pappso Namespace Reference

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

Namespaces
namespace	masschroq
namespace	cbor
namespace	specglob
namespace	specpeptidoms
namespace	specself
namespace	spectree
namespace	Enums

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
struct	CodeToMass
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...
class	AtomNumberInterface
struct	IsotopeCount
class	ChemicalFormula
class	ExceptionInterrupted
class	ExceptionNotFound
class	ExceptionNotImplemented
class	ExceptionNotPossible
class	ExceptionNotRecognized
	excetion to use when an item type is not recognized More...
class	ExceptionOutOfRange
class	FastaFileIndexerInterface
class	FastaFileIndexer
class	FastaHandlerInterface
class	FastaSeqHandler
class	FastaOutputStream
class	FastaReader
class	FastaWriterInterface
class	GrpExperiment
class	GrpGroup
class	GrpGroupingMonitorInterface
class	GrpGroupingMonitor
class	GrpMapPeptideToGroup
class	GrpMapPeptideToSubGroupSet
class	GrpPeptide
class	GrpPeptideSet
class	GrpProtein
class	GrpSubGroup
class	GrpSubGroupSet
class	DataPointJs
struct	NamespaceClassnameAsKeyHash
struct	AreNamespaceClassnamePairsEqual
class	MassSpectrumJs
	The MassSpectrumJs class provides a JavaScript wrapper around MassSpectrum. More...
class	QPointFJs
class	TraceJs
class	MassSpectrum
	Class to represent a mass spectrum. More...
class	MassSpectrumId
struct	PrecursorIonData
class	QualifiedMassSpectrum
	Class representing a fully specified mass spectrum. More...
class	BafAsciiFileReader
class	MsFileAccessor
class	MsFileReader
class	MzcborMsFileReader
class	MsDataFormatEnumStr
	static functions to convert mz file formats More...
class	PwizMsFileReader
class	TimsMsFileReader
class	XyMsFileReader
struct	MsRunRetentionTimeSeamarkPoint
class	MsRunRetentionTime
struct	MassSpectrumLineData
class	BafAsciiMsRunReader
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	MsRunReadConfig
class	MsRunReader
	base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More...
class	MgfOutput
class	MzxmlOutput
class	MzcborMsRunReader
class	PwizMsRunReader
class	TimsFramesMsRunReader
class	TimsMsRunReader
class	TimsMsRunReaderBase
class	TimsMsRunReaderDia
class	TimsMsRunReaderMs2
class	TimsMsRunReaderMs2Selected
class	SpectrumCollectionHandlerInterface
	interface to collect spectrums from the MsRunReader class More...
class	MsRunSimpleStatistics
	example of interface to count MS levels of all spectrum in an MSrun More...
class	MsRunReaderScanNumberMultiMap
	provides a multimap to find quickly spectrum index from scan number More...
class	MsRunReaderRetentionTimeLine
	collect retention times along MS run More...
class	MsRunReaderTicChromatogram
	calculate a TIC chromatogram More...
class	MsRunQualifiedSpectrumLoader
	Load all qualified spectrum into a vector. More...
class	IonMobilityGrid
struct	XicCoord
	coordinates of the XIC to extract and the resulting XIC after extraction More...
struct	XicCoordTims
	coordinates of the XIC to extract and the resulting XIC after extraction More...
class	XyMsRunReader
class	MzRange
class	FilterOboPsiModMap
class	FilterOboPsiModSink
class	FilterOboPsiModTermAccession
class	FilterOboPsiModTermDiffMono
class	FilterOboPsiModTermLabel
class	FilterOboPsiModTermName
class	OboPsiMod
class	OboPsiModHandlerInterface
class	OboPsiModTerm
class	OboPsiMs
class	OboUnimod
class	PappsoException
class	Ion
class	Peptide
class	PeptideFragment
class	PeptideFragmentIon
class	PeptideFragmentIonListBase
class	PeptideInterface
class	PeptideNaturalIsotope
class	PeptideNaturalIsotopeAverage
class	PeptideNaturalIsotopeList
class	PeptideProFormaParser
struct	SimplePeakIonMatch
class	PeptideRawFragmentMasses
class	PeptideStrParser
class	PrecisionBase
class	DaltonPrecision
class	PpmPrecision
class	ResPrecision
class	PrecisionFactory
class	IntegrationScope
class	IntegrationScopeBase
