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

Namespaces
namespace	cbor

namespace	Enums

namespace	masschroq

namespace	specglob

namespace	specpeptidoms

namespace	specself

namespace	spectree

Classes
class	Aa

class	AaBase

class	AaCode
	collection of integer code for each amino acid 0 => null 1 to 20 => amino acid sorted by there mass (lower to higher). Leucine is replaced by Isoleucine More...

class	AaModification

class	AaStringCodec
	code and decode amino acid string sequence to unique integer More...

class	AaStringCodeMassMatching
	convert a list of mass to amino acid string codes More...

struct	AreNamespaceClassnamePairsEqual

class	AtomNumberInterface

class	BafAsciiFileReader

class	BafAsciiMsRunReader

class	BaseColorMapPlotWidget

class	BasePlotContext

class	BasePlotWidget

class	BaseTracePlotWidget

class	ChemicalFormula

struct	CodeToMass

struct	ColorMapPlotConfig

class	CosineSimilarity

class	DaltonPrecision

struct	DataPoint

class	DataPointJs

class	DeepProtEnumStr

class	DriftSpecMassSpecColorMapPlotWidget

class	DriftSpecTracePlotWidget

class	Enzyme

class	EnzymeProductInterface

class	ExceptionInterrupted

class	ExceptionNotFound

class	ExceptionNotImplemented

class	ExceptionNotPossible

class	ExceptionNotRecognized
	excetion to use when an item type is not recognized More...

class	ExceptionOutOfRange

class	FastaFileIndexer

class	FastaFileIndexerInterface

class	FastaHandlerInterface

class	FastaOutputStream

class	FastaReader

class	FastaSeqHandler

class	FastaWriterInterface

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	FilterFloorAmplitudePercentage
	Redefines the floor intensity of the Trace. More...

class	FilterFloorY
	apply std::floor (round to lowest integer) to all Y values More...

class	FilterGreatestY
	keep N datapoints form the greatest intensities to the lowest More...

class	FilterGreatestYperWindow
	keep N datapoints form the greatest intensities to the lowest within a mass range in dalton More...

class	FilterHighPass
	remove datapoints below a given Y value (intensity) More...

class	FilterHighPassPercentage
	remove datapoints below a given intensity percentage (ratio) of the maximum intensity More...

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

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

class	FilterLowIntensitySignalRemoval
	Redefines the floor intensity of the Trace. More...

class	FilterLowPass
	remove datapoints higher than a given Y value (intensity) More...

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

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

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

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

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

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

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

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

class	FilterMorphoSum
	test purpose More...

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

class	FilterMzExclusion

class	FilterNameInterface
	Interface that allows to build filter objects from strings. More...

class	FilterNormalizeIntensities
	Sets the maximum intensity of the trace to the provided value. More...

class	FilterOboPsiModMap

class	FilterOboPsiModSink

class	FilterOboPsiModTermAccession

class	FilterOboPsiModTermDiffMono

class	FilterOboPsiModTermLabel

class	FilterOboPsiModTermName

class	FilterPeakDelta

class	FilterQuantileBasedRemoveY
	removes a value found by quantile to all Y values More...

class	FilterRemoveC13

class	FilterRemoveY
	removes a value to all Y values More...

class	FilterResampleKeepGreater

class	FilterResampleKeepPointInPolygon

class	FilterResampleKeepSmaller

class	FilterResampleKeepXRange

class	FilterResampleRemoveXRange

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

class	FilterRoundY
	apply std::round (round to nearest integer) to all Y values More...

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

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

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

class	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	FrameIdDescr

class	GrpExperiment

class	GrpGroup

class	GrpGroupingMonitor

class	GrpGroupingMonitorInterface

class	GrpMapPeptideToGroup

class	GrpMapPeptideToSubGroupSet

class	GrpPeptide

class	GrpPeptideSet

class	GrpProtein

class	GrpSubGroup

class	GrpSubGroupSet

class	HttpButton

class	IntegrationScope

class	IntegrationScopeBase

class	IntegrationScopeRect

class	IntegrationScopeRhomb

struct	IntegrationScopeSpec

class	Ion

class	IonIsotopeRatioScore

class	IonMobilityGrid

struct	IsotopeCount

class	LinearRegression

class	MapTrace

class	MassDataCombinerInterface

class	MassSpecTracePlotContext

class	MassSpecTracePlotWidget

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

class	MassSpectrumCombiner

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	MassSpectrumJs
	The MassSpectrumJs class provides a JavaScript wrapper around MassSpectrum. More...

struct	MassSpectrumLineData

class	MassSpectrumMinusCombiner

class	MassSpectrumPlusCombiner

class	MassSpectrumWidget

class	MgfOutput

class	MorpheusScore

class	MsDataFormatEnumStr
	static functions to convert mz file formats More...

class	MsFileAccessor

class	MsFileReader

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	MsRunQualifiedSpectrumLoader
	Load all qualified spectrum into a vector. More...

class	MsRunReadConfig

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

class	MsRunReaderRetentionTimeLine
	collect retention times along MS run More...

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

class	MsRunReaderTicChromatogram
	calculate a TIC chromatogram 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	MzCalibrationInterface

class	MzCalibrationModel1

class	MzCalibrationModel1Cached

class	MzCalibrationStore

class	MzIdentMlWriter

class	MzIntegrationParams
	The MzIntegrationParams class provides the parameters definining how m/z ! More...

class	MzRange

class	MzxmlOutput

struct	NamespaceClassnameAsKeyHash

class	OboChooserWidget

class	OboListModel

class	OboListProxyModel

class	OboListWidget

class	OboPsiMod

class	OboPsiModHandlerInterface

class	OboPsiModTerm

class	OboPsiMs

class	OboTermForm

class	OboUnimod

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	PeptideProFormaParser

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

struct	PrecursorIonData

struct	ProjectParam

class	ProjectParameters

class	Protein

class	ProteinIntegerCode

class	ProteinPresenceAbsenceMatrix

class	PsmFeatures

class	PwizMsFileReader

class	PwizMsRunReader

class	QCPSpectrum

class	QCPXic

class	QPointFJs

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

class	QualifiedXic

class	ResPrecision

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

class	SelectionPolygon

struct	SelectionPolygonSpec

struct	SimplePeakIonMatch

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

class	SwitchWidget

class	TandemWrapperRun

class	TicXicChromDriftSpecColorMapPlotWidget

class	TicXicChromMassSpecColorMapPlotWidget

class	TicXicChromTracePlotWidget

class	TimsBinDec

class	TimsData

class	TimsDataFastMap
	replacement for std::map More...

class	TimsDdaPrecursors

class	TimsDiaSlices

class	TimsDirectXicExtractor

class	TimsFrame

class	TimsFrameBase

class	TimsFrameMobilityTraces

class	TimsFrameRawDataChunck

struct	TimsFrameRecord

class	TimsFramesMsRunReader

class	TimsFrameType1

class	TimsMs2CentroidFilter

class	TimsMsFileReader

class	TimsMsRunReader

class	TimsMsRunReaderBase

class	TimsMsRunReaderDia

class	TimsMsRunReaderMs2

class	TimsMsRunReaderMs2Selected

class	TimsXicExtractorInterface

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

class	TraceCombiner

class	TraceDetectionInterface

class	TraceDetectionMoulon

class	TraceDetectionSinkInterface

class	TraceDetectionZivy

class	TraceJs

class	TraceMinusCombiner

class	TracePeak

class	TracePeakList

class	TracePlusCombiner

class	UiMonitorInterface

class	UiMonitorText

class	UiMonitorTextPercent

class	UiMonitorVoid

class	Utils

class	WrapTandemInput

class	WrapTandemResults

class	Xic

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	XicPeptideFragmentIon

class	XicPeptideFragmentIonNaturalIsotope

class	XicPeptideInterface

class	XicWidget

class	XmlStreamReaderInterface
	convenient xml reader helper More...

