Classes
class	Aa

class	AaBase

class	AaModification

class	AtomNumberInterface

class	BaseColorMapPlotWidget

struct	BasePlotContext

class	BasePlotWidget

class	BaseTracePlotWidget

struct	ColorMapPlotConfig

class	DaltonPrecision

struct	DataPoint

class	DriftSpecMassSpecColorMapPlotWidget

class	DriftSpecTracePlotWidget

class	Enzyme

class	EnzymeProductInterface

class	ExceptionNotFound

class	ExceptionNotImplemented

class	ExceptionNotPossible

class	ExceptionOutOfRange

class	FastaFileIndexer

class	FastaFileIndexerInterface

class	FastaHandlerInterface

class	FastaOutputStream

class	FastaReader

class	FastaWriterInterface

class	FilterFloorY

class	FilterGreatestY

class	FilterHighPass

class	FilterHighPassPercentage

class	FilterInterface
	generic interface to apply a filter on a trace More...

class	FilterLocalMaximum
	finds all local maxima, i.e. any point that has a greater y value than both of its neighboring points and only keep those points More...

class	FilterLowPass

class	FilterMorphoAntiSpike
	anti spike filter set to zero alone values inside the window More...

class	FilterMorphoBackground
	compute background of a trace compute background noise on a trace More...

class	FilterMorphoMax
	transform the trace into its maximum over a window More...

class	FilterMorphoMaxMin
	transform the trace with the maximum of the minimum equivalent of the erode filter for pictures More...

class	FilterMorphoMean
	mean filter apply mean of y values inside the window : this results in a kind of smoothing More...

class	FilterMorphoMedian
	median filter apply median of y values inside the window More...

class	FilterMorphoMin
	transform the trace into its minimum over a window More...

class	FilterMorphoMinMax
	transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures More...

class	FilterMorphoSum
	test purpose More...

class	FilterMorphoWindowBase
	base class that apply a signal treatment based on a window More...

class	FilterOboPsiModSink

class	FilterOboPsiModTermAccession

class	FilterOboPsiModTermDiffMono

class	FilterOboPsiModTermLabel

class	FilterOboPsiModTermName

class	FilterPseudoCentroid

class	FilterResampleKeepGreater

class	FilterResampleKeepSmaller

class	FilterResampleKeepXRange

class	FilterResampleRemoveXRange

class	FilterRescaleY
	rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored More...

class	FilterRoundY

class	FilterSavitzkyGolay
	uses Savitsky-Golay filter on trace More...

class	FilterScaleFactorY
	rescales Y values given a tranformation factor More...

class	FilterSuite
	apply a suite of filters from a vector More...

class	FilterTandemDeisotope
	Deisotope the mass spectrum `this` mass spectrum is iterated over and according to a data point-based moving window progression does the following tests: More...

class	FilterTandemRemoveC13
	clean probable C13 isotopes as in X!Tandem algorithm More...

class	FilterTriangle

class	GrpExperiment

class	GrpGroup

class	GrpGroupingMonitor

class	GrpGroupingMonitorInterface

class	GrpMapPeptideToGroup

class	GrpMapPeptideToSubGroupSet

class	GrpPeptide

class	GrpPeptideSet

class	GrpProtein

class	GrpSubGroup

class	GrpSubGroupSet

class	Ion

class	IonIsotopeRatioScore

class	LinearRegression

class	MapTrace

class	MassDataCombinerInterface

struct	MassSpecTracePlotContext

class	MassSpecTracePlotWidget

class	MassSpectrum
	Class to represent a mass spectrum. More...

class	MassSpectrumCombiner

class	MassSpectrumCombinerFactory

class	MassSpectrumFilterGreatestItensities

class	MassSpectrumFilterInterface
	generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface, but some filter are only relevant if they are used on MassSpectrum using this interface means the filter can only be applied on MassSpectrum and not on Trace More...

class	MassSpectrumFilterResampleKeepMzRange

class	MassSpectrumFilterResampleRemoveMzRange

class	MassSpectrumId

class	MassSpectrumMinusCombiner

class	MassSpectrumPlusCombiner

class	MassSpectrumWidget

class	MorpheusScore

class	MsFileAccessor

class	MsFileReader

class	MsRunAlignment

class	MsRunDataSetTree

class	MsRunDataSetTreeNode

class	MsRunDataSetTreeNodeVisitorInterface

class	MsRunId
	MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL) More...

class	MsRunReader
	base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More...

class	MsRunReaderScanNumberMultiMap
	provides a multimap to find quickly spectrum index from scan number More...

class	MsRunRetentionTime

struct	MsRunRetentionTimeSeamarkPoint

class	MsRunSimpleStatistics
	example of interface to count MS levels of all spectrum in an MSrun More...

class	MsRunSlice

class	MsRunXicExtractor

class	MsRunXicExtractorDisk

class	MsRunXicExtractorDiskBuffer

class	MsRunXicExtractorFactory
	factory to build different kinds of XIC extractors More...

class	MsRunXicExtractorInterface

class	MzPrecision

class	MzRange

class	MzxmlOutput

class	OboPsiMod

class	OboPsiModHandlerInterface

class	OboPsiModTerm

class	PappsoException

class	PeakIonIsotopeMatch

class	PeakIonMatch

class	Peptide

class	PeptideBuilder
	builds a peptide shared pointer from peptide string and adds fixed modifications More...

