

◆ MPROTON()

◆ ONEMILLION()

const pappso_double pappso::ONEMILLION ( 1000000  )

◆ operator<()

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

Definition at line 285 of file aa.cpp.

287 {
288  return l.isLesser(r);
289 }

References pappso::Aa::isLesser().

◆ operator<<() [1/3]

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

Definition at line 152 of file datapoint.cpp.

154 {
155  out << dataPoint.x;
156  out << dataPoint.y;
157 
158  return out;
159 }

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

◆ operator<<() [2/3]

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

Definition at line 32 of file trace.cpp.

34 {
35  for(auto &dataPoint : trace)
36  {
37  out << dataPoint.x;
38  out << dataPoint.y;
39  out << "\n";
40  }
41  out << "\n";
42 
43  return out;
44 }

◆ operator<<() [3/3]

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

Definition at line 348 of file massspectrum.cpp.

350 {
351  quint32 vector_size = massSpectrum.size();
352  outstream << vector_size;
353  for(auto &&peak : massSpectrum)
354  {
355  outstream << peak;
356  }
357 
358  return outstream;
359 }

◆ operator==()

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

Definition at line 280 of file aa.cpp.

281 {
282  return l.isAaEqual(r);
283 }

References pappso::Aa::isAaEqual().

◆ operator>>() [1/4]

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

Definition at line 163 of file datapoint.cpp.

164 {
165 
166  if(in.atEnd())
167  {
168  throw PappsoException(
169  QString("error in QDataStream unserialize operator>> of massSpectrum "
170  "dataPoint:\nread datastream failed status=%1")
171  .arg(in.status()));
172  }
173  in >> dataPoint.x;
174  in >> dataPoint.y;
175 
176  return in;
177 }

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

◆ operator>>() [2/4]

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

Definition at line 363 of file massspectrum.cpp.

364 {
365 
366  quint32 vector_size;
367  DataPoint peak;
368 
369  if(!instream.atEnd())
370  {
371  instream >> vector_size;
372  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
373  << " vector_size=" << vector_size;
374 
375  for(quint32 i = 0; i < vector_size; i++)
376  {
377 
378  if(instream.status() != QDataStream::Ok)
379  {
380  throw PappsoException(
381  QString("error in QDataStream unserialize operator>> of "
382  "massSpectrum :\nread datastream failed status=%1 "
383  "massSpectrum "
384  "i=%2 on size=%3")
385  .arg(instream.status())
386  .arg(i)
387  .arg(vector_size));
388  }
389  instream >> peak;
390  massSpectrum.push_back(peak);
391  }
392  if(instream.status() != QDataStream::Ok)
393  {
394  throw PappsoException(
395  QString(
396  "error in QDataStream unserialize operator>> of massSpectrum "
397  ":\nread datastream failed status=%1")
398  .arg(instream.status()));
399  }
400  }
401 
402  return instream;
403 }

◆ operator>>() [3/4]

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

Definition at line 158 of file msrunslice.cpp.

159 {
160 
161  quint32 vector_size = 0;
162  quint32 slice_number = 0;
163  quint32 spectrum_position = 0;
164  DataPoint peak;
165 
166  if(!instream.atEnd())
167  {
168  instream >> slice_number;
169  instream >> vector_size;
170  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
171  << " vector_size=" << vector_size;
172  slice.setSize(vector_size);
173 
174  slice.setSliceNumber(slice_number);
175  while(!instream.atEnd())
176  {
177  instream >> spectrum_position;
178  MassSpectrum spectrum;
179  try
180  {
181  instream >> spectrum;
182  }
183  catch(PappsoException &error)
184  {
185  throw PappsoException(
186  QString("error in QDataStream unserialize operator>> of "
187  "MsRunSlice %2 on %3:\n%1")
188  .arg(error.qwhat())
189  .arg(spectrum_position)
190  .arg(vector_size));
191  }
192  slice.setSpectrum(spectrum_position, spectrum);
193 
194  if(instream.status() != QDataStream::Ok)
195  {
196  throw PappsoException(
197  QString("error in QDataStream unserialize operator>> of "
198  "MsRunSlice :\nread datastream failed status=%1")
199  .arg(instream.status()));
200  }
201  }
202  }
203 
204  if(slice.size() != vector_size)
205  {
206  throw PappsoException(
207  QString("error in QDataStream unserialize operator>> of MsRunSlice "
208  "slice.size() != vector_size :\n %1 %2:")
209  .arg(slice.size())
210  .arg(vector_size));
211  }
212 
213  return instream;
214 }

References pappso::PappsoException::qwhat(), pappso::MsRunSlice::setSize(), pappso::MsRunSlice::setSliceNumber(), pappso::MsRunSlice::setSpectrum(), and pappso::MsRunSlice::size().