struct	IntegrationScopeSpec
class	IntegrationScopeRect
class	IntegrationScopeRhomb
class	MassDataCombinerInterface
class	MassSpectrumCombiner
class	MassSpectrumMinusCombiner
class	MassSpectrumPlusCombiner
class	MzIntegrationParams
	The MzIntegrationParams class provides the parameters definining how m/z integrations must be performed. More...
class	SelectionPolygon
struct	SelectionPolygonSpec
class	TraceCombiner
class	TraceMinusCombiner
class	TracePlusCombiner
class	CosineSimilarity
class	CubicSplineModel
class	HighResPeakPicker
class	LocalSignalToNoiseEstimator
class	TraceDetectionSinkInterface
class	TraceDetectionInterface
class	TraceDetectionMoulon
class	TraceDetectionZivy
class	TracePeak
class	TracePeakList
class	FilterCeilingAmplitudePercentage
	Redefines the ceiling intensity of the Trace. More...
class	FilterChargeDeconvolution
class	FilterComplementIonEnhancer
	try to detect complementary ions and assign maximum intensity of both elements More...
class	FilterMzExclusion
class	FilterFloorAmplitudePercentage
	Redefines the floor intensity of the Trace. More...
class	FilterInterface
	generic interface to apply a filter on a trace More...
class	MassSpectrumFilterInterface
	generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface, but some filter are only relevant if they are used on MassSpectrum using this interface means the filter can only be applied on MassSpectrum and not on Trace More...
class	FilterLocalMaximum
	finds all local maxima, i.e. any point that has a greater y value than both of its neighboring points and only keep those points More...
class	FilterLowIntensitySignalRemoval
	Redefines the floor intensity of the Trace. More...
class	FilterMorphoWindowBase
	base class that apply a signal treatment based on a window More...
class	FilterMorphoSum
	test purpose More...
class	FilterMorphoMax
	transform the trace into its maximum over a window More...
class	FilterMorphoMin
	transform the trace into its minimum over a window More...
class	FilterMorphoMinMax
	transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures More...
class	FilterMorphoMaxMin
	transform the trace with the maximum of the minimum equivalent of the erode filter for pictures More...
class	FilterMorphoAntiSpike
	anti spike filter set to zero alone values inside the window More...
class	FilterMorphoMedian
	median filter apply median of y values inside the window More...
class	FilterMorphoMean
	mean filter apply mean of y values inside the window : this results in a kind of smoothing More...
class	FilterMorphoBackground
	compute background of a trace compute background noise on a trace More...
class	FilterNameInterface
	Interface that allows to build filter objects from strings. More...
class	FilterNormalizeIntensities
	Sets the maximum intensity of the trace to the provided value. More...
class	FilterLowPass
	remove datapoints higher or equal to a given Y value (intensity) More...
class	FilterHighPass
	remove datapoints below or equal to the given Y value (intensity) More...
class	FilterHighPassPercentage
	remove datapoints below a given intensity percentage (ratio) of the maximum intensity More...
class	FilterGreatestY
	keep N datapoints form the greatest intensities to the lowest More...
class	FilterGreatestYperWindow
	keep N datapoints form the greatest intensities to the lowest within a mass range in dalton More...
class	MassSpectrumFilterGreatestItensities
class	FilterFloorY
	apply std::floor (round to lowest integer) to all Y values More...
class	FilterRoundY
	apply std::round (round to nearest integer) to all Y values More...
class	FilterRescaleY
	rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored More...
class	FilterScaleFactorY
	rescales Y values given a tranformation factor More...
class	FilterRemoveY
	removes a value to all Y values More...