class	PeptideFixedModificationBuilder

class	PeptideFragment

class	PeptideFragmentIon

class	PeptideFragmentIonListBase

class	PeptideInterface

class	PeptideIsotopeSpectrumMatch

class	PeptideMethioninRemove
	potential remove Nter Methionin More...

class	PeptideModificatorBase

class	PeptideModificatorInterface

class	PeptideModificatorPipeline

class	PeptideModificatorTee

class	PeptideNaturalIsotope

class	PeptideNaturalIsotopeAverage

class	PeptideNaturalIsotopeList

class	PeptideRawFragmentMasses

class	PeptideSemiEnzyme
	cut a regular peptide obtained with an enzyme at any position from Nter or Cter More...

class	PeptideSinkInterface

class	PeptideSizeFilter
	filter peptide string by size More...

class	PeptideSpectrumMatch

class	PeptideSpSinkInterface

class	PeptideStrParser

class	PeptideVariableModificationBuilder
	Modify a peptide shared pointer with a variable modification on one AA. More...

class	PeptideVariableModificationReplacement

class	PpmPrecision

class	PrecisionBase

class	PrecisionFactory

class	PrecisionWidget

class	Protein

class	PwizMsFileReader

class	PwizMsRunReader

class	QCPSpectrum

class	QCPXic

class	QualifiedMassSpectrum
	Class representing a fully specified mass spectrum. More...

class	QualifiedXic

class	ResPrecision

struct	RtPoint

struct	SavGolParams
	Parameters for the Savitzky-Golay filter. More...

struct	SimplePeakIonMatch

class	SpectrumCollectionHandlerInterface
	interface to collect spectrums from the MsRunReader class More...

class	TandemWrapperRun

class	TicXicChromMassSpecColorMapPlotWidget

class	TicXicChromTracePlotWidget

class	TimsBinDec

class	TimsData

class	TimsDirectXicExtractor

class	TimsFrame

class	TimsFrameBase

class	TimsMs2CentroidFilter

class	TimsMsFileReader

class	TimsMsRunReader

class	TimsMsRunReaderMs2

class	TimsXicExtractorInterface

struct	TimsXicStructure

class	Trace
	A simple container of DataPoint instances. More...

class	TraceCombiner

class	TraceDetectionInterface

class	TraceDetectionMoulon

class	TraceDetectionSinkInterface

class	TraceDetectionZivy

class	TraceMinusCombiner

class	TracePeak

class	TracePlusCombiner

class	Utils

class	Xic

class	XicPeptideFragmentIon

class	XicPeptideFragmentIonNaturalIsotope

class	XicPeptideInterface

class	XicWidget

class	XtandemHyperscore

class	XtandemHyperscoreBis

class	XtandemInputSaxHandler

class	XtandemOutputSaxHandler

class	XtandemPresetSaxHandler

class	XtandemSpectrumProcess

class	XyMsFileReader

class	XyMsRunReader

Typedefs
typedef std::shared_ptr< const Peptide >	PeptideSp

typedef std::unique_ptr< const AaModification >	AaModificationUp

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< 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 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< FilterInterface >	FilterInterfaceSPtr

typedef std::shared_ptr< const FilterInterface >	FilterInterfaceCstSPtr

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< 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	QualifiedMassSpectrumParameter { QualifiedMassSpectrumParameter::OneOverK0, QualifiedMassSpectrumParameter::OneOverK0begin, QualifiedMassSpectrumParameter::OneOverK0end, QualifiedMassSpectrumParameter::IsolationMz, QualifiedMassSpectrumParameter::IsolationWidth, QualifiedMassSpectrumParameter::CollisionEnergy, QualifiedMassSpectrumParameter::BrukerPrecursorIndex, QualifiedMassSpectrumParameter::last }

enum	FileReaderType { FileReaderType::pwiz, FileReaderType::xy, FileReaderType::tims, FileReaderType::tims_ms2 }

enum	PeptideDirection : std::int8_t { PeptideDirection::Nter = 0, PeptideDirection::Cter = 1 }

enum	PeptideIonNter { PeptideIonNter::b, PeptideIonNter::bstar, PeptideIonNter::bo, PeptideIonNter::a, PeptideIonNter::astar, PeptideIonNter::ao, PeptideIonNter::bp, PeptideIonNter::c }

enum	PeptideIonCter { PeptideIonCter::y, PeptideIonCter::ystar, PeptideIonCter::yo, PeptideIonCter::z, PeptideIonCter::yp, PeptideIonCter::x }

enum	AtomIsotope { AtomIsotope::C, AtomIsotope::H, AtomIsotope::O, AtomIsotope::N, AtomIsotope::S }

enum	RawFragmentationMode : std::int8_t { RawFragmentationMode::full = 0, RawFragmentationMode::proline_effect = 1 }

enum	PrecisionUnit { PrecisionUnit::none, PrecisionUnit::dalton, PrecisionUnit::ppm, PrecisionUnit::res, PrecisionUnit::mz, PrecisionUnit::last }