◆ operator>>() [4/4]

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

Definition at line 48 of file trace.cpp.

49 {
50  if(in.atEnd())
51  {
52  throw PappsoException(
53  QString("error in QDataStream unserialize operator>> of trace:\n"
54  "read datastream failed status=%1")
55  .arg(in.status()));
56  }
57 
58  for(auto &dataPoint : trace)
59  {
60  in >> dataPoint.x;
61  in >> dataPoint.y;
62  }
63 
64  return in;
65 }

◆ peptideIonIsNter()

PMSPP_LIB_DECL bool pappso::peptideIonIsNter ( PeptideIon  ion_type)

tells if an ion is Nter

Parameters
ion_typethe ion to test

Definition at line 60 of file peptide.cpp.

61 {
62  if((std::int8_t)ion_type < (std::int8_t)8)
63  {
64  return true;
65  }
66  return false;
67 }

Referenced by pappso::PsmFeatures::findComplementIonPairs(), getPeptideIonDirection(), pappso::XtandemHyperscoreBis::getXtandemPredictedIonIntensityFactor(), peptideIonTypeIsComplement(), pappso::PeptideRawFragmentMasses::pushBackIonMasses(), and pappso::PeptideRawFragmentMasses::pushBackIonMz().

◆ peptideIonTypeIsComplement()

PMSPP_LIB_DECL bool pappso::peptideIonTypeIsComplement ( PeptideIon  ion_type_ref,
PeptideIon  ion_type 
)

tells if an ion type is the complement ion of the other

Parameters
ion_type_refthe ion type reference
ion_typethe ion to test

Definition at line 43 of file peptide.cpp.

44 {
45  if(peptideIonIsNter(ion_type))
46  std::swap(ion_type_ref, ion_type);
47  if(peptideIonIsNter(ion_type))
48  return false;
49  if((ion_type_ref == PeptideIon::b) && (ion_type == PeptideIon::y))
50  return true;
51  if((ion_type_ref == PeptideIon::ao) && (ion_type == PeptideIon::yo))
52  return true;
53  if((ion_type_ref == PeptideIon::bstar) && (ion_type == PeptideIon::ystar))
54  return true;
55 
56  return false;
57 }

References ao, b, bstar, peptideIonIsNter(), y, yo, and ystar.

◆ quantileYTrace()

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

calculate the quantile of y value of a trace

Parameters
beginbegin iterator
endend iterator
quantilethe quantile value between 0 and 1
Returns
Y value at the quantile

Definition at line 265 of file trace.cpp.

268 {
269  std::size_t nb_element = distance(begin, end);
270  if(nb_element == 0)
271  throw ExceptionOutOfRange(
272  QObject::tr("unable to compute quantile on a trace of size 0"));
273 
274 
275  std::size_t ieth_element = std::round((double)nb_element * quantile);
276  if(ieth_element > nb_element)
277  throw ExceptionOutOfRange(
278  QObject::tr("quantile value must be lower than 1"));
279 
280 
281  std::vector<DataPoint> data(begin, end);
282  std::nth_element(
283  data.begin(),
284  data.begin() + ieth_element,
285  data.end(),
286  [](const DataPoint &a, const DataPoint &b) { return a.y < b.y; });
287  return data[ieth_element].y;
288 }

References a, and b.

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

◆ 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 244 of file trace.cpp.

247 {
248  return std::accumulate(
249  begin, end, init, [](double a, const DataPoint &b) { return a + b.y; });
250 }

References a, and b.

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

Variable Documentation

◆ binningTypeMap

std::map< BinningType, QString > pappso::binningTypeMap
Initial value:
{
{BinningType::NONE, "NONE"},
{BinningType::DATA_BASED, "DATA_BASED"},
{BinningType::ARBITRARY, "ARBITRARY"}}

Map relating the BinningType to a textual representation.

Definition at line 67 of file mzintegrationparams.cpp.

Referenced by pappso::MzIntegrationParams::toString().

◆ 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 320 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().