class	FilterQuantileBasedRemoveY
	removes a value found by quantile to all Y values More...
class	FilterPeakDelta
class	FilterRemoveC13
class	FilterResampleKeepSmaller
class	FilterResampleKeepGreater
class	FilterResampleRemoveXRange
class	FilterResampleKeepXRange
class	FilterResampleKeepPointInPolygon
class	MassSpectrumFilterResampleRemoveMzRange
class	MassSpectrumFilterResampleKeepMzRange
class	FilterSuite
	apply a suite of filters from a vector More...
class	FilterSuiteString
class	FilterTandemDeisotope
	Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based moving window progression does the following tests: More...
class	FilterTriangle
struct	SavGolParams
	Parameters for the Savitzky-Golay filter. More...
class	FilterSavitzkyGolay
	uses Savitsky-Golay filter on trace More...
struct	ProjectParam
class	ProjectParameters
class	XtandemError
class	TandemWrapperRun
class	WrapTandemInput
class	WrapTandemResults
class	XtandemPresetReader
class	UiMonitorInterface
class	UiMonitorText
class	UiMonitorTextPercent
class	UiMonitorVoid
class	MzIdentMlWriter
class	XmlStreamReaderInterface
	convenient xml reader helper More...
class	Enzyme
class	EnzymeProductInterface
class	PeptideModificatorInterface
class	PeptideSinkInterface
class	PeptideSpSinkInterface
class	PeptideBuilder
	builds a peptide shared pointer from peptide string and adds fixed modifications More...
class	PeptideFixedModificationBuilder
class	PeptideMethioninRemove
	potential remove Nter Methionin More...
class	PeptideModificatorBase
class	PeptideModificatorPipeline
class	PeptideModificatorTee
class	PeptideSemiEnzyme
	cut a regular peptide obtained with an enzyme at any position from Nter or Cter More...
class	PeptideSizeFilter
	filter peptide string by size More...
class	PeptideVariableModificationBuilder
	Modify a peptide shared pointer with a variable modification on one AA. More...
class	PeptideVariableModificationReplacement
class	Protein
class	ProteinIntegerCode
class	ProteinPresenceAbsenceMatrix
class	DeepProtEnumStr
class	IonIsotopeRatioScore
class	PsmFeatures
class	MorpheusScore
class	PeakIonIsotopeMatch
class	PeakIonMatch
class	PeptideIsotopeSpectrumMatch
class	PeptideSpectrumMatch
class	XtandemHyperscore
class	XtandemHyperscoreBis
class	XtandemSpectrumProcess
struct	DataPoint
class	LinearRegression
class	MapTrace
class	Trace
	A simple container of DataPoint instances. More...
class	Utils
class	TimsFrameMobilityTraces
class	MzCalibrationInterface
class	MzCalibrationModel1
class	MzCalibrationModel1Cached
class	MzCalibrationStore
class	TimsBinDec
struct	FrameIdDescr
class	TimsData
class	TimsDataFastMap
	replacement for std::map More...
class	TimsDdaPrecursors
class	TimsDiaSlices
class	TimsFrame
class	TimsFrameBase
class	TimsFrameRawDataChunck
struct	TimsFrameRecord
class	TimsFrameType1
class	TimsMs2CentroidFilter
class	TimsDirectXicExtractor
class	TimsXicExtractorInterface
class	QualifiedXic
class	Xic
class	XicPeptideFragmentIon
class	XicPeptideFragmentIonNaturalIsotope
class	XicPeptideInterface
class	MsRunXicExtractorFactory
	factory to build different kinds of XIC extractors More...
class	MsRunXicExtractorInterface
class	MsRunSlice
class	MsRunXicExtractor
class	MsRunXicExtractorDisk
class	MsRunXicExtractorDiskBuffer
class	HttpButton
class	MassSpectrumWidget
class	QCPSpectrum
class	OboChooserWidget
class	OboListModel
class	OboListProxyModel
class	OboListWidget
class	OboTermForm
class	BaseColorMapPlotWidget
class	BasePlotContext
class	BasePlotWidget
class	BaseTracePlotWidget
struct	ColorMapPlotConfig
class	DriftSpecMassSpecColorMapPlotWidget
class	DriftSpecTracePlotWidget
class	MassSpecTracePlotContext
class	MassSpecTracePlotWidget
class	TicXicChromDriftSpecColorMapPlotWidget
class	TicXicChromMassSpecColorMapPlotWidget
class	TicXicChromTracePlotWidget
class	PrecisionWidget
class	SwitchWidget
class	QCPXic
class	XicWidget