enum	AtomIsotopeSurvey : std::int8_t { AtomIsotopeSurvey::C, AtomIsotopeSurvey::H, AtomIsotopeSurvey::O, AtomIsotopeSurvey::N, AtomIsotopeSurvey::S, AtomIsotopeSurvey::last }

enum	Isotope { Isotope::C13, Isotope::H2, Isotope::O17, Isotope::O18, Isotope::N15, Isotope::S33, Isotope::S34, Isotope::S36 }

enum	MzFormat : std::int8_t { MzFormat::unknown = 0, MzFormat::mzML = 1, MzFormat::mzXML = 2, MzFormat::MGF = 3, MzFormat::SQLite3 = 4, MzFormat::xy = 5, MzFormat::mz5 = 6, MzFormat::msn = 7, MzFormat::abSciexWiff = 8, MzFormat::abSciexT2D = 9, MzFormat::agilentMassHunter = 10, MzFormat::thermoRaw = 11, MzFormat::watersRaw = 12, MzFormat::brukerFid = 13, MzFormat::brukerYep = 14, MzFormat::brukerBaf = 15, MzFormat::brukerTims = 16, MzFormat::last = 17 }

enum	AminoAcidChar : char { AminoAcidChar::alanine = 'A', AminoAcidChar::cysteine = 'C', AminoAcidChar::aspartic_acid = 'D', AminoAcidChar::glutamic_acid = 'E', AminoAcidChar::phenylalanine = 'F', AminoAcidChar::glycine = 'G', AminoAcidChar::histidine = 'H', AminoAcidChar::isoleucine = 'I', AminoAcidChar::lysine = 'K', AminoAcidChar::leucine = 'L', AminoAcidChar::methionine = 'M', AminoAcidChar::asparagine = 'N', AminoAcidChar::proline = 'P', AminoAcidChar::glutamine = 'Q', AminoAcidChar::arginine = 'R', AminoAcidChar::serine = 'S', AminoAcidChar::threonine = 'T', AminoAcidChar::valine = 'V', AminoAcidChar::tryptophan = 'W', AminoAcidChar::tyrosine = 'Y', AminoAcidChar::selenocysteine = 'U', AminoAcidChar::pyrrolysine = 'O' }

enum	DataCompression : std::int8_t { DataCompression::unset = -1, DataCompression::none = 0, DataCompression::zlib = 1 }

enum	DataKind : std::int8_t { DataKind::unset = -1, DataKind::rt = 0, DataKind::dt = 1, DataKind::mz = 2 }

enum	XicExtractMethod : std::int8_t { XicExtractMethod::sum = 1, XicExtractMethod::max = 2 }

enum	PeptideIon : std::int8_t { PeptideIon::b = 0, PeptideIon::bstar = 1, PeptideIon::bo = 2, PeptideIon::a = 3, PeptideIon::astar = 4, PeptideIon::ao = 5, PeptideIon::bp = 6, PeptideIon::c = 7, PeptideIon::y = 8, PeptideIon::ystar = 9, PeptideIon::yo = 10, PeptideIon::z = 11, PeptideIon::yp = 12, PeptideIon::x = 13 }
	PeptideIon enum defines all types of ions (Nter or Cter) More...

enum	PlotAxis { PlotAxis::none = 0x000, PlotAxis::x_axis = 1 << 1, PlotAxis::y_axis = 1 << 2, PlotAxis::both = (x_axis \| y_axis) }

enum	RangeType { RangeType::outermost = 1, RangeType::innermost = 2 }

Functions
bool	operator== (Aa const &l, Aa const &r)

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

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

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

bool	peptideIonIsNter (PeptideIon ion_type)
	tells if an ion is Nter More...

PeptideDirection	getPeptideIonDirection (PeptideIon ion_type)
	get the direction of a peptide ion More...

uint64_t	Combinations (unsigned int n, unsigned int k)

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

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

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

unsigned int	factorial (unsigned int n)

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

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

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

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

std::vector< DataPoint >::iterator	findFirstEqualOrGreaterX (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
	find the first element in which X is equal or greater than the value searched important : it implies that Trace is sorted by X More...

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

std::vector< DataPoint >::iterator	findFirstGreaterX (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
	find the first element in which X is greater than the value searched important : it implies that Trace is sorted by X More...

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

std::vector< DataPoint >::iterator	findDifferentYvalue (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &y_value)
	find the first element in which Y is different of value More...

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

std::vector< DataPoint >::const_iterator	minYDataPoint (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
	find the element with the smallest Y value (intensity) More...

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

std::vector< DataPoint >::iterator	maxYDataPoint (std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end)
	find the element with the greatest Y value (intensity) More...

std::vector< DataPoint >::const_iterator	moveLowerYRigthDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin)
	Move right to the lower value. More...

std::vector< DataPoint >::const_iterator	moveLowerYLeftDataPoint (const Trace &trace, std::vector< DataPoint >::const_iterator begin)
	Move left to the lower value. More...

double	sumYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
	calculate the sum of y value of a trace More...

double	meanYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
	calculate the mean of y value of a trace More...

double	medianYTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
	calculate the median of y value of a trace More...

double	areaTrace (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
	calculate the area of a trace More...

