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 | 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 | 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
class | TimsData
class | TimsFrame
class | TimsFrameBase
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 Peptide > | PeptideSp
typedef std::unique_ptr< const AaModification > | AaModificationUp
typedef const AaModification * | AaModificationP
typedef std::shared_ptr< FastaFileIndexer > | FastaFileIndexerSPtr
typedef std::shared_ptr< GrpGroup > | GrpGroupSp
typedef std::shared_ptr< const GrpGroup > | GrpGroupSpConst
typedef std::shared_ptr< const GrpPeptide > | GrpPeptideSpConst
typedef std::shared_ptr< GrpPeptide > | GrpPeptideSp
typedef std::shared_ptr< const GrpProtein > | GrpProteinSpConst
typedef std::shared_ptr< GrpProtein > | GrpProteinSp
typedef std::shared_ptr< const GrpSubGroup > | GrpSubGroupSpConst
typedef std::shared_ptr< GrpSubGroup > | GrpSubGroupSp
typedef std::shared_ptr< MassSpectrum > | MassSpectrumSPtr
typedef std::shared_ptr< const MassSpectrum > | MassSpectrumCstSPtr
typedef std::shared_ptr< QualifiedMassSpectrum > | QualifiedMassSpectrumSPtr
typedef std::shared_ptr< const QualifiedMassSpectrum > | QualifiedMassSpectrumCstSPtr
typedef std::shared_ptr< TimsMsRunReaderMs2 > | TimsMsRunReaderMs2SPtr
typedef std::shared_ptr< MsRunDataSetTree > | MsRunDataSetTreeSPtr
typedef std::shared_ptr< const MsRunDataSetTree > | MsRunDataSetTreeCstSPtr
typedef std::shared_ptr< MsRunDataSetTreeNode > | MsRunDataSetTreeNodeSPtr
typedef std::shared_ptr< const MsRunDataSetTreeNode > | MsRunDataSetTreeNodeCstSPtr
typedef std::shared_ptr< const MsRunId > | MsRunIdCstSPtr
typedef std::shared_ptr< MsRunReader > | MsRunReaderSPtr
typedef std::shared_ptr< const MsRunReader > | MsRunReaderCstSPtr
typedef std::shared_ptr< XicCoord > | XicCoordSPtr
typedef std::shared_ptr< XicCoordTims > | XicCoordTimsSPtr
typedef std::shared_ptr< Peptide > | NoConstPeptideSp
typedef std::shared_ptr< const PeptideFragment > | PeptideFragmentSp
typedef std::shared_ptr< const PeptideFragmentIon > | PeptideFragmentIonSp
typedef std::shared_ptr< const PeptideFragmentIonListBase > | PeptideFragmentIonListBaseSp
typedef std::shared_ptr< const PeptideInterface > | PeptideInterfaceSp
typedef std::shared_ptr< const PeptideNaturalIsotope > | PeptideNaturalIsotopeSp
typedef std::shared_ptr< const PeptideNaturalIsotopeAverage > | PeptideNaturalIsotopeAverageSp
typedef std::shared_ptr< const PeptideNaturalIsotopeList > | PeptideNaturalIsotopeListSp
typedef const PrecisionBase * | PrecisionPtr
typedef std::shared_ptr< const MassSpectrumCombiner > | MassSpectrumCombinerCstSPtr
typedef std::shared_ptr< MassSpectrumCombiner > | MassSpectrumCombinerSPtr
typedef std::shared_ptr< const MassSpectrumMinusCombiner > | MassSpectrumMinusCombinerCstSPtr
typedef std::shared_ptr< MassSpectrumMinusCombiner > | MassSpectrumMinusCombinerSPtr
typedef std::shared_ptr< const MassSpectrumPlusCombiner > | MassSpectrumPlusCombinerCstSPtr
typedef std::shared_ptr< MassSpectrumPlusCombiner > | MassSpectrumPlusCombinerSPtr
typedef std::shared_ptr< const TraceCombiner > | TraceCombinerCstSPtr
typedef std::shared_ptr< TraceCombiner > | TraceCombinerSPtr
typedef std::shared_ptr< const TraceMinusCombiner > | TraceMinusCombinerCstSPtr
typedef std::shared_ptr< TraceMinusCombiner > | TraceMinusCombinerSPtr
typedef std::shared_ptr< const TracePlusCombiner > | TracePlusCombinerCstSPtr
typedef std::shared_ptr< TracePlusCombiner > | TracePlusCombinerSPtr
typedef std::shared_ptr< TraceDetectionInterface > | TraceDetectionInterfaceSPtr
typedef std::shared_ptr< const TraceDetectionInterface > | TraceDetectionInterfaceCstSPtr
typedef std::shared_ptr< const TracePeak > | TracePeakCstSPtr
typedef std::shared_ptr< FilterCeilingAmplitudePercentage > | FilterCeilingAmplitudePercentageSPtr
typedef std::shared_ptr< const FilterCeilingAmplitudePercentage > | FilterCeilingAmplitudePercentageCstSPtr
typedef std::shared_ptr< FilterFloorAmplitudePercentage > | FilterFloorAmplitudePercentageSPtr
typedef std::shared_ptr< const FilterFloorAmplitudePercentage > | FilterFloorAmplitudePercentageCstSPtr
typedef std::shared_ptr< FilterInterface > | FilterInterfaceSPtr
typedef std::shared_ptr< const FilterInterface > | FilterInterfaceCstSPtr
typedef std::shared_ptr< FilterLowIntensitySignalRemoval > | FilterLowIntensitySignalRemovalSPtr
typedef std::shared_ptr< const FilterLowIntensitySignalRemoval > | FilterLowIntensitySignalRemovalCstSPtr
typedef std::shared_ptr< FilterNameInterface > | FilterNameInterfaceSPtr
typedef std::shared_ptr< const FilterNameInterface > | FilterNameInterfaceCstSPtr
using | SelectionPolygonSpecVector = std::vector< SelectionPolygonSpec >
typedef std::shared_ptr< FilterSuiteString > | FilterSuiteStringSPtr
typedef std::shared_ptr< FilterSavitzkyGolay > | FilterSavitzkyGolaySPtr
typedef std::shared_ptr< const FilterSavitzkyGolay > | FilterSavitzkyGolayCstSPtr
typedef std::shared_ptr< const Protein > | ProteinSp
| shared pointer on a Protein object More...
typedef std::shared_ptr< const PeakIonIsotopeMatch > | PeakIonIsotopeMatchCstSPtr
typedef std::shared_ptr< const DataPoint > | DataPointCstSPtr
typedef std::shared_ptr< MapTrace > | MapTraceSPtr
typedef std::shared_ptr< const MapTrace > | MapTraceCstSPtr
typedef std::shared_ptr< Trace > | TraceSPtr
typedef std::shared_ptr< const Trace > | TraceCstSPtr
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< MzCalibrationInterface > | MzCalibrationInterfaceSPtr
typedef std::shared_ptr< TimsData > | TimsDataSp
| shared pointer on a TimsData object More...
typedef std::shared_ptr< TimsFrame > | TimsFrameSPtr
typedef std::shared_ptr< const TimsFrame > | TimsFrameCstSPtr
typedef std::shared_ptr< TimsFrameBase > | TimsFrameBaseSPtr
typedef std::shared_ptr< const TimsFrameBase > | TimsFrameBaseCstSPtr
typedef std::shared_ptr< BaseColorMapPlotWidget > | BaseColorMapPlotWidgetSPtr
typedef std::shared_ptr< const BaseColorMapPlotWidget > | BaseColorMapPlotWidgetCstSPtr
typedef std::shared_ptr< BasePlotWidget > | BasePlotWidgetSPtr
typedef std::shared_ptr< const BasePlotWidget > | BasePlotWidgetCstSPtr
typedef std::shared_ptr< BaseTracePlotWidget > | BaseTracePlotWidgetSPtr
typedef std::shared_ptr< const BaseTracePlotWidget > | BaseTracePlotWidgetCstSPtr
typedef std::vector< std::pair< XicCstSPtr, TracePeakCstSPtr > > | XicXicPeakPairList
typedef std::shared_ptr< Xic > | QualifiedXicSp
typedef std::shared_ptr< const Xic > | XicCstSPtr
typedef std::shared_ptr< Xic > | XicSPtr
typedef std::shared_ptr< MsRunXicExtractorInterface > | MsRunXicExtractorInterfaceSp
typedef std::shared_ptr< const MsRunSlice > | MsRunSliceSPtr