class	XtandemError

class	XtandemHyperscore

class	XtandemHyperscoreBis

class	XtandemPresetReader

class	XtandemSpectrumProcess

class	XyMsFileReader

class	XyMsRunReader

Typedefs
typedef std::shared_ptr< const Peptide >	PeptideSp

typedef std::unique_ptr< const AaModification >	AaModificationUp

typedef const AaModification *	AaModificationP

typedef std::shared_ptr< const AaStringCodec >	AaStringCodecSp
	shared pointer on a Protein object

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

using	NamespaceClassnamePairAsKey = std::pair<QString, QString>

using	RegisterFunc = std::function<void(QJSEngine *)>

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< MsFileAccessor >	MsFileAccessorSPtr

typedef std::shared_ptr< const MsFileAccessor >	MsFileAccessorCstSPtr

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< MsRunId >	MsRunIdSPtr

typedef std::shared_ptr< const MsRunId >	MsRunIdCstSPtr

typedef std::shared_ptr< MsRunReader >	MsRunReaderSPtr

typedef std::shared_ptr< const MsRunReader >	MsRunReaderCstSPtr

typedef std::shared_ptr< TimsFramesMsRunReader >	TimsFramesMsRunReaderSPtr

typedef std::shared_ptr< const TimsFramesMsRunReader >	TimsFramesMsRunReaderCstSPtr

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< IntegrationScope >	IntegrationScopeSPtr

typedef std::shared_ptr< const IntegrationScope >	IntegrationScopeCstSPtr

typedef std::shared_ptr< IntegrationScopeBase >	IntegrationScopeBaseSPtr

typedef std::shared_ptr< const IntegrationScopeBase >	IntegrationScopeBaseCstSPtr

typedef std::shared_ptr< IntegrationScopeSpec >	IntegrationScopeSpecSPtr

typedef std::shared_ptr< const IntegrationScopeSpec >	IntegrationScopeSpecCstSPtr

typedef std::shared_ptr< IntegrationScopeRect >	IntegrationScopeRectSPtr

typedef std::shared_ptr< const IntegrationScopeRect >	IntegrationScopeRectCstSPtr

typedef std::shared_ptr< IntegrationScopeRhomb >	IntegrationScopeRhombSPtr

typedef std::shared_ptr< const IntegrationScopeRhomb >	IntegrationScopeRhombCstSPtr

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

typedef std::shared_ptr< FilterNormalizeIntensities >	FilterNormalizeIntensitiesSPtr

typedef std::shared_ptr< const FilterNormalizeIntensities >	FilterNormalizeIntensitiesCstSPtr

using	IntegrationScopeSpecVector = std::vector<IntegrationScopeSpec>

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

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.

typedef double	pappso_double
	A type definition for doubles.

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

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< 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

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

Enumerations
enum class	QualifiedMassSpectrumParameter { IonMobOneOverK0 , IonMobOneOverK0Begin , IonMobOneOverK0End , TimsIonMobScanIndex , TimsFrameIonMobScanIndexBegin , TimsFrameIonMobScanIndexEnd , IsolationMz , IsolationMzWidth , CollisionEnergy , BrukerPrecursorIndex , TimsFrameScansCount , TimsFrameMzIndexBegin , TimsFrameMzIndexEnd , ScanNumber , last }

enum class	MsRunReadConfigParameter { TimsFrameIonMobScanIndexBegin , TimsFrameIonMobScanIndexEnd , TimsFrameIonMobOneOverK0Begin , TimsFrameIonMobOneOverK0End , MzRangeBegin , MzRangeEnd , TimsFrameMzIndexMergeWindow }

enum class	XicCoordParam : std::int8_t { TimsTofIonMobilityScanNumberStart , TimsTofIonMobilityScanNumberStop }

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	IntegrationScopeFeatures { FAILURE = 0x0000 , SUCCESS = 1 << 1 , FLAT_ON_X_AXIS = 1 << 2 , FLAT_ON_Y_AXIS = 1 << 3 , RHOMBOID_VERTICAL = 1 << 4 , RHOMBOID_HORIZONTAL = 1 << 5 , NOT_PRINTABLE = 1 << 6 , FLAT_ON_ANY_AXIS = (FLAT_ON_X_AXIS \| FLAT_ON_Y_AXIS) }

enum class	PointSpec { 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	ProjectParamCategory : std::int8_t { undefined = 0 , general = 1 , identification = 2 , filter = 3 , quantification = 4 , instrument = 5 }

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	MsRunXicExtractorFactoryType : std::int8_t { nose = 0 , direct = 1 , disk = 2 , diskbuffer }

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	SelectionDrawingLines { 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	RangeType { outermost = 1 , innermost = 2 }

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

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

std::unordered_map< NamespaceClassnamePairAsKey, RegisterFunc, NamespaceClassnameAsKeyHash, AreNamespaceClassnamePairsEqual > &	getNameSpaceClassNameJsConstructorRegistrarMap ()

void	registerJsConstructorForEachClassInRegistrarMap (QJSEngine *engine)

void	registerJsConstructorForNameSpaceClassNameInRegistrarMap (const QString &name_space, const QString &class_name, QJSEngine *engine)

void	registerQmlTypes (const char *uri, int versionMajor, int versionMinor)

void	registerEnumsToQJSEngine (QJSEngine *engine)

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

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

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

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

bool	peptideIonTypeIsComplement (Enums::PeptideIon ion_type_ref, Enums::PeptideIon ion_type)
	tells if an ion type is the complement ion of the other

bool	peptideIonIsNter (Enums::PeptideIon ion_type)
	tells if an ion is Nter

PeptideDirection	getPeptideIonDirection (Enums::PeptideIon ion_type)
	get the direction of a peptide ion

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 (Enums::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)

MzIntegrationParams::BinningType	getBinningTypeFromString (const QString &text)

constexpr MzIntegrationParams::InitializationResult	operator\| (MzIntegrationParams::InitializationResult a, MzIntegrationParams::InitializationResult b)

constexpr MzIntegrationParams::InitializationResult	operator& (MzIntegrationParams::InitializationResult a, MzIntegrationParams::InitializationResult b)

constexpr MzIntegrationParams::InitializationResult	operator\|= (MzIntegrationParams::InitializationResult &a, MzIntegrationParams::InitializationResult b)

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

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

std::vector< PeakIonIsotopeMatch >::iterator	findComplementIonType (std::vector< PeakIonIsotopeMatch >::iterator begin, std::vector< PeakIonIsotopeMatch >::iterator end, const PeakIonIsotopeMatch &peak_ion, std::size_t peptide_size)
	find the first element containing the complementary ion complementary ion of y1 is b(n-1) for instance

unsigned int	factorial (unsigned int n)

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

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

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

PMSPP_LIB_DECL 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

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

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

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)

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)

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

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

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

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

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

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

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

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
static const std::size_t	CHECKED_LINES_COUNT = 10

constexpr std::size_t	MAX_MS_LEVELS = 12

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< Enums::PrecisionUnit, QString >	precisionUnitMap

std::map< MzIntegrationParams::BinningType, QString >	binningTypeMap
	Map relating the BinningType to a textual representation.

std::map< Enums::DataKind, QString >	dataKindMap

std::map< Qt::MouseButton, QString >	qtMouseButtonMap

std::map< Qt::MouseButtons, QString >	qtMouseButtonsMap

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.