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

const pappso_double	MHPLUS (1.007276466879)

const pappso_double	MPROTON (1.007276466879)

const pappso_double	MPROTIUM (1.007825032241)

const pappso_double	ONEMILLION (1000000)

const pappso_double	MASSOXYGEN (15.99491461956)

const pappso_double	MASSCARBON (12)

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

const pappso_double	MASSNITROGEN (14.0030740048)

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

const pappso_double	MASSCO (MASSCARBON+MASSOXYGEN)

const pappso_double	MASSPHOSPHORUS (30.973761998)

const pappso_double	MASSSULFUR (31.97207100)

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

const pappso_double	MASSSELENIUM (79.916520)

const pappso_double	DIFFC12C13 (1.0033548378)

const pappso_double	DIFFS32S33 (32.97145876 - MASSSULFUR)

const pappso_double	DIFFS32S34 (33.96786690 - MASSSULFUR)

const pappso_double	DIFFS32S36 (35.96708076 - MASSSULFUR)

const pappso_double	DIFFH1H2 (2.0141017778 - MPROTIUM)

const pappso_double	DIFFO16O18 (17.9991610 - MASSOXYGEN)

const pappso_double	DIFFO16O17 (16.99913150 - MASSOXYGEN)

const pappso_double	DIFFN14N15 (15.0001088982 - MASSNITROGEN)

const pappso_double	ABUNDANCEH2 (0.00015574)

const pappso_double	ABUNDANCEN15 (0.003663)

const pappso_double	ABUNDANCEO17 (0.000372)

const pappso_double	ABUNDANCEO18 (0.0020004)

const pappso_double	ABUNDANCEC13 (0.011078)

const pappso_double	ABUNDANCEC12 (0.988922)

const pappso_double	ABUNDANCES33 (0.00750)

const pappso_double	ABUNDANCES34 (0.04215)

const pappso_double	ABUNDANCES36 (0.00020)

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

Variables
const typedef AaModification *	AaModificationP

const typedef PrecisionBase *	PrecisionPtr

class PMSPP_LIB_DECL	MsRunReader

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

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

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

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

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

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

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

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

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

Detailed Description

Todo:: write docs

Todo:: write docs

Todo:: write docs

Todo:: write docs

Typedef Documentation

◆ AaModificationUp

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

Definition at line 69 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 55 of file basecolormapplotwidget.h.

◆ BasePlotWidgetCstSPtr

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

Definition at line 133 of file baseplotwidget.h.

◆ BasePlotWidgetSPtr

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

Definition at line 130 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 54 of file basetraceplotwidget.h.

◆ DataPointCstSPtr

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

Definition at line 16 of file datapoint.h.

◆ FastaFileIndexerSPtr

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

Definition at line 64 of file fastafileindexer.h.

◆ FilterInterfaceCstSPtr

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

Definition at line 62 of file filterinterface.h.

◆ FilterInterfaceSPtr

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

Definition at line 61 of file filterinterface.h.

◆ GrpGroupSp

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

Definition at line 57 of file grpgroup.h.

◆ GrpGroupSpConst

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

Definition at line 59 of file grpgroup.h.

◆ GrpPeptideSp

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

Definition at line 59 of file grppeptide.h.

◆ GrpPeptideSpConst

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

Definition at line 55 of file grppeptide.h.

◆ GrpProteinSp

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

Definition at line 56 of file grpprotein.h.

◆ GrpProteinSpConst

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

Definition at line 54 of file grpprotein.h.

◆ GrpSubGroupSp

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

Definition at line 58 of file grpsubgroup.h.

◆ GrpSubGroupSpConst

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

Definition at line 56 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 23 of file massspectrumcombiner.h.

◆ MassSpectrumCombinerSPtr

typedef std::shared_ptr<MassSpectrumCombiner> pappso::MassSpectrumCombinerSPtr

Definition at line 26 of file massspectrumcombiner.h.

◆ MassSpectrumCstSPtr

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

Definition at line 74 of file massspectrum.h.

◆ MassSpectrumMinusCombinerCstSPtr

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

Definition at line 17 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 16 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 73 of file massspectrum.h.

◆ MsRunDataSetTreeCstSPtr

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

Definition at line 28 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 27 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 63 of file msrunid.h.

◆ MsRunReaderCstSPtr

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

Definition at line 169 of file msrunreader.h.

◆ MsRunReaderSPtr

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

Definition at line 168 of file msrunreader.h.

◆ MsRunSliceSPtr

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

Definition at line 58 of file msrunslice.h.

◆ MsRunXicExtractorInterfaceSp

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

Definition at line 57 of file msrunxicextractorinterface.h.

◆ NoConstPeptideSp

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

Definition at line 109 of file peptide.h.

◆ pappso_double

typedef double pappso::pappso_double

A type definition for doubles.

Definition at line 67 of file types.h.

◆ pappso_float

typedef float pappso::pappso_float

Definition at line 72 of file types.h.

◆ PeakIonIsotopeMatchCstSPtr

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

Definition at line 33 of file peakionisotopematch.h.

◆ PeptideFragmentIonListBaseSp

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

Definition at line 60 of file peptidefragmentionlistbase.h.

◆ PeptideFragmentIonSp

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

Definition at line 63 of file peptidefragmention.h.

◆ PeptideFragmentSp

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

Definition at line 62 of file peptidefragment.h.

◆ PeptideInterfaceSp

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

Definition at line 57 of file peptideinterface.h.