## Enumerations

enum class | QualifiedMassSpectrumParameter { OneOverK0 , OneOverK0begin , OneOverK0end , IsolationMz , IsolationWidth , CollisionEnergy , BrukerPrecursorIndex , last }
enum class | FileReaderType { pwiz , xy , tims , 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 | 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< PeptideNaturalIsotopeAverageSp > | getByIntensityRatioByIsotopeNumber (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...
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

typedef const AaModification* pappso::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

typedef std::shared_ptr<const BaseColorMapPlotWidget> pappso::BaseColorMapPlotWidgetCstSPtr

Definition at line 59 of file basecolormapplotwidget.h.

## BaseColorMapPlotWidgetSPtr

typedef std::shared_ptr<BaseColorMapPlotWidget> pappso::BaseColorMapPlotWidgetSPtr

Definition at line 57 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

typedef std::shared_ptr<const BaseTracePlotWidget> pappso::BaseTracePlotWidgetCstSPtr

Definition at line 57 of file basetraceplotwidget.h.

## BaseTracePlotWidgetSPtr

typedef std::shared_ptr<BaseTracePlotWidget> pappso::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

typedef std::shared_ptr<FastaFileIndexer> pappso::FastaFileIndexerSPtr

Definition at line 49 of file fastafileindexer.h.

## FilterCeilingAmplitudePercentageCstSPtr

typedef std::shared_ptr<const FilterCeilingAmplitudePercentage> pappso::FilterCeilingAmplitudePercentageCstSPtr

Definition at line 51 of file filterceilingamplitudepercentage.h.

## FilterCeilingAmplitudePercentageSPtr

typedef std::shared_ptr<FilterCeilingAmplitudePercentage> pappso::FilterCeilingAmplitudePercentageSPtr

Definition at line 50 of file filterceilingamplitudepercentage.h.

## FilterFloorAmplitudePercentageCstSPtr

typedef std::shared_ptr<const FilterFloorAmplitudePercentage> pappso::FilterFloorAmplitudePercentageCstSPtr

Definition at line 53 of file filterflooramplitudepercentage.h.

## FilterFloorAmplitudePercentageSPtr

typedef std::shared_ptr<FilterFloorAmplitudePercentage> pappso::FilterFloorAmplitudePercentageSPtr

Definition at line 51 of file filterflooramplitudepercentage.h.

## 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

typedef std::shared_ptr<const FilterLowIntensitySignalRemoval> pappso::FilterLowIntensitySignalRemovalCstSPtr

Definition at line 53 of file filterlowintensitysignalremoval.h.

## FilterLowIntensitySignalRemovalSPtr

typedef std::shared_ptr<FilterLowIntensitySignalRemoval> pappso::FilterLowIntensitySignalRemovalSPtr

Definition at line 51 of file filterlowintensitysignalremoval.h.

## FilterNameInterfaceCstSPtr

typedef std::shared_ptr<const FilterNameInterface> pappso::FilterNameInterfaceCstSPtr

Definition at line 60 of file filternameinterface.h.

## FilterNameInterfaceSPtr

typedef std::shared_ptr<FilterNameInterface> pappso::FilterNameInterfaceSPtr

Definition at line 59 of file filternameinterface.h.

## FilterSavitzkyGolayCstSPtr

typedef std::shared_ptr<const FilterSavitzkyGolay> pappso::FilterSavitzkyGolayCstSPtr

Definition at line 122 of file savgolfilter.h.

## FilterSavitzkyGolaySPtr

typedef std::shared_ptr<FilterSavitzkyGolay> pappso::FilterSavitzkyGolaySPtr

Definition at line 121 of file savgolfilter.h.

## FilterSuiteStringSPtr

typedef std::shared_ptr<FilterSuiteString> pappso::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 26 of file maptrace.h.

## MapTraceSPtr

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

Definition at line 25 of file maptrace.h.

## MassSpectrumCombinerCstSPtr

typedef std::shared_ptr<const MassSpectrumCombiner> pappso::MassSpectrumCombinerCstSPtr

Definition at line 24 of file massspectrumcombiner.h.

## MassSpectrumCombinerSPtr

typedef std::shared_ptr<MassSpectrumCombiner> pappso::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

typedef std::shared_ptr<const MassSpectrumMinusCombiner> pappso::MassSpectrumMinusCombinerCstSPtr

Definition at line 20 of file massspectrumminuscombiner.h.

## MassSpectrumMinusCombinerSPtr

typedef std::shared_ptr<MassSpectrumMinusCombiner> pappso::MassSpectrumMinusCombinerSPtr

Definition at line 22 of file massspectrumminuscombiner.h.

## MassSpectrumPlusCombinerCstSPtr

typedef std::shared_ptr<const MassSpectrumPlusCombiner> pappso::MassSpectrumPlusCombinerCstSPtr

Definition at line 19 of file massspectrumpluscombiner.h.

## MassSpectrumPlusCombinerSPtr

typedef std::shared_ptr<MassSpectrumPlusCombiner> pappso::MassSpectrumPlusCombinerSPtr

Definition at line 21 of file massspectrumpluscombiner.h.

## 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

typedef std::shared_ptr<const MsRunDataSetTreeNode> pappso::MsRunDataSetTreeNodeCstSPtr

Definition at line 30 of file msrundatasettreenode.h.

## MsRunDataSetTreeNodeSPtr

typedef std::shared_ptr<MsRunDataSetTreeNode> pappso::MsRunDataSetTreeNodeSPtr

Definition at line 29 of file msrundatasettreenode.h.

## MsRunDataSetTreeSPtr

typedef std::shared_ptr<MsRunDataSetTree> pappso::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 185 of file msrunreader.h.

## MsRunReaderSPtr

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

Definition at line 184 of file msrunreader.h.

## MsRunSliceSPtr

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

Definition at line 40 of file msrunslice.h.

## MsRunXicExtractorInterfaceSp

typedef std::shared_ptr<MsRunXicExtractorInterface> pappso::MsRunXicExtractorInterfaceSp

Definition at line 46 of file msrunxicextractorinterface.h.