◆ AaStringCodecSp

typedef std::shared_ptr<const AaStringCodec> pappso::AaStringCodecSp

shared pointer on a Protein object

Definition at line 41 of file aastringcodec.h.

◆ BaseColorMapPlotWidgetCstSPtr

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

Definition at line 61 of file basecolormapplotwidget.h.

◆ BaseColorMapPlotWidgetSPtr

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

Definition at line 59 of file basecolormapplotwidget.h.

◆ BasePlotWidgetCstSPtr

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

Definition at line 81 of file baseplotwidget.h.

◆ BasePlotWidgetSPtr

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

Definition at line 80 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 18 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 53 of file filterceilingamplitudepercentage.h.

◆ FilterCeilingAmplitudePercentageSPtr

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

Definition at line 51 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.

◆ FilterNormalizeIntensitiesCstSPtr

typedef std::shared_ptr<const FilterNormalizeIntensities> pappso::FilterNormalizeIntensitiesCstSPtr

Definition at line 53 of file filternormalizeintensities.h.

◆ FilterNormalizeIntensitiesSPtr

typedef std::shared_ptr<FilterNormalizeIntensities> pappso::FilterNormalizeIntensitiesSPtr

Definition at line 51 of file filternormalizeintensities.h.

◆ FilterSavitzkyGolayCstSPtr

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

Definition at line 137 of file savgolfilter.h.

◆ FilterSavitzkyGolaySPtr

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

Definition at line 136 of file savgolfilter.h.

◆ FilterSuiteStringSPtr

typedef std::shared_ptr<FilterSuiteString> pappso::FilterSuiteStringSPtr

Definition at line 83 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.

◆ IntegrationScopeBaseCstSPtr

typedef std::shared_ptr<const IntegrationScopeBase> pappso::IntegrationScopeBaseCstSPtr

Definition at line 120 of file integrationscopebase.h.

◆ IntegrationScopeBaseSPtr

typedef std::shared_ptr<IntegrationScopeBase> pappso::IntegrationScopeBaseSPtr

Definition at line 119 of file integrationscopebase.h.

◆ IntegrationScopeCstSPtr

typedef std::shared_ptr<const IntegrationScope> pappso::IntegrationScopeCstSPtr

Definition at line 89 of file integrationscope.h.

◆ IntegrationScopeRectCstSPtr

typedef std::shared_ptr<const IntegrationScopeRect> pappso::IntegrationScopeRectCstSPtr

Definition at line 94 of file integrationscoperect.h.

◆ IntegrationScopeRectSPtr

typedef std::shared_ptr<IntegrationScopeRect> pappso::IntegrationScopeRectSPtr

Definition at line 93 of file integrationscoperect.h.

◆ IntegrationScopeRhombCstSPtr

typedef std::shared_ptr<const IntegrationScopeRhomb> pappso::IntegrationScopeRhombCstSPtr

Definition at line 149 of file integrationscoperhomb.h.

◆ IntegrationScopeRhombSPtr

typedef std::shared_ptr<IntegrationScopeRhomb> pappso::IntegrationScopeRhombSPtr

Definition at line 147 of file integrationscoperhomb.h.

◆ IntegrationScopeSpecCstSPtr

typedef std::shared_ptr<const IntegrationScopeSpec> pappso::IntegrationScopeSpecCstSPtr

Definition at line 179 of file integrationscopebase.h.

◆ IntegrationScopeSpecSPtr

typedef std::shared_ptr<IntegrationScopeSpec> pappso::IntegrationScopeSpecSPtr

Definition at line 178 of file integrationscopebase.h.

◆ IntegrationScopeSpecVector

using pappso::IntegrationScopeSpecVector = std::vector<IntegrationScopeSpec>

Definition at line 105 of file filterresample.h.

◆ IntegrationScopeSPtr

typedef std::shared_ptr<IntegrationScope> pappso::IntegrationScopeSPtr

Definition at line 88 of file integrationscope.h.

◆ MapTraceCstSPtr

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

Definition at line 29 of file maptrace.h.

◆ MapTraceSPtr

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

Definition at line 28 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 57 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 56 of file massspectrum.h.

◆ MsFileAccessorCstSPtr

typedef std::shared_ptr<const MsFileAccessor> pappso::MsFileAccessorCstSPtr

Definition at line 128 of file msfileaccessor.h.

◆ MsFileAccessorSPtr

typedef std::shared_ptr<MsFileAccessor> pappso::MsFileAccessorSPtr

Definition at line 127 of file msfileaccessor.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 46 of file msrunid.h.

◆ MsRunIdSPtr

typedef std::shared_ptr<MsRunId> pappso::MsRunIdSPtr

Definition at line 45 of file msrunid.h.

◆ MsRunReaderCstSPtr

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

Definition at line 58 of file msrunreader.h.

◆ MsRunReaderSPtr

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

Definition at line 57 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.

◆ NamespaceClassnamePairAsKey

using pappso::NamespaceClassnamePairAsKey = std::pair<QString, QString>

Definition at line 49 of file jsclassregistrar.h.

◆ NoConstPeptideSp

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

Definition at line 96 of file peptide.h.

◆ pappso_double

typedef double pappso::pappso_double

A type definition for doubles.

Definition at line 61 of file types.h.

◆ pappso_float

typedef float pappso::pappso_float

Definition at line 66 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 42 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 40 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 56 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.

◆ RegisterFunc

using pappso::RegisterFunc = std::function<void(QJSEngine *)>

Definition at line 50 of file jsclassregistrar.h.

◆ TimsDataSp

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

shared pointer on a TimsData object

Definition at line 54 of file timsdata.h.

◆ TimsFrameBaseCstSPtr

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

Definition at line 43 of file timsframebase.h.

◆ TimsFrameBaseSPtr

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

Definition at line 42 of file timsframebase.h.

◆ TimsFrameCstSPtr

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

Definition at line 44 of file timsframe.h.

◆ TimsFramesMsRunReaderCstSPtr

typedef std::shared_ptr<const TimsFramesMsRunReader> pappso::TimsFramesMsRunReaderCstSPtr

Definition at line 76 of file timsframesmsrunreader.h.

◆ TimsFramesMsRunReaderSPtr

typedef std::shared_ptr<TimsFramesMsRunReader> pappso::TimsFramesMsRunReaderSPtr

Definition at line 75 of file timsframesmsrunreader.h.

◆ TimsFrameSPtr

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

Definition at line 43 of file timsframe.h.

◆ TimsMsRunReaderMs2SPtr

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

Definition at line 19 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 68 of file types.h.

◆ XicCoordSPtr

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

Definition at line 44 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

◆ AtomIsotope

enum class pappso::AtomIsotope

strong

Enumerator
C
H
O
N
S

Definition at line 69 of file peptidenaturalisotope.cpp.

{
  C,
  H,
  O,
  N,
  S
};

◆ DataDimension

enum class pappso::DataDimension

strong

Enumerator
NOT_SET
HORIZONTAL
VERTICAL

Definition at line 34 of file selectionpolygon.h.

{
  NOT_SET = 0,
  HORIZONTAL,
  VERTICAL
};

◆ DeepProtMatchType

enum class 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
};

◆ DeepProtPeptideCandidateStatus

enum class 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
};

◆ DragDirections

enum class pappso::DragDirections

strong

Enumerator
NOT_SET
LEFT_TO_RIGHT
RIGHT_TO_LEFT
TOP_TO_BOTTOM
BOTTOM_TO_TOP

Definition at line 34 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
};

◆ IntegrationScopeFeatures

enum pappso::IntegrationScopeFeatures

Enumerator
FAILURE
SUCCESS
FLAT_ON_X_AXIS
FLAT_ON_Y_AXIS
RHOMBOID_VERTICAL
RHOMBOID_HORIZONTAL
NOT_PRINTABLE
FLAT_ON_ANY_AXIS

Definition at line 45 of file integrationscopebase.h.