◆ PeptideNaturalIsotopeAverageSp

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

Definition at line 56 of file peptidenaturalisotopeaverage.h.

◆ PeptideNaturalIsotopeListSp

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

Definition at line 62 of file peptidenaturalisotopelist.h.

◆ PeptideNaturalIsotopeSp

typedef std::shared_ptr<const PeptideNaturalIsotope> pappso::PeptideNaturalIsotopeSp

Definition at line 60 of file peptidenaturalisotope.h.

◆ PeptideSp

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

Definition at line 66 of file aamodification.h.

◆ PeptideStr

typedef QString pappso::PeptideStr

A type definition for PeptideStr.

Definition at line 62 of file types.h.

◆ ProteinSp

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

shared pointer on a Protein object

Definition at line 62 of file protein.h.

◆ QualifiedMassSpectrumCstSPtr

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

Definition at line 61 of file qualifiedmassspectrum.h.

◆ QualifiedMassSpectrumSPtr

typedef std::shared_ptr<QualifiedMassSpectrum> pappso::QualifiedMassSpectrumSPtr

Definition at line 57 of file qualifiedmassspectrum.h.

◆ QualifiedXicSp

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

Definition at line 41 of file qualifiedxic.h.

◆ TimsFrameBaseCstSPtr

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

Definition at line 56 of file timsframebase.h.

◆ TimsFrameBaseSPtr

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

Definition at line 54 of file timsframebase.h.

◆ TimsFrameCstSPtr

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

Definition at line 57 of file timsframe.h.

◆ TimsFrameSPtr

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

Definition at line 55 of file timsframe.h.

◆ TimsMsRunReaderMs2SPtr

typedef std::shared_ptr<TimsMsRunReaderMs2> pappso::TimsMsRunReaderMs2SPtr

Definition at line 17 of file msfileaccessor.h.

◆ TraceCombinerCstSPtr

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

Definition at line 21 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 114 of file trace.h.

◆ TraceDetectionInterfaceCstSPtr

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

Definition at line 55 of file tracedetectioninterface.h.

◆ TraceDetectionInterfaceSPtr

typedef std::shared_ptr<TraceDetectionInterface> pappso::TraceDetectionInterfaceSPtr

Definition at line 51 of file tracedetectioninterface.h.

◆ TraceMinusCombinerCstSPtr

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

Definition at line 20 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 53 of file tracepeak.h.

◆ TracePlusCombinerCstSPtr

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

Definition at line 20 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 113 of file trace.h.

◆ uint

typedef unsigned int pappso::uint

Definition at line 74 of file types.h.

◆ XicCstSPtr

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

Definition at line 56 of file xic.h.

◆ XicSPtr

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

Definition at line 58 of file xic.h.

◆ XicXicPeakPairList

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

Definition at line 61 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 151 of file types.h.

                            : std::int8_t
 {
   unset = -1, ///< not net
   none  = 0,  ///< no compression
   zlib  = 1,  ///< zlib compresssion
 };
  
  
 enum class DataKind : std::int8_t
 {
   unset = -1, ///< not set
   rt    = 0,  ///< Retention time
   dt    = 1,  ///< Drift time
   mz    = 2,  ///< m/z

◆ AtomIsotope

enum pappso::AtomIsotope

strong

Enumerator
C
H
O
N
S

Definition at line 68 of file peptidenaturalisotope.cpp.

 {
   C,
   H,
   O,
   N,
   S

◆ AtomIsotopeSurvey

enum pappso::AtomIsotopeSurvey : std::int8_t

strong

Enumerator
C
H
O
N
S
last

Definition at line 94 of file types.h.

106 : std::int8_t

◆ DataCompression

enum pappso::DataCompression : std::int8_t

strong

Enumerator
unset	not net
none	no compression
zlib	zlib compresssion

Definition at line 181 of file types.h.

                             : std::int8_t
 {
   sum = 1, ///< sum of intensities
   max = 2  ///< maximum of intensities
 };

◆ DataKind

enum pappso::DataKind : std::int8_t

strong

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

Definition at line 189 of file types.h.

333 : std::int8_t

◆ FileReaderType

enum pappso::FileReaderType

strong

Enumerator
pwiz
xy
tims
tims_ms2

Definition at line 20 of file msfileaccessor.h.

 {
   pwiz,
   xy,
   tims,
   tims_ms2,
 };

◆ Isotope

enum pappso::Isotope

strong

Enumerator
C13
H2
O17
O18
N15
S33
S34
S36

Definition at line 109 of file types.h.

132 : char

◆ MzFormat

enum pappso::MzFormat : std::int8_t

strong

Enumerator
unknown	unknown format
mzML	mzML
mzXML	mzXML
MGF	Mascot format.
SQLite3	SQLite3 format.
xy	(x,y) format
mz5
msn
abSciexWiff
abSciexT2D
agilentMassHunter
thermoRaw
watersRaw
brukerFid
brukerYep
brukerBaf
brukerTims
last

Definition at line 125 of file types.h.

                          : 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',

◆ PeptideDirection

enum pappso::PeptideDirection : std::int8_t

strong

Enumerator
Nter
Cter

Definition at line 64 of file peptide.h.

 {
   b,
   bstar,
   bo,

◆ 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 352 of file types.h.