## MzCalibrationInterfaceSPtr

typedef std::shared_ptr<MzCalibrationInterface> pappso::MzCalibrationInterfaceSPtr

Definition at line 38 of file mzcalibrationinterface.h.

## NoConstPeptideSp

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

Definition at line 90 of file peptide.h.

## pappso_double

typedef double pappso::pappso_double

A type definition for doubles.

Definition at line 48 of file types.h.

## pappso_float

typedef float pappso::pappso_float

Definition at line 53 of file types.h.

## PeakIonIsotopeMatchCstSPtr

typedef std::shared_ptr<const PeakIonIsotopeMatch> pappso::PeakIonIsotopeMatchCstSPtr

Definition at line 34 of file peakionisotopematch.h.

## PeptideFragmentIonListBaseSp

typedef std::shared_ptr<const PeptideFragmentIonListBase> pappso::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

typedef std::shared_ptr<const PeptideNaturalIsotopeAverage> pappso::PeptideNaturalIsotopeAverageSp

Definition at line 40 of file peptidenaturalisotopeaverage.h.

## PeptideNaturalIsotopeListSp

typedef std::shared_ptr<const PeptideNaturalIsotopeList> pappso::PeptideNaturalIsotopeListSp

Definition at line 45 of file peptidenaturalisotopelist.h.

## PeptideNaturalIsotopeSp

typedef std::shared_ptr<const PeptideNaturalIsotope> pappso::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 43 of file types.h.

## PrecisionPtr

typedef const PrecisionBase* pappso::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

typedef std::shared_ptr<const QualifiedMassSpectrum> pappso::QualifiedMassSpectrumCstSPtr

Definition at line 45 of file qualifiedmassspectrum.h.

## QualifiedMassSpectrumSPtr

typedef std::shared_ptr<QualifiedMassSpectrum> pappso::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

using pappso::SelectionPolygonSpecVector = typedef std::vector<SelectionPolygonSpec>

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 43 of file timsframe.h.

## TimsFrameSPtr

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

Definition at line 42 of file timsframe.h.

## TimsMsRunReaderMs2SPtr

typedef std::shared_ptr<TimsMsRunReaderMs2> pappso::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

typedef std::shared_ptr<const TraceDetectionInterface> pappso::TraceDetectionInterfaceCstSPtr

Definition at line 35 of file tracedetectioninterface.h.

## TraceDetectionInterfaceSPtr

typedef std::shared_ptr<TraceDetectionInterface> pappso::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

typedef std::shared_ptr<TraceMinusCombiner> pappso::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

typedef std::shared_ptr<TracePlusCombiner> pappso::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 55 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 132 of file types.h.

{
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',
};
pappso::AminoAcidChar::lysine
@ lysine
pappso::AminoAcidChar::tyrosine
@ tyrosine
pappso::AminoAcidChar::glycine
@ glycine
pappso::AminoAcidChar::methionine
@ methionine
pappso::AminoAcidChar::cysteine
@ cysteine
pappso::AminoAcidChar::proline
@ proline
pappso::AminoAcidChar::asparagine
@ asparagine
pappso::AminoAcidChar::histidine
@ histidine
pappso::AminoAcidChar::alanine
@ alanine
pappso::AminoAcidChar::glutamic_acid
@ glutamic_acid
pappso::AminoAcidChar::pyrrolysine
@ pyrrolysine
pappso::AminoAcidChar::leucine
@ leucine
pappso::AminoAcidChar::arginine
@ arginine
pappso::AminoAcidChar::threonine
@ threonine
pappso::AminoAcidChar::serine
@ serine
pappso::AminoAcidChar::phenylalanine
@ phenylalanine
pappso::AminoAcidChar::selenocysteine
@ selenocysteine
pappso::AminoAcidChar::valine
@ valine
pappso::AminoAcidChar::aspartic_acid
@ aspartic_acid
pappso::AminoAcidChar::tryptophan
@ tryptophan
pappso::AminoAcidChar::isoleucine
@ isoleucine
pappso::AminoAcidChar::glutamine
@ glutamine

## AtomIsotope

enum pappso::AtomIsotope

strong

Enumerator
C |
H |
O |
N |
S |

Definition at line 69 of file peptidenaturalisotope.cpp.

{
C,
H,
O,
N,
S
};
pappso::AtomIsotope::C
@ C
pappso::AtomIsotope::S
@ S
pappso::AtomIsotope::N
@ N
pappso::AtomIsotope::H
@ H
pappso::AtomIsotope::O
@ O

## AtomIsotopeSurvey

enum pappso::AtomIsotopeSurvey : std::int8_t

strong

Enumerator
C |
H |
O |
N |
S |
last |

Definition at line 75 of file types.h.

{
C,
H,
O,
N,
S,
last
};
pappso::QualifiedMassSpectrumParameter::last
@ last

## Axis

enum pappso::Axis : std::int8_t

strong

Enumerator
unset |
x |
y |
z |

Definition at line 179 of file types.h.

{
unset = 0x000,
x = 1 << 0,
y = 1 << 1,
z = 1 << 2,
};
pappso::DataCompression::unset
@ unset
not net
pappso::PeptideIonCter::y
@ y
pappso::PeptideIonCter::x
@ x
pappso::PeptideIonCter::z
@ z

## AxisScale

enum pappso::AxisScale : std::int8_t

strong

Enumerator
unset |
orig |
log10 |

Definition at line 188 of file types.h.

{
unset = 0,
orig = 1,
log10 = 2,
};
pappso::AxisScale::orig
@ orig
pappso::AxisScale::log10
@ log10

## 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 46 of file mzintegrationparams.h.

{
//! < no binning
NONE = 0,
//! binning based on mass spectral data
DATA_BASED,
//! binning based on arbitrary bin size value
ARBITRARY,
LAST,
};
pappso::BinningType::DATA_BASED
@ DATA_BASED
binning based on mass spectral data
pappso::BinningType::ARBITRARY
@ ARBITRARY
binning based on arbitrary bin size value
pappso::BinningType::NONE
@ NONE
< no binning
pappso::BinningType::LAST
@ LAST

## DataCompression

enum pappso::DataCompression : std::int8_t

strong

Enumerator
unset | not net
none | no compression
zlib | zlib compresssion

Definition at line 162 of file types.h.

{
unset = -1, ///< not net
none = 0, ///< no compression
zlib = 1, ///< zlib compresssion
};
pappso::PrecisionUnit::none
@ none
pappso::DataCompression::zlib
@ zlib
zlib compresssion

## DataDimension

enum pappso::DataDimension

strong

Enumerator
NOT_SET |
HORIZONTAL |
VERTICAL |

Definition at line 34 of file selectionpolygon.h.

{
NOT_SET = 0,
HORIZONTAL,
VERTICAL
};
pappso::DataDimension::NOT_SET
@ NOT_SET
pappso::DataDimension::VERTICAL
@ VERTICAL
pappso::DataDimension::HORIZONTAL
@ HORIZONTAL

## DataKind

enum pappso::DataKind : std::int8_t

strong

Enumerator
unset | not set
rt | Retention time.
dt | Drift time.
mz | m/z

Definition at line 170 of file types.h.