{
  // This one needs to be 0 because of (if!<function>() syntax)
  FAILURE = 0x0000,
  // As soon as not 0, success and potentially with more info.
  SUCCESS             = 1 << 1,
  FLAT_ON_X_AXIS      = 1 << 2,
  FLAT_ON_Y_AXIS      = 1 << 3,
  RHOMBOID_VERTICAL   = 1 << 4,
  RHOMBOID_HORIZONTAL = 1 << 5,
  NOT_PRINTABLE       = 1 << 6,
  FLAT_ON_ANY_AXIS    = (FLAT_ON_X_AXIS | FLAT_ON_Y_AXIS)
};

◆ MsRunReadConfigParameter

enum class pappso::MsRunReadConfigParameter

strong

Enumerator
TimsFrameIonMobScanIndexBegin
TimsFrameIonMobScanIndexEnd
TimsFrameIonMobOneOverK0Begin
TimsFrameIonMobOneOverK0End
MzRangeBegin
MzRangeEnd
TimsFrameMzIndexMergeWindow

Definition at line 35 of file msrunreadconfig.h.

{
  // Only process mobility scans contained in the
  // scan index range below.
  TimsFrameIonMobScanIndexBegin,
  TimsFrameIonMobScanIndexEnd,
 
  // Only process mobility scans contained in the
  // inverse mobility range below.
  TimsFrameIonMobOneOverK0Begin,
  TimsFrameIonMobOneOverK0End,
 
  // Only process mass spectra for m/z values contained
  // in the following m/z range.
  MzRangeBegin,
  MzRangeEnd,
 
  // Merge m/z (TOF, really) indices on the basis of this
  // count of m/z (TOF, really) indices.
  TimsFrameMzIndexMergeWindow,
};

◆ MsRunXicExtractorFactoryType

enum class 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
};

◆ PeptideDirection

enum class pappso::PeptideDirection : std::int8_t

strong

Enumerator
Nter
Cter

Definition at line 45 of file peptide.h.

{
  Nter = 0,
  Cter = 1
};

◆ PeptideIonCter

enum class pappso::PeptideIonCter

strong

Enumerator
y
ystar
yo
z
yp
x

Definition at line 83 of file peptide.h.

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

◆ PeptideIonNter

enum class pappso::PeptideIonNter

strong

Enumerator
b
bstar
bo
a
astar
ao
bp
c

Definition at line 70 of file peptide.h.

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

◆ PointSpec

enum class pappso::PointSpec

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,
};

◆ ProjectParamCategory

enum class pappso::ProjectParamCategory : std::int8_t

strong

Enumerator
undefined	undefined
general	concerning the whole process
identification	concerning identification
filter	concerning filters (psm, peptide, protein validation)
quantification	quantification
instrument	information about instrument

Definition at line 43 of file projectparameters.h.

{
  undefined      = 0, ///< undefined
  general        = 1, ///< concerning the whole process
  identification = 2, ///< concerning identification
  filter         = 3, ///< concerning filters (psm, peptide, protein validation)
  quantification = 4, ///< quantification
  instrument     = 5, ///< information about instrument
};

◆ QualifiedMassSpectrumParameter

enum class pappso::QualifiedMassSpectrumParameter

strong

Enumerator
IonMobOneOverK0	1/kO value
IonMobOneOverK0Begin	1/K0 range's begin value
IonMobOneOverK0End	1/K0 range's end value
TimsIonMobScanIndex
TimsFrameIonMobScanIndexBegin
TimsFrameIonMobScanIndexEnd
IsolationMz	Isolation m/z value.
IsolationMzWidth	m/z isolation window width (left + right)
CollisionEnergy	Bruker's timsTOF collision energy.
BrukerPrecursorIndex	Bruker's timsTOF precursor index.
TimsFrameScansCount	Bruker's timsTOF frame's total ion mobility slots.
TimsFrameMzIndexBegin	Bruker's timsTOF mz index frame start range.
TimsFrameMzIndexEnd	Bruker's timsTOF mz index frame end range.
ScanNumber	Scan number: Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run. MS_scan_number = 1003057,
last

Definition at line 47 of file qualifiedmassspectrum.h.

{
 
  IonMobOneOverK0,      ///< 1/kO value
  IonMobOneOverK0Begin, ///< 1/K0 range's begin value
  IonMobOneOverK0End,   ///< 1/K0 range's end value
 
  TimsIonMobScanIndex,
  TimsFrameIonMobScanIndexBegin,
  TimsFrameIonMobScanIndexEnd,
 
  IsolationMz,      ///< Isolation m/z value
  IsolationMzWidth, ///< m/z isolation window width (left + right)
 
  CollisionEnergy,      ///< Bruker's timsTOF collision energy
  BrukerPrecursorIndex, ///< Bruker's timsTOF precursor index
  TimsFrameScansCount,  ///< Bruker's timsTOF frame's total ion mobility slots
 
  TimsFrameMzIndexBegin, ///< Bruker's timsTOF mz index frame start range
  TimsFrameMzIndexEnd,   ///< Bruker's timsTOF mz index frame end range
 
  ScanNumber, ///< Scan number: Ordinal number of the scan indicating its order
              ///< of acquisition within a mass spectrometry acquisition run.
              ///< MS_scan_number = 1003057,
  last
};

◆ RangeType

enum class pappso::RangeType

strong

Enumerator
outermost
innermost

Definition at line 72 of file baseplotwidget.h.

{
  outermost = 1,
  innermost = 2,
};

◆ RawFragmentationMode

enum class pappso::RawFragmentationMode : std::int8_t

strong

Enumerator
full
proline_effect

Definition at line 42 of file peptiderawfragmentmasses.h.

{
  full           = 0,
  proline_effect = 1
};

◆ SelectionDrawingLines

enum class pappso::SelectionDrawingLines

strong

Enumerator
NOT_SET
TOP_LINE
BOTTOM_LINE
HORIZONTAL_LINES
RIGHT_LINE
LEFT_LINE
VERTICAL_LINES
FULL_POLYGON

Definition at line 55 of file baseplotwidget.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)
 };

◆ XicCoordParam

enum class pappso::XicCoordParam : std::int8_t

strong

Enumerator
TimsTofIonMobilityScanNumberStart	TimsTOF specific ion mobility start range
TimsTofIonMobilityScanNumberStop	TimsTOF specific ion mobility stop range

Definition at line 50 of file xiccoord.h.

{
  TimsTofIonMobilityScanNumberStart, ///< TimsTOF specific ion mobility start
                                     ///< range
  TimsTofIonMobilityScanNumberStop,  ///< TimsTOF specific ion mobility stop
                                     ///< range
};

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 288 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(), and 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;
}

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::FilterChargeDeconvolution::FilterChargeDeconvolution(), pappso::FilterRemoveC13::FilterRemoveC13(), pappso::FilterRemoveC13::FilterRemoveC13(), pappso::PeptideNaturalIsotope::PeptideNaturalIsotope(), pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage(), pappso::FilterChargeDeconvolution::buildFilterFromString(), pappso::AaModification::calculateMassFromChemicalComponents(), pappso::ChemicalFormula::getMass(), and pappso::QCPSpectrum::highlightPrecursorPeaks().