                             : it is used to define static array size
  */
 #define PEPTIDE_ION_TYPE_COUNT 14
 } // namespace pappso

◆ PeptideIonCter

enum pappso::PeptideIonCter

strong

Enumerator
y
ystar
yo
z
yp
x

Definition at line 96 of file peptide.h.

         :
   Peptide(const QString &pepstr);
   virtual ~Peptide();
   Peptide(const Peptide &peptide);
   friend bool
   operator<(const Peptide &l, const Peptide &r)
   {

◆ PeptideIonNter

enum pappso::PeptideIonNter

strong

Enumerator
b
bstar
bo
a
astar
ao
bp
c

Definition at line 83 of file peptide.h.

92 : public PeptideInterface

93 {

◆ PlotAxis

enum pappso::PlotAxis

strong

Enumerator
none
x_axis
y_axis
both

Definition at line 53 of file baseplotwidget.h.

 {
   none   = 0x000,
   x_axis = 1 << 1,
   y_axis = 1 << 2,
   both   = (x_axis | y_axis)
 };

◆ PrecisionUnit

enum pappso::PrecisionUnit

strong

Enumerator
none
dalton
ppm
res
mz
last

Definition at line 81 of file types.h.

91 {

◆ 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 63 of file qualifiedmassspectrum.h.

 {
   public:
   QualifiedMassSpectrum();
   QualifiedMassSpectrum(const MassSpectrumId &id);
   QualifiedMassSpectrum(MassSpectrumSPtr mass_spectrum_SPtr);
   QualifiedMassSpectrum(const QualifiedMassSpectrum &other);
   ~QualifiedMassSpectrum();
  

◆ RangeType

enum pappso::RangeType

strong

Enumerator
outermost
innermost

Definition at line 62 of file baseplotwidget.h.

 {
   outermost = 1,
   innermost = 2,
 };

◆ RawFragmentationMode

enum pappso::RawFragmentationMode : std::int8_t

strong

Enumerator
full
proline_effect

Definition at line 61 of file peptiderawfragmentmasses.h.

          :
   static ionDeltatMzMassMap m_ionDeltaMz;
  

◆ XicExtractMethod

enum pappso::XicExtractMethod : std::int8_t

strong

Enumerator
sum	sum of intensities
max	maximum of intensities

Definition at line 201 of file types.h.

       ://en.wikipedia.org/wiki/Isotopes_of_hydrogen (One proton + One electron)
  1.00782503207
  
  Note that as of 20191028, that same page says: 1.007825032241
  */

Function Documentation

◆ ABUNDANCEC12()

const pappso_double pappso::ABUNDANCEC12 ( 0. 988922 )

◆ ABUNDANCEC13()

const pappso_double pappso::ABUNDANCEC13 ( 0. 011078 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEH2()

const pappso_double pappso::ABUNDANCEH2 ( 0. 00015574 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEN15()

const pappso_double pappso::ABUNDANCEN15 ( 0. 003663 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEO17()

const pappso_double pappso::ABUNDANCEO17 ( 0. 000372 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCEO18()

const pappso_double pappso::ABUNDANCEO18 ( 0. 0020004 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES33()

const pappso_double pappso::ABUNDANCES33 ( 0. 00750 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES34()

const pappso_double pappso::ABUNDANCES34 ( 0. 04215 )

Referenced by isotopem_ratio_cache().

◆ ABUNDANCES36()

const pappso_double pappso::ABUNDANCES36 ( 0. 00020 )

Referenced by isotopem_ratio_cache().

◆ areaTrace()

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

calculate the area of a trace

Definition at line 219 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;
 }

◆ Combinations()

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

Definition at line 46 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;

References CACHE_ARRAY_SIZE, and combinations_cache.

Referenced by isotopem_ratio().

◆ DIFFC12C13()

const pappso_double pappso::DIFFC12C13 ( 1. 0033548378 )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFH1H2()

const pappso_double pappso::DIFFH1H2 ( 2.0141017778 - MPROTIUM )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFN14N15()

const pappso_double pappso::DIFFN14N15 ( 15.0001088982 - MASSNITROGEN )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFO16O17()

const pappso_double pappso::DIFFO16O17 ( 16.99913150 - MASSOXYGEN )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFO16O18()

const pappso_double pappso::DIFFO16O18 ( 17.9991610 - MASSOXYGEN )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFS32S33()

const pappso_double pappso::DIFFS32S33 ( 32.97145876 - MASSSULFUR )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFS32S34()

const pappso_double pappso::DIFFS32S34 ( 33.96786690 - MASSSULFUR )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ DIFFS32S36()

const pappso_double pappso::DIFFS32S36 ( 35.96708076 - MASSSULFUR )

Referenced by pappso::PeptideNaturalIsotope::PeptideNaturalIsotope().

◆ factorial()

unsigned int pappso::factorial ( unsigned int n )

Definition at line 63 of file xtandemhyperscore.cpp.

                                                                   {
                     if(current_max_charge > 2)  {
                         current_max_charge--;
                     }
                 }*/
       unsigned int max_charge = parent_charge;
       if(parent_charge > 1)

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

◆ findDifferentYvalue() [1/2]

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

Definition at line 100 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 86 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 43 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 29 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::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 71 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 57 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(), and pappso::Trace::sumY().