{
unset = -1, ///< not set
rt = 0, ///< Retention time
dt = 1, ///< Drift time
mz = 2, ///< m/z
};
pappso::PrecisionUnit::mz
@ mz
pappso::DataKind::dt
@ dt
Drift time.
pappso::DataKind::rt
@ 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.

{
uncategorized = 0, ///< precursor mass was not compared
ZeroMassDelta = 1, ///< peptide candidate is in precursor mz range
ZeroMassDeltaMissedCleavage =
2, ///< peptide candidate with missed cleavage is in precursor mz range
ZeroMassDeltaSemiTryptic =
3, ///< semi tryptic peptide candidate is in precursor mz range
DeltaPosition = 4, ///< spectrum shifter on peptide candidate has detected a
///< position for the mass delta
NoDeltaPosition = 5, ///< spectrum shifter on peptide candidate has not
///< detected a position for the mass delta
last = 6
};
pappso::DeepProtMatchType::ZeroMassDeltaMissedCleavage
@ ZeroMassDeltaMissedCleavage
peptide candidate with missed cleavage is in precursor mz range
pappso::DeepProtMatchType::uncategorized
@ uncategorized
precursor mass was not compared
pappso::DeepProtMatchType::NoDeltaPosition
@ NoDeltaPosition
pappso::DeepProtMatchType::DeltaPosition
@ DeltaPosition
pappso::DeepProtMatchType::ZeroMassDelta
@ ZeroMassDelta
peptide candidate is in precursor mz range
pappso::DeepProtMatchType::ZeroMassDeltaSemiTryptic
@ 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.

{
unmodified = 0, ///< precursor mass was not compared
ZeroMassDelta = 1,
CterRemoval = 2,
NterRemoval = 3,
MissedCleavage = 4,
DeltaPosition = 5,
NoDeltaPosition = 6,
last = 7
};
pappso::DeepProtPeptideCandidateStatus::CterRemoval
@ CterRemoval
pappso::DeepProtPeptideCandidateStatus::unmodified
@ unmodified
precursor mass was not compared
pappso::DeepProtPeptideCandidateStatus::MissedCleavage
@ MissedCleavage
pappso::DeepProtPeptideCandidateStatus::NterRemoval
@ NterRemoval

## DragDirections

enum pappso::DragDirections

strong

Enumerator
NOT_SET |
LEFT_TO_RIGHT |
RIGHT_TO_LEFT |
TOP_TO_BOTTOM |
BOTTOM_TO_TOP |

Definition at line 25 of file baseplotcontext.h.

{
NOT_SET = 0x0000,
LEFT_TO_RIGHT = 1 << 0,
RIGHT_TO_LEFT = 1 << 1,
TOP_TO_BOTTOM = 1 << 2,
BOTTOM_TO_TOP = 1 << 3
};
pappso::DragDirections::RIGHT_TO_LEFT
@ RIGHT_TO_LEFT
pappso::DragDirections::LEFT_TO_RIGHT
@ LEFT_TO_RIGHT
pappso::DragDirections::BOTTOM_TO_TOP
@ BOTTOM_TO_TOP
pappso::DragDirections::TOP_TO_BOTTOM
@ TOP_TO_BOTTOM

## FileReaderType

enum pappso::FileReaderType

strong

Enumerator
pwiz |
xy |
tims |
tims_ms2 |

Definition at line 20 of file msfileaccessor.h.

{
pwiz,
xy,
tims,
tims_ms2,
};
pappso::FileReaderType::pwiz
@ pwiz
pappso::FileReaderType::xy
@ xy
pappso::FileReaderType::tims_ms2
@ tims_ms2
pappso::FileReaderType::tims
@ tims

## Isotope

enum pappso::Isotope

strong

Enumerator
C13 |
H2 |
O17 |
O18 |
N15 |
S33 |
S34 |
S36 |

Definition at line 90 of file types.h.

{
C13,
H2,
O17,
O18,
N15,
S33,
S34,
S36
};
pappso::Isotope::S36
@ S36
pappso::Isotope::C13
@ C13
pappso::Isotope::N15
@ N15
pappso::Isotope::S33
@ S33
pappso::Isotope::O18
@ O18
pappso::Isotope::O17
@ O17
pappso::Isotope::S34
@ S34
pappso::Isotope::H2
@ H2

## 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.

{
nose = 0, ///< default factory
direct = 1, ///< 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 = 2, ///< 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 =
3, ///< 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
};
pappso::MsRunXicExtractorFactoryType::diskbuffer
@ diskbuffer
pappso::MsRunXicExtractorFactoryType::nose
@ nose
default factory
pappso::MsRunXicExtractorFactoryType::disk
@ disk
pappso::MsRunXicExtractorFactoryType::direct
@ direct

## 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 106 of file types.h.

{
unknown = 0, ///< unknown format
mzML = 1, ///< mzML
mzXML = 2, ///< mzXML
MGF = 3, ///< Mascot format
SQLite3 = 4, ///< SQLite3 format
xy = 5, ///< (x,y) format
mz5 = 6, //< MZ5 format
msn = 7, //< MS_MS2 format
abSciexWiff = 8,
abSciexT2D = 9,
agilentMassHunter = 10,
thermoRaw = 11,
watersRaw = 12,
brukerFid = 13,
brukerYep = 14,
brukerBaf = 15,
brukerTims = 16,
last = 17
};
pappso::MzFormat::brukerTims
@ brukerTims
pappso::MzFormat::msn
@ msn
pappso::MzFormat::agilentMassHunter
@ agilentMassHunter
pappso::MzFormat::abSciexT2D
@ abSciexT2D
pappso::MzFormat::mzXML
@ mzXML
mzXML
pappso::MzFormat::watersRaw
@ watersRaw
pappso::MzFormat::mz5
@ mz5
pappso::MzFormat::brukerBaf
@ brukerBaf
pappso::MzFormat::mzML
@ mzML
mzML
pappso::MzFormat::abSciexWiff
@ abSciexWiff
pappso::MzFormat::brukerFid
@ brukerFid
pappso::MzFormat::unknown
@ unknown
unknown format
pappso::MzFormat::SQLite3
@ SQLite3
SQLite3 format.
pappso::MzFormat::MGF
@ MGF
Mascot format.
pappso::MzFormat::thermoRaw
@ thermoRaw
pappso::MzFormat::brukerYep
@ brukerYep

## PeptideDirection

enum pappso::PeptideDirection : std::int8_t

strong

Enumerator
Nter |
Cter |

Definition at line 45 of file peptide.h.

{
Nter = 0,
Cter = 1
};
pappso::PeptideDirection::Cter
@ Cter
pappso::PeptideDirection::Nter
@ Nter

## PeptideIon

enum pappso::PeptideIon : std::int8_t

strong

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

Enumerator
b | Nter acylium ions.
bstar | Nter acylium ions + NH3 loss.
bo | Nter acylium ions + H2O loss.
a | Nter aldimine ions.
astar | Nter aldimine ions + NH3 loss.
ao | Nter aldimine ions + H2O loss.
bp |
c | Nter amino ions.
y | Cter amino ions.
ystar | Cter amino ions + NH3 loss.
yo | Cter amino ions + H2O loss.
z | Cter carbocations.
yp |
x | Cter acylium ions.

Definition at line 384 of file types.h.