◆ DIFFH1H2()

const pappso_double pappso::DIFFH1H2 ( 2.0141017778 - MPROTIUM )

References MPROTIUM().

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

◆ DIFFN14N15()

const pappso_double pappso::DIFFN14N15 ( 15.0001088982 - MASSNITROGEN )

References MASSNITROGEN().

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

◆ DIFFO16O17()

const pappso_double pappso::DIFFO16O17 ( 16.99913150 - MASSOXYGEN )

References MASSOXYGEN().

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

◆ DIFFO16O18()

const pappso_double pappso::DIFFO16O18 ( 17.9991610 - MASSOXYGEN )

References MASSOXYGEN().

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

◆ DIFFS32S33()

const pappso_double pappso::DIFFS32S33 ( 32.9714589101 - MASSSULFUR )

References MASSSULFUR().

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

◆ DIFFS32S34()

const pappso_double pappso::DIFFS32S34 ( 33.9678670300 - MASSSULFUR )

References MASSSULFUR().

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

◆ DIFFS32S36()

const pappso_double pappso::DIFFS32S36 ( 35.9670812000 - MASSSULFUR )

References MASSSULFUR().

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

◆ 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();
    });
}

References a, and b.

Referenced by pappso::masschroq::PeptideMeasurements::detectQuantifyPeaks().

◆ findComplementIonType()

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

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

Definition at line 30 of file peakionisotopematch.cpp.

{
 
  return std::find_if(
    begin,
    end,
    [peak_ion, peptide_size](const PeakIonIsotopeMatch &to_compare) {
      if(to_compare.getCharge() == peak_ion.getCharge())
        {
          if((to_compare.getPeptideFragmentIonSp().get()->size() +
              peak_ion.getPeptideFragmentIonSp().get()->size()) == peptide_size)
            {
              if(peptideIonTypeIsComplement(to_compare.getPeptideIonType(),
                                            peak_ion.getPeptideIonType()))
                {
                  if(to_compare.getPeptideNaturalIsotopeAverageSp()
                       .get()
                       ->getIsotopeNumber() ==
                     peak_ion.getPeptideNaturalIsotopeAverageSp()
                       .get()
                       ->getIsotopeNumber())
                    {
                      return true;
                    }
                }
            }
        }
 
      return false;
    });
}

References pappso::PeakIonMatch::getCharge(), pappso::PeptideNaturalIsotopeAverage::getIsotopeNumber(), pappso::PeakIonMatch::getPeptideFragmentIonSp(), pappso::PeakIonMatch::getPeptideIonType(), pappso::PeakIonIsotopeMatch::getPeptideNaturalIsotopeAverageSp(), peptideIonTypeIsComplement(), and pappso::PeptideFragmentIon::size().

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

◆ findDifferentYvalue() [1/2]

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

Definition at line 141 of file trace.cpp.

{
  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 126 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 84 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 70 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::FilterResampleKeepXRange::filter(), pappso::FilterResampleRemoveXRange::filter(), pappso::specglob::ExperimentalSpectrum::findMz(), 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 112 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 98 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::FilterResampleKeepXRange::filter(), pappso::FilterResampleRemoveXRange::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.

Referenced by pappso::masschroq::MbrPeptideMeasurements::detectQuantifyPeaks().

◆ 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 307 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.

◆ getBinningTypeFromString()

MzIntegrationParams::BinningType pappso::getBinningTypeFromString ( const QString & text )

Definition at line 73 of file mzintegrationparams.cpp.

{
  std::map<MzIntegrationParams::MzIntegrationParams::BinningType, QString>::const_iterator
    the_iterator_const =
      std::find_if(binningTypeMap.begin(),
                   binningTypeMap.end(),
                   [text](const std::pair<MzIntegrationParams::BinningType, QString> &pair) {
                     return pair.second == text;
                   });
 
  if(the_iterator_const != binningTypeMap.end())
    return the_iterator_const->first;
 
  return MzIntegrationParams::BinningType::NONE;
}

References binningTypeMap, and pappso::MzIntegrationParams::NONE.

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

◆ 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;
}

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

◆ getNameSpaceClassNameJsConstructorRegistrarMap()

PMSPP_LIB_DECL std::unordered_map< NamespaceClassnamePairAsKey, RegisterFunc, NamespaceClassnameAsKeyHash, AreNamespaceClassnamePairsEqual > & pappso::getNameSpaceClassNameJsConstructorRegistrarMap ( )

Definition at line 10 of file jsclassregistrar.cpp.

{
  static std::unordered_map<NamespaceClassnamePairAsKey,
                            RegisterFunc,
                            NamespaceClassnameAsKeyHash,
                            AreNamespaceClassnamePairsEqual>
    map;
  return map;
}

Referenced by registerJsConstructorForEachClassInRegistrarMap(), and registerJsConstructorForNameSpaceClassNameInRegistrarMap().

◆ getPeptideIonDirection()

PMSPP_LIB_DECL PeptideDirection pappso::getPeptideIonDirection ( Enums::PeptideIon ion_type )

get the direction of a peptide ion

Parameters

ion_type the ion to test

Returns: the peptide direction

Definition at line 95 of file peptide.cpp.

{
  if(peptideIonIsNter(ion_type))
    {
      return PeptideDirection::Nter;
    }
  return PeptideDirection::Cter;
}

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));
}

References Combinations().

Referenced by isotopem_ratio_cache().

◆ isotopem_ratio_cache()

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

Definition at line 95 of file peptidenaturalisotope.cpp.

{
  pappso_double abundance = 1;
  switch(isotope)
    {
      case Enums::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 Enums::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 Enums::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 Enums::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 Enums::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 Enums::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 Enums::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 Enums::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;
      default:
        break;
    }
  return isotopem_ratio(abundance, total, heavy);
}

References ABUNDANCEC13(), ABUNDANCEH2(), ABUNDANCEN15(), ABUNDANCEO17(), ABUNDANCEO18(), ABUNDANCES33(), ABUNDANCES34(), ABUNDANCES36(), pappso::Enums::C13, CACHE_ARRAY_SIZE, pappso::Enums::H2, isotopem_ratio(), pappso::Enums::N15, pappso::Enums::O17, pappso::Enums::O18, ratioC13_cache, ratioH2_cache, ratioN15_cache, ratioO17_cache, ratioO18_cache, ratioS33_cache, ratioS34_cache, ratioS36_cache, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

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

◆ MASSCARBON()

const pappso_double pappso::MASSCARBON ( 12 )

Referenced by pappso::AaModification::calculateMassFromChemicalComponents(), pappso::ChemicalFormula::getMass(), and MASSCO().

◆ MASSCO()

const pappso_double pappso::MASSCO ( MASSCARBON+ MASSOXYGEN )

References MASSCARBON(), and MASSOXYGEN().

◆ MASSH2O()

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

References MASSOXYGEN(), and MPROTIUM().

Referenced by pappso::PeptideFragmentIon::PeptideFragmentIon(), pappso::specglob::PeptideSpectrum::PeptideSpectrum(), and pappso::specglob::ExperimentalSpectrum::createSymetricPeakList().

◆ MASSNH3()

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

References MASSNITROGEN(), and MPROTIUM().

◆ MASSNITROGEN()

const pappso_double pappso::MASSNITROGEN ( 14. 0030740048 )

Referenced by pappso::AaModification::calculateMassFromChemicalComponents(), DIFFN14N15(), pappso::ChemicalFormula::getMass(), and MASSNH3().