◆ flooredLocalMaxima()

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

Definition at line 239 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 370 of file peptidenaturalisotopelist.cpp.

     {
       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;
 }
  
  
 /** /brief get a sorted (by expected intensity) vector of natural isotope
  * average
  *
  * */
 std::vector<PeptideNaturalIsotopeAverageSp>
 PeptideNaturalIsotopeList::getByIntensityRatio(
   unsigned int charge,
   PrecisionPtr precision,
   pappso_double minimumIntensityRatio) const
 {
  
   // qDebug() << "PeptideNaturalIsotopeList::getByIntensityRatio begin";
   std::vector<PeptideNaturalIsotopeAverageSp>
     peptide_natural_isotope_average_list;
  
   std::map<unsigned int, pappso::pappso_double> map_isotope_number =
     getIntensityRatioPerIsotopeNumber();

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 74 of file peptide.cpp.

                                            :Nter_hydrolytic_cleavage_H"));
       m_aaVec.push_back(nter_aa);
       it++;
  
       while(it != pepstr.end())
         {
           m_aaVec.push_back(Aa(it->toLatin1()));
           it++;

References pappso::Peptide::m_aaVec.

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

◆ isotopem_ratio()

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

Definition at line 78 of file peptidenaturalisotope.cpp.

 {
   return (pow(abundance, heavy) * pow((double)1 - abundance, (total - heavy)) *
           (double)Combinations(total, heavy));

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 94 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);

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

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

◆ MASSCARBON()

const pappso_double pappso::MASSCARBON ( 12 )

◆ MASSCO()

const pappso_double pappso::MASSCO ( MASSCARBON+ MASSOXYGEN )

◆ MASSH2O()

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

◆ MASSNH3()

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

◆ MASSNITROGEN()

const pappso_double pappso::MASSNITROGEN ( 14. 0030740048 )

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

◆ MASSOXYGEN()

const pappso_double pappso::MASSOXYGEN ( 15. 99491461956 )

◆ MASSPHOSPHORUS()

const pappso_double pappso::MASSPHOSPHORUS ( 30. 973761998 )

◆ MASSPHOSPHORYLATEDR()

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

◆ MASSSELENIUM()

const pappso_double pappso::MASSSELENIUM ( 79. 916520 )

◆ MASSSULFUR()

const pappso_double pappso::MASSSULFUR ( 31. 97207100 )

◆ maxYDataPoint() [1/2]

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

Definition at line 126 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::FilterHighPassPercentage::filter(), pappso::FilterTriangle::filter(), pappso::FilterLocalMaximum::filter(), pappso::FilterRescaleY::filter(), pappso::LinearRegression::getNrmsd(), pappso::FilterMorphoMax::getWindowValue(), and pappso::MsRunXicExtractor::getXicCstSPtr().

◆ maxYDataPoint() [2/2]

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

find the element with the greatest Y value (intensity)

Definition at line 137 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 190 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);
 }

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 201 of file trace.cpp.

 {
   pappso_double 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::PeptideRawFragmentMasses::pushBackIonMasses().

◆ minYDataPoint()

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

find the element with the smallest Y value (intensity)

Definition at line 115 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::LinearRegression::getNrmsd(), and pappso::FilterMorphoMin::getWindowValue().

◆ 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 164 of file trace.cpp.

 {
   if(begin == trace.begin())
     return begin;
   auto it     = begin - 1;
   auto result = begin;
   while((it != trace.begin()) && (it->y <= result->y))
     {
       it--;
       result--;
     }
   return result;
 }

◆ 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 148 of file trace.cpp.

 {
   if(begin == trace.end())
     return begin;
   auto it     = begin + 1;
   auto result = begin;
   while((it != trace.end()) && (it->y <= result->y))
     {
       it++;
       result++;
     }
   return result;
 }

◆ MPROTIUM()

const pappso_double pappso::MPROTIUM ( 1. 007825032241 )

◆ MPROTON()

const pappso_double pappso::MPROTON ( 1. 007276466879 )

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

◆ ONEMILLION()

const pappso_double pappso::ONEMILLION ( 1000000 )

◆ operator<()

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

Definition at line 305 of file aa.cpp.

◆ operator<<() [1/3]

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

Definition at line 131 of file datapoint.cpp.

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

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

◆ operator<<() [2/3]

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

◆ operator<<() [3/3]

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

Definition at line 358 of file massspectrum.cpp.

     {
       instream >> vector_size;
       qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
                << " vector_size=" << vector_size;
  
       for(quint32 i = 0; i < vector_size; i++)
         {
  
           if(instream.status() != QDataStream::Ok)
             {

◆ operator==()

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

Definition at line 299 of file aa.cpp.

◆ operator>>() [1/4]

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

Definition at line 141 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 372 of file massspectrum.cpp.

         {
           throw PappsoException(
             QString(
               "error in QDataStream unserialize operator>> of massSpectrum "
               ":\nread datastream failed status=%1")
               .arg(instream.status()));
         }
     }
  
   return instream;
 }
  
  
 MassSpectrum &
 MassSpectrum::massSpectrumFilter(const MassSpectrumFilterInterface &filter)
 {
   return filter.filter(*this);
 }
  
 } // namespace pappso

◆ operator>>() [3/4]

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

Definition at line 175 of file msrunslice.cpp.