{
b = 0, ///< Nter acylium ions
bstar = 1, ///< Nter acylium ions + NH3 loss
bo = 2, ///< Nter acylium ions + H2O loss
a = 3, ///< Nter aldimine ions
astar = 4, ///< Nter aldimine ions + NH3 loss
ao = 5, ///< Nter aldimine ions + H2O loss
bp = 6,
c = 7, ///< Nter amino ions
y = 8, ///< Cter amino ions
ystar = 9, ///< Cter amino ions + NH3 loss
yo = 10, ///< Cter amino ions + H2O loss
z = 11, ///< Cter carbocations
yp = 12,
x = 13 ///< Cter acylium ions
};
pappso::PeptideIonNter::a
@ a
pappso::PeptideIonNter::c
@ c
pappso::PeptideIonNter::astar
@ astar
pappso::PeptideIonNter::bp
@ bp
pappso::PeptideIonNter::bstar
@ bstar
pappso::PeptideIonNter::b
@ b
pappso::PeptideIonNter::bo
@ bo
pappso::PeptideIonNter::ao
@ ao
pappso::PeptideIonCter::yp
@ yp
pappso::PeptideIonCter::ystar
@ ystar
pappso::PeptideIonCter::yo
@ yo

## PeptideIonCter

enum pappso::PeptideIonCter

strong

Enumerator
y |
ystar |
yo |
z |
yp |
x |

Definition at line 77 of file peptide.h.

{
y,
ystar,
yo,
z,
yp,
x
};

## PeptideIonNter

enum pappso::PeptideIonNter

strong

Enumerator
b |
bstar |
bo |
a |
astar |
ao |
bp |
c |

Definition at line 64 of file peptide.h.

{
b,
bstar,
bo,
a,
astar,
ao,
bp,
c
};

## 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.

{
// Starting top left and then clockwise
TOP_LEFT_POINT = 0,
TOP_RIGHT_POINT = 1,
BOTTOM_RIGHT_POINT = 2,
BOTTOM_LEFT_POINT = 3,
ENUM_LAST = 4,
};
pappso::PointSpecs::BOTTOM_RIGHT_POINT
@ BOTTOM_RIGHT_POINT
pappso::PointSpecs::TOP_LEFT_POINT
@ TOP_LEFT_POINT
pappso::PointSpecs::BOTTOM_LEFT_POINT
@ BOTTOM_LEFT_POINT
pappso::PointSpecs::ENUM_LAST
@ ENUM_LAST
pappso::PointSpecs::TOP_RIGHT_POINT
@ TOP_RIGHT_POINT

## 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.

{
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)
};
pappso::PolygonType::VERTICAL_LINES
@ VERTICAL_LINES
pappso::PolygonType::FULL_POLYGON
@ FULL_POLYGON
pappso::PolygonType::TOP_LINE
@ TOP_LINE
pappso::PolygonType::BOTTOM_LINE
@ BOTTOM_LINE
pappso::PolygonType::HORIZONTAL_LINES
@ HORIZONTAL_LINES

## PrecisionUnit

enum pappso::PrecisionUnit

strong

Enumerator
none |
dalton |
ppm |
res |
mz |
last |

Definition at line 62 of file types.h.

{
none,
dalton,
ppm,
res,
mz,
last
};
pappso::PrecisionUnit::res
@ res
pappso::PrecisionUnit::ppm
@ ppm
pappso::PrecisionUnit::dalton
@ dalton

## QualifiedMassSpectrumParameter

enum pappso::QualifiedMassSpectrumParameter

strong

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.

{
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
};
pappso::QualifiedMassSpectrumParameter::CollisionEnergy
@ CollisionEnergy
Bruker's Tims tof collision energy.
pappso::QualifiedMassSpectrumParameter::IsolationMz
@ IsolationMz
isolation window
pappso::QualifiedMassSpectrumParameter::OneOverK0
@ OneOverK0
1/kO of a simple scan
pappso::QualifiedMassSpectrumParameter::OneOverK0end
@ OneOverK0end
1/k0 of last acquisition for composite pasef MS/MS spectrum
pappso::QualifiedMassSpectrumParameter::OneOverK0begin
@ OneOverK0begin
pappso::QualifiedMassSpectrumParameter::IsolationWidth
@ IsolationWidth
isolation window width
pappso::QualifiedMassSpectrumParameter::BrukerPrecursorIndex
@ BrukerPrecursorIndex
Bruker's Tims tof precursor index.

## RangeType

enum pappso::RangeType

strong

Enumerator
outermost |
innermost |

Definition at line 55 of file baseplotwidget.h.

{
outermost = 1,
innermost = 2,
};
pappso::RangeType::innermost
@ innermost
pappso::RangeType::outermost
@ outermost

## RawFragmentationMode

enum pappso::RawFragmentationMode : std::int8_t

strong

Enumerator
full |
proline_effect |

Definition at line 42 of file peptiderawfragmentmasses.h.

{
full = 0,
proline_effect = 1
};
pappso::RawFragmentationMode::full
@ full
pappso::RawFragmentationMode::proline_effect
@ proline_effect

## XicExtractMethod

enum pappso::XicExtractMethod : std::int8_t

strong

Enumerator
sum | sum of intensities
max | maximum of intensities

Definition at line 199 of file types.h.

{
sum = 1, ///< sum of intensities
max = 2 ///< maximum of intensities
};
pappso::XicExtractMethod::sum
@ sum
sum of intensities
pappso::XicExtractMethod::max
@ 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 268 of file trace.cpp.

{
if(begin == end)
return 0;
auto previous = begin;
auto next = begin + 1;
double area = 0;
while(next != end)
{
area += ((next->x - previous->x) * (previous->y + next->y)) / (double)2;
previous++;
next++;
}
return area;
}

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

## Combinations()

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

Definition at line 47 of file peptidenaturalisotope.cpp.

{
if(k > n)
return 0;
uint64_t r = 1;
if((n < CACHE_ARRAY_SIZE) && (combinations_cache[n][k] != 0))
{
return combinations_cache[n][k];
}
for(unsigned int d = 1; d <= k; ++d)
{
r *= n--;
r /= d;
}
if(n < CACHE_ARRAY_SIZE)
{
combinations_cache[n][k] = r;
}
return r;
}
pappso::combinations_cache
uint64_t combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:44
CACHE_ARRAY_SIZE
#define CACHE_ARRAY_SIZE
Definition: peptidenaturalisotope.cpp:42

References CACHE_ARRAY_SIZE, and combinations_cache.

Referenced by isotopem_ratio().

## DIFFC12C13()

const pappso_double pappso::DIFFC12C13 | ( | 1. | 0033548378 | ) |

Referenced by pappso::FilterChargeDeconvolution::FilterChargeDeconvolution(), pappso::FilterRemoveC13::FilterRemoveC13(), pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), pappso::FilterChargeDeconvolution::buildFilterFromString(), pappso::AaModification::calculateMassFromChemicalComponents(), and pappso::QCPSpectrum::highlightPrecursorPeaks().