◆ MASSOXYGEN()

const pappso_double pappso::MASSOXYGEN ( 15. 99491461956 )

Referenced by pappso::specpeptidoms::SpOMSSpectrum::SpOMSSpectrum(), pappso::specpeptidoms::SpOMSSpectrum::SpOMSSpectrum(), pappso::AaModification::calculateMassFromChemicalComponents(), pappso::AaModification::createInstance(), DIFFO16O17(), DIFFO16O18(), pappso::ChemicalFormula::getMass(), MASSCO(), MASSH2O(), and MASSPHOSPHORYLATEDR().

◆ MASSPHOSPHORUS()

const pappso_double pappso::MASSPHOSPHORUS ( 30. 973761998 )

Referenced by pappso::ChemicalFormula::getMass(), and MASSPHOSPHORYLATEDR().

◆ MASSPHOSPHORYLATEDR()

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

References MASSOXYGEN(), MASSPHOSPHORUS(), and MPROTIUM().

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(), DIFFS32S33(), DIFFS32S34(), DIFFS32S36(), and pappso::ChemicalFormula::getMass().

◆ 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 174 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::TracePeak::TracePeak(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::FilterCeilingAmplitudePercentage::filter(), pappso::FilterFloorAmplitudePercentage::filter(), pappso::FilterHighPassPercentage::filter(), pappso::FilterLocalMaximum::filter(), pappso::FilterNormalizeIntensities::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 183 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 239 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 272 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::FilterComplementIonEnhancer::FilterComplementIonEnhancer(), pappso::specglob::PeptideSpectrum::PeptideSpectrum(), pappso::specpeptidoms::SpOMSSpectrum::SpOMSSpectrum(), pappso::specpeptidoms::SpOMSSpectrum::SpOMSSpectrum(), pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), pappso::specself::SelfSpectrumDataPoint::fillAntiSpectrumDataPoint(), pappso::specpeptidoms::SpOMSSpectrum::fillComplementaryPeakIndexes(), pappso::specglob::PeptideModel::generateTheoreticalPeaks(), pappso::PsmFeatures::getIonPairPrecursorMassDelta(), pappso::specpeptidoms::SpOMSSpectrum::getMissingMass(), pappso::Ion::getMz(), pappso::specglob::PeptideModel::getMz(), pappso::cbor::psm::PsmFileReaderBase::getPrecursorMass(), pappso::QualifiedMassSpectrum::getPrecursorMass(), 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 157 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 166 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 211 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 194 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::specpeptidoms::SpOMSSpectrum::SpOMSSpectrum(), pappso::specpeptidoms::SpOMSSpectrum::SpOMSSpectrum(), pappso::AaModification::calculateMassFromChemicalComponents(), pappso::AaModification::createInstance(), pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), DIFFH1H2(), pappso::specglob::PeptideModel::generateTheoreticalPeaks(), pappso::ChemicalFormula::getMass(), MASSH2O(), MASSNH3(), and MASSPHOSPHORYLATEDR().

◆ 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&()

MzIntegrationParams::InitializationResult pappso::operator&	(	MzIntegrationParams::InitializationResult	a,
		MzIntegrationParams::InitializationResult	b )

constexpr

Definition at line 263 of file mzintegrationparams.h.

{
  return static_cast<MzIntegrationParams::InitializationResult>(static_cast<uint32_t>(a) &
                                                                static_cast<uint32_t>(b));
}

References a, and b.

◆ operator<() [1/2]

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

Definition at line 291 of file aa.cpp.

{
  return l.isLesser(r);
}

References pappso::Aa::isLesser().

◆ operator<() [2/2]

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

Definition at line 44 of file peptide.cpp.

{
  return (l.m_aaVec < r.m_aaVec);
}

◆ operator<<() [1/3]

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

Definition at line 151 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 )

Definition at line 34 of file trace.cpp.

{
  for(auto &dataPoint : trace)
    {
      out << dataPoint.x;
      out << dataPoint.y;
      out << "\n";
    }
  out << "\n";
 
  return out;
}

◆ operator<<() [3/3]

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

Definition at line 345 of file massspectrum.cpp.

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

◆ operator==() [1/2]

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

Definition at line 286 of file aa.cpp.

{
  return l.isAaEqual(r);
}

References pappso::Aa::isAaEqual().

◆ operator==() [2/2]

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

Definition at line 51 of file peptide.cpp.

{
  if(l.getCleavageNterModification() != r.getCleavageNterModification())
    return false;
  if(l.getCleavageCterModification() != r.getCleavageCterModification())
    return false;
  if(l.getNterModification() && r.getNterModification() &&
     (l.getNterModification() != r.getNterModification()))
    return false;
  if(l.getCterModification() && r.getCterModification() &&
     (l.getCterModification() != r.getCterModification()))
    return false;
 
  return (l.m_aaVec == r.m_aaVec);
}

◆ operator>>() [1/4]

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

Definition at line 162 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]

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

Definition at line 360 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 158 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 )

Definition at line 50 of file trace.cpp.

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

◆ operator|()

MzIntegrationParams::InitializationResult pappso::operator\|	(	MzIntegrationParams::InitializationResult	a,
		MzIntegrationParams::InitializationResult	b )

constexpr

Definition at line 256 of file mzintegrationparams.h.

{
  return static_cast<MzIntegrationParams::InitializationResult>(static_cast<uint32_t>(a) |
                                                                static_cast<uint32_t>(b));
}

References a, and b.

◆ operator|=()

MzIntegrationParams::InitializationResult pappso::operator\|=	(	MzIntegrationParams::InitializationResult &	a,
		MzIntegrationParams::InitializationResult	b )

constexpr

Definition at line 270 of file mzintegrationparams.h.

{
  a = a | b;
  return a;
}

References a, and b.

◆ peptideIonIsNter()

PMSPP_LIB_DECL bool pappso::peptideIonIsNter ( Enums::PeptideIon ion_type )

tells if an ion is Nter

Parameters

ion_type the ion to test

Definition at line 85 of file peptide.cpp.

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

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

◆ peptideIonTypeIsComplement()

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

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

Parameters

ion_type_ref	the ion type reference
ion_type	the ion to test

Definition at line 68 of file peptide.cpp.

{
  if(peptideIonIsNter(ion_type))
    std::swap(ion_type_ref, ion_type);
  if(peptideIonIsNter(ion_type))
    return false;
  if((ion_type_ref == Enums::PeptideIon::b) && (ion_type == Enums::PeptideIon::y))
    return true;
  if((ion_type_ref == Enums::PeptideIon::ao) && (ion_type == Enums::PeptideIon::yo))
    return true;
  if((ion_type_ref == Enums::PeptideIon::bstar) && (ion_type == Enums::PeptideIon::ystar))
    return true;
 
  return false;
}

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

Referenced by findComplementIonType().

◆ 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 249 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().

◆ registerEnumsToQJSEngine()

PMSPP_LIB_DECL void pappso::registerEnumsToQJSEngine ( QJSEngine * engine )

Definition at line 32 of file pappsojsqml.cpp.