             {
               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;
 }
  
  
 } // namespace pappso

◆ operator>>() [4/4]

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

◆ peptideIonIsNter()

bool pappso::peptideIonIsNter ( PeptideIon ion_type )

tells if an ion is Nter

Parameters

ion_type the ion to test

Definition at line 64 of file peptide.cpp.

 {
  
   QString::const_iterator it(pepstr.begin());
   if(it != pepstr.end())
     {
       // first amino acid is the Nter one
       // by default, it is obtained by hydrolytic cleavage in normal water
       // and it is loaded with one Hydrogen

References pappso::Aa::addAaModification().

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

◆ sumYTrace()

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

calculate the sum of y value of a trace

Definition at line 181 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::FilterMorphoSum::getWindowValue(), pappso::LinearRegression::LinearRegression(), meanYTrace(), and pappso::Trace::sumY().

Variable Documentation

◆ AaModificationP

const typedef AaModification* pappso::AaModificationP

Definition at line 71 of file aamodification.h.

Referenced by pappso::AaModification::createInstance(), pappso::PeptideFragmentIonListBase::getETDionList(), pappso::Aa::getInternalCterModification(), pappso::Aa::getInternalNterModification(), pappso::PeptideModificatorPipeline::parseFixedModification(), pappso::PeptideModificatorPipeline::parseLabeledModification(), pappso::PeptideModificatorPipeline::parsePotentialModification(), and pappso::Peptide::removeNterAminoAcid().

◆ combinations_cache

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

Definition at line 43 of file peptidenaturalisotope.cpp.

Referenced by Combinations().

◆ MsRunReader

class PMSPP_LIB_DECL pappso::MsRunReader

Definition at line 167 of file msrunreader.h.

◆ PrecisionPtr

const typedef PrecisionBase * pappso::PrecisionPtr

Definition at line 141 of file precision.h.

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

◆ ratioC13_cache

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

Definition at line 84 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 91 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 85 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 89 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 90 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 88 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 87 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 86 of file peptidenaturalisotope.cpp.

Referenced by isotopem_ratio_cache().

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ AaModificationUp

◆ BaseColorMapPlotWidgetCstSPtr

◆ BaseColorMapPlotWidgetSPtr

◆ BasePlotWidgetCstSPtr

◆ BasePlotWidgetSPtr

◆ BaseTracePlotWidgetCstSPtr

◆ BaseTracePlotWidgetSPtr

◆ DataPointCstSPtr

◆ FastaFileIndexerSPtr

◆ FilterInterfaceCstSPtr

◆ FilterInterfaceSPtr

◆ GrpGroupSp

◆ GrpGroupSpConst

◆ GrpPeptideSp

◆ GrpPeptideSpConst

◆ GrpProteinSp

◆ GrpProteinSpConst

◆ GrpSubGroupSp

◆ GrpSubGroupSpConst

◆ MapTraceCstSPtr

◆ MapTraceSPtr

◆ MassSpectrumCombinerCstSPtr

◆ MassSpectrumCombinerSPtr

◆ MassSpectrumCstSPtr

◆ MassSpectrumMinusCombinerCstSPtr

◆ MassSpectrumMinusCombinerSPtr

◆ MassSpectrumPlusCombinerCstSPtr

◆ MassSpectrumPlusCombinerSPtr

◆ MassSpectrumSPtr

◆ MsRunDataSetTreeCstSPtr

◆ MsRunDataSetTreeNodeCstSPtr

◆ MsRunDataSetTreeNodeSPtr

◆ MsRunDataSetTreeSPtr

◆ MsRunIdCstSPtr

◆ MsRunReaderCstSPtr

◆ MsRunReaderSPtr

◆ MsRunSliceSPtr

◆ MsRunXicExtractorInterfaceSp

◆ NoConstPeptideSp

◆ pappso_double

◆ pappso_float

◆ PeakIonIsotopeMatchCstSPtr

◆ PeptideFragmentIonListBaseSp

◆ PeptideFragmentIonSp

◆ PeptideFragmentSp

◆ PeptideInterfaceSp

◆ PeptideNaturalIsotopeAverageSp

◆ PeptideNaturalIsotopeListSp

◆ PeptideNaturalIsotopeSp

◆ PeptideSp

◆ PeptideStr

◆ ProteinSp

◆ QualifiedMassSpectrumCstSPtr

◆ QualifiedMassSpectrumSPtr

◆ QualifiedXicSp

◆ TimsFrameBaseCstSPtr

◆ TimsFrameBaseSPtr

◆ TimsFrameCstSPtr

◆ TimsFrameSPtr

◆ TimsMsRunReaderMs2SPtr

◆ TraceCombinerCstSPtr

◆ TraceCombinerSPtr

◆ TraceCstSPtr

◆ TraceDetectionInterfaceCstSPtr

◆ TraceDetectionInterfaceSPtr

◆ TraceMinusCombinerCstSPtr

◆ TraceMinusCombinerSPtr

◆ TracePeakCstSPtr

◆ TracePlusCombinerCstSPtr

◆ TracePlusCombinerSPtr

◆ TraceSPtr

◆ uint

◆ XicCstSPtr