## DIFFH1H2()

const pappso_double pappso::DIFFH1H2 | ( | 2.0141017778 - | MPROTIUM | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## DIFFN14N15()

const pappso_double pappso::DIFFN14N15 | ( | 15.0001088982 - | MASSNITROGEN | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## DIFFO16O17()

const pappso_double pappso::DIFFO16O17 | ( | 16.99913150 - | MASSOXYGEN | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## DIFFO16O18()

const pappso_double pappso::DIFFO16O18 | ( | 17.9991610 - | MASSOXYGEN | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## DIFFS32S33()

const pappso_double pappso::DIFFS32S33 | ( | 32.9714589101 - | MASSSULFUR | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## DIFFS32S34()

const pappso_double pappso::DIFFS32S34 | ( | 33.9678670300 - | MASSSULFUR | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## DIFFS32S36()

const pappso_double pappso::DIFFS32S36 | ( | 35.9670812000 - | MASSSULFUR | ) |

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), and pappso::AaModification::calculateMassFromChemicalComponents().

## factorial()

unsigned int pappso::factorial | ( | unsigned int | n | ) |

Definition at line 43 of file xtandemhyperscore.cpp.

{
unsigned int retval = 1;
for(int i = n; i > 1; --i)
retval *= i;
return retval;
}

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

  begin | begin iterator
  end | end iterator
  rt_list | retention time list in seconds
  nb_peaks | retrieve 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.

{
// get peak containing rt ahead :
auto itend = std::partition(begin, end, [rt_list](const TracePeak &a) {
for(double rt : rt_list)
{
if(a.containsRt(rt))
{
return true;
};
}
return false;
});
nb_peaks = std::distance(begin, itend);
if(nb_peaks == 0)
return end;
return std::max_element(
begin, itend, [](const TracePeak &a, const TracePeak &b) {
return a.getArea() < b.getArea();
});
}
pappso::TracePeak
Definition: tracepeak.h:40

References a, b, and rt.

## 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 102 of file trace.cpp.

{
return std::find_if(begin, end, [y_value](const DataPoint &to_compare) {
if(to_compare.y != y_value)
{
return true;
}
return false;
});
}

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 88 of file trace.cpp.

{
return std::find_if(begin, end, [y_value](const DataPoint &to_compare) {
if(to_compare.y != y_value)
{
return true;
}
return false;
});
}

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 46 of file trace.cpp.

{
return std::find_if(begin, end, [value](const DataPoint &to_compare) {
if(to_compare.x < value)
{
return false;
}
return true;
});
}

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 32 of file trace.cpp.

{
return std::find_if(begin, end, [value](const DataPoint &to_compare) {
if(to_compare.x < value)
{
return false;
}
return true;
});
}

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 74 of file trace.cpp.

{
return std::find_if(begin, end, [value](const DataPoint &to_compare) {
if(to_compare.x > value)
{
return true;
}
return false;
});
}

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 60 of file trace.cpp.

{
return std::find_if(begin, end, [value](const DataPoint &to_compare) {
if(to_compare.x > value)
{
return true;
}
return false;
});
}

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

  begin | begin iterator
  end | end iterator
  rt | retention time in seconds

Returns
  iterator on the peak concerned by the retention time

Definition at line 81 of file tracepeaklist.cpp.

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

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 288 of file trace.cpp.

{
Trace local_maxima_trace;
Trace single_peak_trace;
DataPoint previous_data_point;
for(auto iter = begin; iter != end; ++iter)
{
DataPoint iterated_data_point(iter->x, iter->y);
// qDebug().noquote() << "Current data point:"
//<< iterated_data_point.toString();
if(iterated_data_point.y < y_floor)
{
// qDebug() << "under the floor";
if(single_peak_trace.size())
{
// qDebug() << "There was a single peak trace cooking";
local_maxima_trace.push_back(single_peak_trace.maxYDataPoint());
// qDebug().noquote() << "pushed back local maximum point:"
//<< local_maxima_trace.back().toString();
// Clean and set the context.
single_peak_trace.clear();
previous_data_point = iterated_data_point;
continue;
}
else
{
// qDebug() << "no single peak trace cooking";
previous_data_point = iterated_data_point;
continue;
}
}
else
{
// qDebug() << "over the floor";
// The iterated value is greater than the y_floor value, so we need to
// handle it.
if(iterated_data_point.y == previous_data_point.y)
{
// We are in a flat region, no need to change anything to the
// context, just skip the point.
continue;
}
else if(iterated_data_point.y > previous_data_point.y)
{
// qDebug().noquote() << "ascending in a peak";
// The previously iterated y value was smaller than the presently
// iterated one, so we are ascending in a peak.
// All we need to do is set the context.
single_peak_trace.push_back(iterated_data_point);
// qDebug().noquote() << "pushed back normal point:"
//<< single_peak_trace.back().toString();
previous_data_point = iterated_data_point;
continue;
}
else
{
// qDebug().noquote() << "started descending in a peak";
// No, the currently iterated y value is less than the previously
// iterated value.
single_peak_trace.push_back(iterated_data_point);
// qDebug().noquote() << "pushed back normal point:"
//<< single_peak_trace.back().toString();
previous_data_point = iterated_data_point;
continue;
}
}
}
// End of
// for(auto iter = begin; iter != end; ++iter)
// Attention, we might arrive here with a peak being created, we need to get
// its maximum if that peak is non-empty;
if(single_peak_trace.size())
{
local_maxima_trace.push_back(single_peak_trace.maxYDataPoint());
// qDebug().noquote()
//<< "was cooking a peak: pushed back local maximum point:"
//<< local_maxima_trace.back().toString();
}
return local_maxima_trace;
}

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.

{
// qDebug() << "getByIntensityRatioByIsotopeNumber begin";
unsigned int askedIsotopeRank;
unsigned int maxAskedIsotopeRank = 10;
pappso_double cumulativeRatio = 0;
std::vector<PeptideNaturalIsotopeAverageSp> v_isotopeAverageList;
std::vector<PeptideNaturalIsotopeAverageSp> v_isotopeAverageListResult;
std::vector<unsigned int> previousIsotopeRank;
bool isEmpty = false;
for(askedIsotopeRank = 1;
(askedIsotopeRank < maxAskedIsotopeRank) && (!isEmpty);
askedIsotopeRank++)
{
PeptideNaturalIsotopeAverage isotopeAverage(
peptide, askedIsotopeRank, isotopeNumber, charge, precision);
isEmpty = isotopeAverage.isEmpty();
if(isEmpty)
{
}
else
{
if(std::find(previousIsotopeRank.begin(),
previousIsotopeRank.end(),
isotopeAverage.getIsotopeRank()) ==
previousIsotopeRank.end())
{ // not Found
previousIsotopeRank.push_back(isotopeAverage.getIsotopeRank());
v_isotopeAverageList.push_back(
isotopeAverage.makePeptideNaturalIsotopeAverageSp());
}
}
}
if(v_isotopeAverageList.size() == 0)
return v_isotopeAverageListResult;
// qDebug() << "getByIntensityRatioByIsotopeNumber comp";
std::sort(v_isotopeAverageList.begin(),
v_isotopeAverageList.end(),
[](const PeptideNaturalIsotopeAverageSp &m,
const PeptideNaturalIsotopeAverageSp &n) {
return (m.get()->getIntensityRatio() >
n.get()->getIntensityRatio());
});
cumulativeRatio = 0;
auto it = v_isotopeAverageList.begin();
v_isotopeAverageListResult.clear();
// qDebug() << "getByIntensityRatioByIsotopeNumber cumul";
while((it != v_isotopeAverageList.end()) &&
(cumulativeRatio < minimumIntensity))
{
cumulativeRatio += it->get()->getIntensityRatio();
v_isotopeAverageListResult.push_back(*it);
it++;
}
// qDebug() << "getByIntensityRatioByIsotopeNumber end";
return v_isotopeAverageListResult;
}
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
pappso::PeptideNaturalIsotopeAverageSp
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp
Definition: peptidenaturalisotopeaverage.h:37

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

## getPeptideIonDirection()

PeptideDirection pappso::getPeptideIonDirection | ( | PeptideIon | ion_type | ) |

get the direction of a peptide ion

Parameters

  ion_type | the ion to test

Returns
  the peptide direction

Definition at line 54 of file peptide.cpp.