{
  qDebug() << "Now registering the Enums:: enums for pappsomspp";
 
  // Get the meta-object for the namespace (generated by Q_NAMESPACE
  // as stated right below the Enums namespace at types.h).
 
  const QMetaObject *metaObject = &Enums::staticMetaObject;
  if(metaObject == nullptr)
    qFatal() << "Programming error. Failed to obtain &Enums::staticMetaObject";
 
  qDebug() << "Found namespace Enums with full name:" << metaObject->className();
 
  QJSValue libraryJsRootProperty;
 
  if(engine->globalObject().hasProperty("pappsomspp"))
    {
      // qDebug() << "Global object property 'pappsomspp' already exists.";
      libraryJsRootProperty = engine->globalObject().property("pappsomspp");
    }
  else
    {
      // qDebug() << "Global object property 'pappsomspp' not found.";
      // Create a JS object for pappsomspp
      libraryJsRootProperty = engine->newObject();
    }
 
  // Create a nested JS object for Enums
  QJSValue all_js_enums = engine->newObject();
 
  // Loop through all enums and populate jsEnums
  for(int i = 0; i < metaObject->enumeratorCount(); ++i)
    {
      QMetaEnum iter_meta_enum = metaObject->enumerator(i);
 
      // qDebug() << "Now iterating in enum:" << iter_meta_enum.enumName();
 
      QJSValue single_js_enum = engine->newObject();
 
      for(int j = 0; j < iter_meta_enum.keyCount(); ++j)
        {
          // qDebug() << "Now iterating in new key:" << iter_meta_enum.key(j)
          //          << "with value:" << iter_meta_enum.value(j);
 
          // key() would be "LEFT", with value() = 1
          single_js_enum.setProperty(iter_meta_enum.key(j), iter_meta_enum.value(j));
        }
 
      // name would be CapType
      all_js_enums.setProperty(iter_meta_enum.enumName(), single_js_enum);
    }
 
  // Attach Enums to pappsomspp
  libraryJsRootProperty.setProperty("Enums", all_js_enums);
 
  engine->globalObject().setProperty("pappsomspp", libraryJsRootProperty);
 
#if 0
 
  qDebug()
    << "Now checking for correct exposition of Enums::enum::<key/value> pairs.";
 
  QJSValue jsEnums =
    engine->globalObject().property("pappsomspp").property("Enums");
 
  if(jsEnums.isUndefined())
    {
      qDebug() << "Error: pappsomspp.Enums not found!";
      return;
    }
  else
    {
      qDebug() << "pappsomspp.Enums JS object exists";
 
      // Get all enum names (properties of the Enums object)
      QJSValue propNames =
        engine->evaluate("Object.getOwnPropertyNames(pappsomspp.Enums)");
 
      if(propNames.isError())
        {
          qDebug() << "JS Error:" << propNames.toString();
          return;
        }
 
      // Iterate through each enum
      QStringList enumNames = propNames.toVariant().toStringList();
      for(const QString &enumName : enumNames)
        {
          QJSValue jsEnum = jsEnums.property(enumName);
 
          if(!jsEnum.isObject())
            {
              qDebug() << "Skipping non-object property:" << enumName;
              continue;
            }
 
          qDebug() << "\nChecking enum:" << enumName;
 
          // Get all keys of the iterated enum
          QJSValue enumKeys = engine->evaluate(
            QString("Object.getOwnPropertyNames(libXpertMass.Enums.%1)")
              .arg(enumName));
 
          if(enumKeys.isError())
            {
              qDebug() << "  JS Error:" << enumKeys.toString();
              continue;
            }
 
          // Print key-value pairs for the iterated enum
          QStringList keys = enumKeys.toVariant().toStringList();
          for(const QString &key : keys)
            {
              QJSValue value = jsEnum.property(key);
              qDebug() << "  " << key << "=" << value.toInt();
              qDebug().noquote() << "\nChecked enum: " << enumName << "member ("
                                 << key << " / " << value.toInt() << ")";
            }
        }
    }
#endif
}

◆ registerJsConstructorForEachClassInRegistrarMap()

PMSPP_LIB_DECL void pappso::registerJsConstructorForEachClassInRegistrarMap ( QJSEngine * engine )

Definition at line 22 of file jsclassregistrar.cpp.

{
  qDebug() << "Registering the constructor of the classes marked for JS.";
 
  qsizetype count = getNameSpaceClassNameJsConstructorRegistrarMap().size();
  qDebug() << "Size of the map: count" << count;
 
  for(const auto &entry : getNameSpaceClassNameJsConstructorRegistrarMap())
    entry.second(engine);
}

References getNameSpaceClassNameJsConstructorRegistrarMap().

◆ registerJsConstructorForNameSpaceClassNameInRegistrarMap()

PMSPP_LIB_DECL void pappso::registerJsConstructorForNameSpaceClassNameInRegistrarMap	(	const QString &	name_space,
		const QString &	class_name,
		QJSEngine *	engine )

Definition at line 35 of file jsclassregistrar.cpp.

{
  // Remember, the registrar map is actually a map of map:
 
  // Key type: pair of namespace and class name
  // using NamespaceClassnamePairAsKey = std::pair<QString, QString>;
  // using RegisterFunc                = std::function<void(QJSEngine *)>;
  //
  // std::unordered_map<NamespaceClassnamePairAsKey,
  //                    RegisterFunc,
  //                    NsClassKeyHash,
  //                    AreNamespaceClassnamePairAsKeyEqual>
 
  // So, first look for a pair<NamespaceClassnamePairAsKey, RegisterFunc>
  // having key = {name_sape, class_name}, that is, a std::pair<QString,
  // QString>. Once we get that map item, run the second member of the
  // outer map item which actually runs the functor.
  auto it = getNameSpaceClassNameJsConstructorRegistrarMap().find({name_space, class_name});
  if(it != getNameSpaceClassNameJsConstructorRegistrarMap().end())
    it->second(engine);
  else
    qWarning().noquote() << "No JS constructor registered for namespace" << name_space
                         << "and class name" << class_name;
}

References getNameSpaceClassNameJsConstructorRegistrarMap().

◆ registerQmlTypes()

PMSPP_LIB_DECL void pappso::registerQmlTypes	(	const char *	uri,
		int	versionMajor,
		int	versionMinor )

Definition at line 8 of file pappsojsqml.cpp.

{
  Q_UNUSED(uri)
  Q_UNUSED(versionMajor)
  Q_UNUSED(versionMinor)
 
  // Register the namespace meta object
#if 0
  // At the moment no need to register namespace pappso as metaobject.
  qmlRegisterUncreatableMetaObject(staticMetaObject,
                                   uri,
                                   versionMajor,
                                   versionMinor,
                                   "Enums",
                                   "Cannot create PappsoMS namespace");
#endif
  // Register other types here too
}

◆ 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 231 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< MzIntegrationParams::BinningType, QString > pappso::binningTypeMap

Initial value:

{
  {MzIntegrationParams::BinningType::NONE, "NONE"},
  {MzIntegrationParams::BinningType::DATA_BASED, "DATA_BASED"},
  {MzIntegrationParams::BinningType::ARBITRARY, "ARBITRARY"}}

Map relating the BinningType to a textual representation.

Definition at line 67 of file mzintegrationparams.cpp.

                                                              {
  {MzIntegrationParams::BinningType::NONE, "NONE"},
  {MzIntegrationParams::BinningType::DATA_BASED, "DATA_BASED"},
  {MzIntegrationParams::BinningType::ARBITRARY, "ARBITRARY"}};

Referenced by getBinningTypeFromString(), pappso::MzIntegrationParams::toString(), and pappso::MzIntegrationParams::toString().

◆ CHECKED_LINES_COUNT

const std::size_t pappso::CHECKED_LINES_COUNT = 10

static

Definition at line 27 of file bafasciifilereader.cpp.

Referenced by pappso::BafAsciiFileReader::initialize().

◆ combinations_cache

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

Definition at line 44 of file peptidenaturalisotope.cpp.

44{0};

Referenced by Combinations().

◆ dataKindMap

std::map< Enums::DataKind, QString > pappso::dataKindMap

Initial value:

{{Enums::DataKind::unset, "unset"},
                                               {Enums::DataKind::dt, "dt"},
                                               {Enums::DataKind::rt, "rt"},
                                               {Enums::DataKind::mz, "mz"}}

Definition at line 8 of file types.cpp.