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
using	TraceIterator = std::vector<DataPoint>::const_iterator
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)
void	spline_bisection (const CubicSplineModel &spline_model, double const mz_at_left, double const mz_at_right, double &center_peak_mz, double &center_peak_intensity, double const threshold)
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)
Trace	incrementByValueX (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double increment)
Trace	incrementByValueY (std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double increment)
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
std::map< Qt::KeyboardModifier, QString >	qtKeyboardModifierMap

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 56 of file basetraceplotwidget.h.

BaseTracePlotWidgetSPtr

typedef std::shared_ptr<BaseTracePlotWidget> pappso::BaseTracePlotWidgetSPtr

Definition at line 55 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 117 of file integrationscopebase.h.

IntegrationScopeBaseSPtr

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

Definition at line 116 of file integrationscopebase.h.

IntegrationScopeCstSPtr

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

Definition at line 98 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 176 of file integrationscopebase.h.

IntegrationScopeSpecSPtr

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

Definition at line 175 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 97 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 22 of file massspectrumcombiner.h.

MassSpectrumCombinerSPtr

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

Definition at line 23 of file massspectrumcombiner.h.

MassSpectrumCstSPtr

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

Definition at line 54 of file massspectrum.h.

MassSpectrumMinusCombinerCstSPtr

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

Definition at line 17 of file massspectrumminuscombiner.h.

MassSpectrumMinusCombinerSPtr

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

Definition at line 19 of file massspectrumminuscombiner.h.

MassSpectrumPlusCombinerCstSPtr

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

Definition at line 16 of file massspectrumpluscombiner.h.

MassSpectrumPlusCombinerSPtr

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

Definition at line 18 of file massspectrumpluscombiner.h.

MassSpectrumSPtr

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

Definition at line 53 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 42 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 98 of file peptide.h.

pappso_double

typedef double pappso::pappso_double

A type definition for doubles.

Definition at line 60 of file types.h.

pappso_float

typedef float pappso::pappso_float

Definition at line 65 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 55 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 19 of file tracecombiner.h.

TraceCombinerSPtr

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

Definition at line 20 of file tracecombiner.h.

TraceCstSPtr

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

Definition at line 140 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.

TraceIterator

using pappso::TraceIterator = std::vector<DataPoint>::const_iterator

Definition at line 23 of file localsignaltonoiseestimator.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 139 of file trace.h.

uint

typedef unsigned int pappso::uint

Definition at line 67 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 32 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 46 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 46 of file peptide.h.

{
  Nter = 0,
  Cter = 1
};

PeptideIonCter

enum class pappso::PeptideIonCter

strong

Enumerator
y
ystar
yo
z
yp
x

Definition at line 85 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 72 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 283 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 54 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 136 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 121 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 79 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 65 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 107 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 93 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 78 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 302 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 68 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 330 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 97 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().

incrementByValueX()

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

Definition at line 418 of file trace.cpp.

{
  Trace trace;
  trace.reserve(std::distance(begin, end) + 1);
 
  std::vector<DataPoint>::const_iterator the_iterator = begin;
 
  while(the_iterator != end)
    {
      trace.append({the_iterator->x + increment, the_iterator->y});
      ++the_iterator;
    }
 
  return trace;
}

References pappso::Trace::append().

incrementByValueY()

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

Definition at line 437 of file trace.cpp.

{
  Trace trace;
  trace.reserve(std::distance(begin, end) + 1);
 
  std::vector<DataPoint>::const_iterator the_iterator = begin;
 
  while(the_iterator != end)
    {
      trace.append({the_iterator->x, the_iterator->y + increment});
      ++the_iterator;
    }
 
  return trace;
}

References pappso::Trace::append().

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(), pappso::specglob::ExperimentalSpectrum::createSymetricPeakList(), pappso::specpeptidoms::PeptideModel::getMass(), and pappso::Peptide::getMassIonSerie().

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(), MASSPHOSPHORYLATEDR(), and pappso::specpeptidoms::SemiGlobalAlignment::updateAlignmentMatrix().

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 169 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 178 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 234 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 267 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::Peptide::getMassIonSerie(), 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(), pappso::cbor::psm::SageTsvHandler::recordLine(), pappso::FilterChargeDeconvolution::transformToMonoChargedForAllDataPoint(), and pappso::specpeptidoms::SemiGlobalAlignment::updateAlignmentMatrix().

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 152 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 161 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 206 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 189 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(), MASSPHOSPHORYLATEDR(), and pappso::specpeptidoms::SemiGlobalAlignment::updateAlignmentMatrix().

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 313 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 46 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 148 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 29 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 338 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 53 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 159 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 353 of file massspectrum.cpp.

{
  DataPoint peak;
 
  if(!instream.atEnd())
    {
      quint32 vector_size;
      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 155 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 45 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 305 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 321 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 87 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 70 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 244 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 30 of file pappsojsqml.cpp.