{
if(peptideIonIsNter(ion_type))
{
return PeptideDirection::Nter;
}
return PeptideDirection::Cter;
}
pappso::peptideIonIsNter
bool peptideIonIsNter(PeptideIon ion_type)
tells if an ion is Nter
Definition: peptide.cpp:44

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.

{
return (pow(abundance, heavy) * pow((double)1 - abundance, (total - heavy)) *
(double)Combinations(total, heavy));
}
pappso::Combinations
uint64_t Combinations(unsigned int n, unsigned int k)
Definition: peptidenaturalisotope.cpp:47

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.

{
pappso_double abundance = 1;
switch(isotope)
{
case Isotope::H2:
abundance = ABUNDANCEH2;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioH2_cache[total][heavy] == 0)
{
ratioH2_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioH2_cache[total][heavy];
}
break;
case Isotope::C13:
abundance = ABUNDANCEC13;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioC13_cache[total][heavy] == 0)
{
ratioC13_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioC13_cache[total][heavy];
}
break;
case Isotope::N15:
abundance = ABUNDANCEN15;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioN15_cache[total][heavy] == 0)
{
ratioN15_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioN15_cache[total][heavy];
}
break;
case Isotope::O18:
abundance = ABUNDANCEO18;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioO18_cache[total][heavy] == 0)
{
ratioO18_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioO18_cache[total][heavy];
}
break;
case Isotope::O17:
abundance = ABUNDANCEO17;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioO17_cache[total][heavy] == 0)
{
ratioO17_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioO17_cache[total][heavy];
}
break;
case Isotope::S33:
abundance = ABUNDANCES33;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioS33_cache[total][heavy] == 0)
{
ratioS33_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioS33_cache[total][heavy];
}
break;
case Isotope::S34:
abundance = ABUNDANCES34;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioS34_cache[total][heavy] == 0)
{
ratioS34_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioS34_cache[total][heavy];
}
break;
case Isotope::S36:
abundance = ABUNDANCES36;
if(total < CACHE_ARRAY_SIZE)
{
if(ratioS36_cache[total][heavy] == 0)
{
ratioS36_cache[total][heavy] =
isotopem_ratio(abundance, total, heavy);
}
return ratioS36_cache[total][heavy];
}
break;
}
return isotopem_ratio(abundance, total, heavy);
}
pappso::ratioO17_cache
pappso_double ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:90
pappso::ABUNDANCES36
const pappso_double ABUNDANCES36(0.00010999120070394368536836893213148869108408689498901367187500)
pappso::ratioS34_cache
pappso_double ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:88
pappso::ABUNDANCEN15
const pappso_double ABUNDANCEN15(0.00364198543205827118818262988497735932469367980957031250000000)
pappso::ratioC13_cache
pappso_double ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:85
pappso::isotopem_ratio
pappso_double isotopem_ratio(pappso_double abundance, unsigned int total, unsigned int heavy)
Definition: peptidenaturalisotope.cpp:79
pappso::ratioH2_cache
pappso_double ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:92
pappso::ABUNDANCEC13
const pappso_double ABUNDANCEC13(0.01078805814953308406245469086570665240287780761718750000000000)
pappso::ABUNDANCEO17
const pappso_double ABUNDANCEO17(0.00038099847600609595965615028489992255344986915588378906250000)
pappso::ABUNDANCEH2
const pappso_double ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250)
pappso::ratioO18_cache
pappso_double ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:91
pappso::ABUNDANCES34
const pappso_double ABUNDANCES34(0.04252059835213182203972337447339668869972229003906250000000000)
pappso::ratioS36_cache
pappso_double ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:87
pappso::ABUNDANCEO18
const pappso_double ABUNDANCEO18(0.00205139179443282221315669744399201590567827224731445312500000)
pappso::ABUNDANCES33
const pappso_double ABUNDANCES33(0.00751939844812414937003097747947322204709053039550781250000000)
pappso::ratioN15_cache
pappso_double ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:86
pappso::ratioS33_cache
pappso_double ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition: peptidenaturalisotope.cpp:89

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 |  | ) |

Referenced by pappso::AaModification::calculateMassFromChemicalComponents().

## MASSCO()

const pappso_double pappso::MASSCO | ( | MASSCARBON+ | MASSOXYGEN | ) |

## MASSH2O()

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

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

## MASSNH3()

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

## MASSNITROGEN()

const pappso_double pappso::MASSNITROGEN | ( | 14. | 0030740048 | ) |

Referenced by pappso::AaModification::calculateMassFromChemicalComponents().

## MASSOXYGEN()

const pappso_double pappso::MASSOXYGEN | ( | 15. | 99491461956 | ) |

Referenced by pappso::AaModification::calculateMassFromChemicalComponents(), and pappso::AaModification::createInstance().

## MASSPHOSPHORUS()

const pappso_double pappso::MASSPHOSPHORUS | ( | 30. | 973761998 | ) |

## MASSPHOSPHORYLATEDR()

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

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

## MASSSELENIUM()

const pappso_double pappso::MASSSELENIUM | ( | 79. | 916520 | ) |

## MASSSULFUR()

const pappso_double pappso::MASSSULFUR | ( | 31. | 9720711741 | ) |

Referenced by pappso::AaModification::calculateMassFromChemicalComponents().

## 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 139 of file trace.cpp.

{
return std::max_element(
begin, end, [](const DataPoint &a, const DataPoint &b) {
return a.y < b.y;
});
}

References a, and b.

Referenced by pappso::TracePeak::TracePeak(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::FilterCeilingAmplitudePercentage::filter(), pappso::FilterFloorAmplitudePercentage::filter(), pappso::FilterLocalMaximum::filter(), pappso::FilterHighPassPercentage::filter(), pappso::FilterRescaleY::filter(), pappso::FilterTriangle::filter(), pappso::LinearRegression::getNrmsd(), and pappso::FilterMorphoMax::getWindowValue().

## 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 150 of file trace.cpp.

{
return std::max_element(
begin, end, [](const DataPoint &a, const DataPoint &b) {
return a.y < b.y;
});
}

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 212 of file trace.cpp.

{
pappso_double nb_element = distance(begin, end);
if(nb_element == 0)
throw ExceptionOutOfRange(
QObject::tr("unable to compute mean on a trace of size 0"));
return (sumYTrace(begin, end, 0) / nb_element);
}
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:203

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 250 of file trace.cpp.