                                          {{Enums::DataKind::unset, "unset"},
                                               {Enums::DataKind::dt, "dt"},
                                               {Enums::DataKind::rt, "rt"},
                                               {Enums::DataKind::mz, "mz"}};

Referenced by pappso::MsRunDataSetTree::addDataSetQualMassSpectraInsideDtOrRtRange(), pappso::MsRunDataSetTree::addDataSetTreeNodesInsideDtOrRtRange(), pappso::MsRunDataSetTree::removeDataSetQualMassSpectraOutsideDtOrRtRange(), and pappso::MsRunDataSetTree::removeDataSetTreeNodesOutsideDtOrRtRange().

◆ MAX_MS_LEVELS

std::size_t pappso::MAX_MS_LEVELS = 12

constexpr

Definition at line 59 of file msrunreadconfig.h.

Referenced by pappso::MsRunReadConfig::MsRunReadConfig(), pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::getMsLevelsAsString(), pappso::MsRunReadConfig::operator=(), pappso::MsRunReadConfig::reset(), pappso::MsRunReadConfig::setMsLevels(), and pappso::MsRunReadConfig::toString().

◆ MsRunReader

class PMSPP_LIB_DECL pappso::MsRunReader

Definition at line 56 of file msrunreader.h.

◆ precisionUnitMap

std::map< Enums::PrecisionUnit, QString > pappso::precisionUnitMap

Initial value:

= {{Enums::PrecisionUnit::none, "none"},
                                                     {Enums::PrecisionUnit::dalton, "dalton"},
                                                     {Enums::PrecisionUnit::ppm, "ppm"},
                                                     {Enums::PrecisionUnit::res, "res"},
                                                     {Enums::PrecisionUnit::mz, "mz"}}

Definition at line 43 of file precision.cpp.

                                                       {{Enums::PrecisionUnit::none, "none"},
                                                     {Enums::PrecisionUnit::dalton, "dalton"},
                                                     {Enums::PrecisionUnit::ppm, "ppm"},
                                                     {Enums::PrecisionUnit::res, "res"},
                                                     {Enums::PrecisionUnit::mz, "mz"}};

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

◆ qtMouseButtonMap

std::map< Qt::MouseButton, QString > pappso::qtMouseButtonMap

Initial value:

{{Qt::NoButton, "NoButton"},
                                                    {Qt::LeftButton, "LeftButton"},
                                                    {Qt::RightButton, "RightButton"},
                                                    {Qt::MiddleButton, "MiddleButton"}}

Definition at line 13 of file baseplotcontext.cpp.

                                               {{Qt::NoButton, "NoButton"},
                                                    {Qt::LeftButton, "LeftButton"},
                                                    {Qt::RightButton, "RightButton"},
                                                    {Qt::MiddleButton, "MiddleButton"}};

◆ qtMouseButtonsMap

std::map< Qt::MouseButtons, QString > pappso::qtMouseButtonsMap

Initial value:

{
  {Qt::NoButton, "NoButton"},
  {Qt::AllButtons, "AllButtons"},
  {Qt::LeftButton, "LeftButton"},
  {Qt::RightButton, "RightButton"},
  {Qt::MiddleButton, "MiddleButton"},
  {Qt::LeftButton | Qt::RightButton, "LeftRightButtons"},
  {Qt::LeftButton | Qt::MiddleButton, "LeftMiddleButtons"},
  {Qt::RightButton | Qt::MiddleButton, "RightMiddleButtons"},
}

Definition at line 19 of file baseplotcontext.cpp.

                                                 {
  {Qt::NoButton, "NoButton"},
  {Qt::AllButtons, "AllButtons"},
  {Qt::LeftButton, "LeftButton"},
  {Qt::RightButton, "RightButton"},
  {Qt::MiddleButton, "MiddleButton"},
  {Qt::LeftButton | Qt::RightButton, "LeftRightButtons"},
  {Qt::LeftButton | Qt::MiddleButton, "LeftMiddleButtons"},
  {Qt::RightButton | Qt::MiddleButton, "RightMiddleButtons"},
};

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

◆ ratioC13_cache

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

Definition at line 85 of file peptidenaturalisotope.cpp.

85{0};

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.

92{0};

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.

86{0};

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.

90{0};

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.

91{0};

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.

89{0};

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.

88{0};

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.

87{0};

Referenced by isotopem_ratio_cache().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ AaModificationP

◆ AaModificationUp

◆ AaStringCodecSp

◆ BaseColorMapPlotWidgetCstSPtr

◆ BaseColorMapPlotWidgetSPtr

◆ BasePlotWidgetCstSPtr

◆ BasePlotWidgetSPtr

◆ BaseTracePlotWidgetCstSPtr

◆ BaseTracePlotWidgetSPtr

◆ DataPointCstSPtr

◆ FastaFileIndexerSPtr

◆ FilterCeilingAmplitudePercentageCstSPtr

◆ FilterCeilingAmplitudePercentageSPtr

◆ FilterFloorAmplitudePercentageCstSPtr

◆ FilterFloorAmplitudePercentageSPtr

◆ FilterInterfaceCstSPtr

◆ FilterInterfaceSPtr

◆ FilterLowIntensitySignalRemovalCstSPtr

◆ FilterLowIntensitySignalRemovalSPtr

◆ FilterNameInterfaceCstSPtr

◆ FilterNameInterfaceSPtr

◆ FilterNormalizeIntensitiesCstSPtr

◆ FilterNormalizeIntensitiesSPtr

◆ FilterSavitzkyGolayCstSPtr

◆ FilterSavitzkyGolaySPtr

◆ FilterSuiteStringSPtr

◆ GrpGroupSp

◆ GrpGroupSpConst

◆ GrpPeptideSp

◆ GrpPeptideSpConst

◆ GrpProteinSp

◆ GrpProteinSpConst

◆ GrpSubGroupSp

◆ GrpSubGroupSpConst

◆ IntegrationScopeBaseCstSPtr

◆ IntegrationScopeBaseSPtr

◆ IntegrationScopeCstSPtr

◆ IntegrationScopeRectCstSPtr

◆ IntegrationScopeRectSPtr

◆ IntegrationScopeRhombCstSPtr

◆ IntegrationScopeRhombSPtr

◆ IntegrationScopeSpecCstSPtr

◆ IntegrationScopeSpecSPtr

◆ IntegrationScopeSpecVector

◆ IntegrationScopeSPtr

◆ MapTraceCstSPtr

◆ MapTraceSPtr

◆ MassSpectrumCombinerCstSPtr

◆ MassSpectrumCombinerSPtr

◆ MassSpectrumCstSPtr

◆ MassSpectrumMinusCombinerCstSPtr

◆ MassSpectrumMinusCombinerSPtr

◆ MassSpectrumPlusCombinerCstSPtr

◆ MassSpectrumPlusCombinerSPtr

◆ MassSpectrumSPtr

◆ MsFileAccessorCstSPtr

◆ MsFileAccessorSPtr

◆ MsRunDataSetTreeCstSPtr

◆ MsRunDataSetTreeNodeCstSPtr

◆ MsRunDataSetTreeNodeSPtr

◆ MsRunDataSetTreeSPtr

◆ MsRunIdCstSPtr

◆ MsRunIdSPtr

◆ MsRunReaderCstSPtr

◆ MsRunReaderSPtr

◆ MsRunSliceSPtr

◆ MsRunXicExtractorInterfaceSp

◆ MzCalibrationInterfaceSPtr

◆ NamespaceClassnamePairAsKey

◆ NoConstPeptideSp

◆ pappso_double

◆ pappso_float