{
  // qDebug() << "Now registering the Enums:: enums for pappso";
 
  // Get the meta-object for the namespace (generated by Q_NAMESPACE
  // as stated right below the Enums namespace at types.h).
 
  if(engine == nullptr)
    {
      qFatal() << "Cannot register class: engine is null";
    }
 
  const QMetaObject *metaObject = &Enums::staticMetaObject;
  // qDebug() << "Namespace Enums with full name:" << metaObject->className();
 
  QJSValue pappso_root_property;
 
  if(engine->globalObject().hasProperty("pappso"))
    {
      // qDebug() << "Global object property 'pappso' already exists.";
      pappso_root_property = engine->globalObject().property("pappso");
    }
  else
    {
      // qDebug() << "Global object property 'pappso' not found.";
      // Create a JS object for pappso
      pappso_root_property = 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
  pappso_root_property.setProperty("Enums", all_js_enums);
 
  engine->globalObject().setProperty("pappso", pappso_root_property);
 
#if 0
 
  qDebug()
    << "Now checking for correct exposition of Enums::enum::<key/value> pairs.";
 
  QJSValue jsEnums =
    engine->globalObject().property("pappso").property("Enums");
 
  if(jsEnums.isUndefined())
    {
      qDebug() << "Error: pappso.Enums not found!";
      return;
    }
  else
    {
      qDebug() << "pappso.Enums JS object exists";
 
      // Get all enum names (properties of the Enums object)
      QJSValue propNames =
        engine->evaluate("Object.getOwnPropertyNames(pappso.Enums)");
 
      if(propNames.isError())
        {
          qDebug() << "JS Error:" << propNames.toString();
          return;
        }
 
      // Iterate through each enum
      const 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(pappso.Enums.%1)")
              .arg(enumName));
 
          if(enumKeys.isError())
            {
              qDebug() << "  JS Error:" << enumKeys.toString();
              continue;
            }
 
          // Print key-value pairs for the iterated enum
          const 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;
 
  // 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>
 
  for(const auto &entry : getNameSpaceClassNameJsConstructorRegistrarMap())
    {
      // qDebug() << "Now registering" << entry.first.first << "-" << entry.first.second;
      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 50 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_space, 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 7 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
}

spline_bisection()

void pappso::spline_bisection	(	const CubicSplineModel &	spline_model,
		double const	mz_at_left,
		double const	mz_at_right,
		double &	center_peak_mz,
		double &	center_peak_intensity,
		double const	threshold )

Definition at line 241 of file cubicsplinemodel.cpp.

{
  // qDebug() << "spline model has" << spline_model.getKnots().size();
 
  // calculate maximum by evaluating the spline's 1st derivative
  // (bisection method)
  double lefthand  = mz_at_left;
  double righthand = mz_at_right;
 
  bool lefthand_sign = true;
  double eps         = std::numeric_limits<double>::epsilon();
 
  // bisection
  do
    {
      double mid                = (lefthand + righthand) / 2.0;
      double midpoint_deriv_val = spline_model.derivative(mid);
 
      // if deriv nearly zero then maximum already found
      if(!(std::fabs(midpoint_deriv_val) > eps))
        {
          break;
        }
 
      bool midpoint_sign = (midpoint_deriv_val < 0.0) ? false : true;
 
      if(lefthand_sign ^ midpoint_sign)
        {
          righthand = mid;
        }
      else
        {
          lefthand = mid;
        }
    }
  while(righthand - lefthand > threshold);
 
  center_peak_mz = (lefthand + righthand) / 2;
 
  center_peak_intensity = spline_model.evalSplineAt(center_peak_mz);
 
  // qDebug() << "center_peak_intensity:" << center_peak_intensity;
}

References pappso::CubicSplineModel::derivative(), and pappso::CubicSplineModel::evalSplineAt().

Referenced by pappso::HighResPeakPicker::pick().

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 226 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 62 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.

{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"}};

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().

qtKeyboardModifierMap

std::map< Qt::KeyboardModifier, QString > pappso::qtKeyboardModifierMap

Initial value:

{
  {Qt::NoModifier, "No modifier"},
  {Qt::ShiftModifier, "A Shift key"},
  {Qt::ControlModifier, "A Ctrl key"},
  {Qt::AltModifier, "An Alt key"},
  {Qt::MetaModifier, "A Meta key"},
  {Qt::KeypadModifier, "A keypad button"},
  {Qt::GroupSwitchModifier, "A Mode_switch key"}}

Definition at line 29 of file baseplotcontext.cpp.

                                                         {
  {Qt::NoModifier, "No modifier"},
  {Qt::ShiftModifier, "A Shift key"},
  {Qt::ControlModifier, "A Ctrl key"},
  {Qt::AltModifier, "An Alt key"},
  {Qt::MetaModifier, "A Meta key"},
  {Qt::KeypadModifier, "A keypad button"},
  {Qt::GroupSwitchModifier, "A Mode_switch key"}};

Referenced by pappso::BasePlotContext::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 12 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 18 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.

{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.

{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.

{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.

{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.

{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.

{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.

{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.

{0};

Referenced by isotopem_ratio_cache().