{
std::size_t nb_element = distance(begin, end);
if(nb_element == 0)
throw ExceptionOutOfRange(
QObject::tr("unable to compute median on a trace of size 0"));
std::vector<DataPoint> data(begin, end);
std::nth_element(
data.begin(),
data.begin() + data.size() / 2,
data.end(),
[](const DataPoint &a, const DataPoint &b) { return a.y < b.y; });
return data[data.size() / 2].y;
}

References a, and b.

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

## MHPLUS()

const pappso_double pappso::MHPLUS | ( | 1. | 007276466879 | ) |

Referenced by pappso::Ion::getMz(), pappso::PeptideInterface::matchPeak(), pappso::XtandemSpectrumProcess::process(), pappso::PeptideRawFragmentMasses::pushBackIonMz(), and pappso::FilterChargeDeconvolution::transformToMonoChargedForAllDataPoint().

## 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 117 of file trace.cpp.

{
return std::min_element(
begin, end, [](const DataPoint &a, const DataPoint &b) {
return a.y < b.y;
});
}

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 128 of file trace.cpp.

{
return std::min_element(
begin, end, [](const DataPoint &a, const DataPoint &b) {
return a.y < b.y;
});
}

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 182 of file trace.cpp.

{
if(begin == trace.begin())
return begin;
auto it = begin - 1;
auto result = begin;
// As long as prev datapoint has y value less or equal to next,
// move along up the container. That is, continue moving if
// direction is downhill to the beginning of the container (its front).
while((it != trace.begin()) && (it->y <= result->y))
{
it--;
result--;
}
return result;
}

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 164 of file trace.cpp.

{
if(begin == trace.end())
return begin;
auto it = begin + 1;
auto result = begin;
// Move along as long as next point's y value is less
// or equal to prev point's y value (FR, check).
while((it != trace.end()) && (it->y <= result->y))
{
it++;
result++;
}
return result;
}

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

## MPROTIUM()

const pappso_double pappso::MPROTIUM | ( | 1. | 007825032241 | ) |

Referenced by pappso::AaModification::calculateMassFromChemicalComponents(), and pappso::AaModification::createInstance().

## MPROTON()

const pappso_double pappso::MPROTON | ( | 1. | 007276466879 | ) |

Referenced by pappso::MassSpecTracePlotWidget::deconvoluteChargedState(), and pappso::MassSpecTracePlotWidget::deconvoluteIsotopicCluster().

## ONEMILLION()

const pappso_double pappso::ONEMILLION | ( | 1000000 |  | ) |

Referenced by pappso::PpmPrecision::delta().

## operator<()

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

Definition at line 285 of file aa.cpp.

{
return l.isLesser(r);
}

References pappso::Aa::isLesser().

## operator<<() [1/3]

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

Definition at line 152 of file datapoint.cpp.

{
out << dataPoint.x;
out << dataPoint.y;
return out;
}

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

## operator<<() [2/3]

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

## operator<<() [3/3]

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

Definition at line 342 of file massspectrum.cpp.

{
quint32 vector_size = massSpectrum.size();
outstream << vector_size;
for(auto &&peak : massSpectrum)
{
outstream << peak;
}
return outstream;
}

## operator==()

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

Definition at line 280 of file aa.cpp.

{
return l.isAaEqual(r);
}

References pappso::Aa::isAaEqual().

## operator>>() [1/4]

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

Definition at line 163 of file datapoint.cpp.

{
if(in.atEnd())
{
throw PappsoException(
QString("error in QDataStream unserialize operator>> of massSpectrum "
"dataPoint:\nread datastream failed status=%1")
.arg(in.status()));
}
in >> dataPoint.x;
in >> dataPoint.y;
return in;
}

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

## operator>>() [2/4]

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

Definition at line 357 of file massspectrum.cpp.

{
quint32 vector_size;
DataPoint peak;
if(!instream.atEnd())
{
instream >> vector_size;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " vector_size=" << vector_size;
for(quint32 i = 0; i < vector_size; i++)
{
if(instream.status() != QDataStream::Ok)
{
throw PappsoException(
QString("error in QDataStream unserialize operator>> of "
"massSpectrum :\nread datastream failed status=%1 "
"massSpectrum "
"i=%2 on size=%3")
.arg(instream.status())
.arg(i)
.arg(vector_size));
}
instream >> peak;
massSpectrum.push_back(peak);
}
if(instream.status() != QDataStream::Ok)
{
throw PappsoException(
QString(
"error in QDataStream unserialize operator>> of massSpectrum "
":\nread datastream failed status=%1")
.arg(instream.status()));
}
}
return instream;
}

## operator>>() [3/4]

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

Definition at line 156 of file msrunslice.cpp.

{
quint32 vector_size = 0;
quint32 slice_number = 0;
quint32 spectrum_position = 0;
DataPoint peak;
if(!instream.atEnd())
{
instream >> slice_number;
instream >> vector_size;
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
<< " vector_size=" << vector_size;
slice.setSize(vector_size);
slice.setSliceNumber(slice_number);
while(!instream.atEnd())
{
instream >> spectrum_position;
MassSpectrum spectrum;
try
{
instream >> spectrum;
}
catch(PappsoException &error)
{
throw PappsoException(
QString("error in QDataStream unserialize operator>> of "
"MsRunSlice %2 on %3:\n%1")
.arg(error.qwhat())
.arg(spectrum_position)
.arg(vector_size));
}
slice.setSpectrum(spectrum_position, spectrum);
if(instream.status() != QDataStream::Ok)
{
throw PappsoException(
QString("error in QDataStream unserialize operator>> of "
"MsRunSlice :\nread datastream failed status=%1")
.arg(instream.status()));
}
}
}
if(slice.size() != vector_size)
{
throw PappsoException(
QString("error in QDataStream unserialize operator>> of MsRunSlice "
"slice.size() != vector_size :\n %1 %2:")
.arg(slice.size())
.arg(vector_size));
}
return instream;
}

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
| ) |  |

## peptideIonIsNter()

bool pappso::peptideIonIsNter | ( | PeptideIon | ion_type | ) |

tells if an ion is Nter

Parameters

  ion_type | the ion to test

Definition at line 44 of file peptide.cpp.

{
if((std::int8_t)ion_type < (std::int8_t)8)
{
return true;
}
return false;
}

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

## 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

  begin | begin iterator
  end | end iterator
  quantile | the quantile value between 0 and 1

Returns
  Y value at the quantile

Definition at line 224 of file trace.cpp.

{
std::size_t nb_element = distance(begin, end);
if(nb_element == 0)
throw ExceptionOutOfRange(
QObject::tr("unable to compute quantile on a trace of size 0"));
std::size_t ieth_element = std::round((double)nb_element * quantile);
if(ieth_element > nb_element)
throw ExceptionOutOfRange(
QObject::tr("quantile value must be lower than 1"));
std::vector<DataPoint> data(begin, end);
std::nth_element(
data.begin(),
data.begin() + ieth_element,
data.end(),
[](const DataPoint &a, const DataPoint &b) { return a.y < b.y; });
return data[ieth_element].y;
}

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 203 of file trace.cpp.

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

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 60 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

class PMSPP_LIB_DECL pappso::MsRunReader

Definition at line 298 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().