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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
};
pappso::AtomIsotope::C
@ C
Definition peptidenaturalisotope.cpp:71
pappso::AtomIsotope::S
@ S
Definition peptidenaturalisotope.cpp:75
pappso::AtomIsotope::N
@ N
Definition peptidenaturalisotope.cpp:74
pappso::AtomIsotope::H
@ H
Definition peptidenaturalisotope.cpp:72
pappso::AtomIsotope::O
@ O
Definition peptidenaturalisotope.cpp:73

## DataDimension

enum class pappso::DataDimension

strong

Enumerator
NOT_SET |
HORIZONTAL |
VERTICAL |

Definition at line 34 of file selectionpolygon.h.

{
NOT_SET = 0,
HORIZONTAL,
VERTICAL
};
pappso::DataDimension::NOT_SET
@ NOT_SET
Definition selectionpolygon.h:36
pappso::DataDimension::VERTICAL
@ VERTICAL
Definition selectionpolygon.h:38
pappso::DataDimension::HORIZONTAL
@ HORIZONTAL
Definition selectionpolygon.h:37

## 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
};
pappso::masschroq::PeakQualityCategory::last
@ last
Definition types.h:61
pappso::DeepProtMatchType::ZeroMassDeltaMissedCleavage
@ ZeroMassDeltaMissedCleavage
peptide candidate with missed cleavage is in precursor mz range
Definition deepprotenum.h:45
pappso::DeepProtMatchType::uncategorized
@ uncategorized
precursor mass was not compared
Definition deepprotenum.h:43
pappso::DeepProtMatchType::NoDeltaPosition
@ NoDeltaPosition
Definition deepprotenum.h:51
pappso::DeepProtMatchType::DeltaPosition
@ DeltaPosition
Definition deepprotenum.h:49
pappso::DeepProtMatchType::ZeroMassDelta
@ ZeroMassDelta
peptide candidate is in precursor mz range
Definition deepprotenum.h:44
pappso::DeepProtMatchType::ZeroMassDeltaSemiTryptic
@ ZeroMassDeltaSemiTryptic
semi tryptic peptide candidate is in precursor mz range
Definition deepprotenum.h:47

## 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
};
pappso::DeepProtPeptideCandidateStatus::CterRemoval
@ CterRemoval
Definition deepprotenum.h:64
pappso::DeepProtPeptideCandidateStatus::unmodified
@ unmodified
precursor mass was not compared
Definition deepprotenum.h:62
pappso::DeepProtPeptideCandidateStatus::MissedCleavage
@ MissedCleavage
Definition deepprotenum.h:66
pappso::DeepProtPeptideCandidateStatus::NterRemoval
@ NterRemoval
Definition deepprotenum.h:65

## 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
};
pappso::DragDirections::RIGHT_TO_LEFT
@ RIGHT_TO_LEFT
Definition baseplotcontext.h:36
pappso::DragDirections::LEFT_TO_RIGHT
@ LEFT_TO_RIGHT
Definition baseplotcontext.h:35
pappso::DragDirections::BOTTOM_TO_TOP
@ BOTTOM_TO_TOP
Definition baseplotcontext.h:38
pappso::DragDirections::TOP_TO_BOTTOM
@ TOP_TO_BOTTOM
Definition baseplotcontext.h:37

## 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)
};
pappso::SUCCESS
@ SUCCESS
Definition integrationscopebase.h:51
pappso::FLAT_ON_X_AXIS
@ FLAT_ON_X_AXIS
Definition integrationscopebase.h:52
pappso::FAILURE
@ FAILURE
Definition integrationscopebase.h:49
pappso::RHOMBOID_VERTICAL
@ RHOMBOID_VERTICAL
Definition integrationscopebase.h:54
pappso::RHOMBOID_HORIZONTAL
@ RHOMBOID_HORIZONTAL
Definition integrationscopebase.h:55
pappso::NOT_PRINTABLE
@ NOT_PRINTABLE
Definition integrationscopebase.h:56
pappso::FLAT_ON_Y_AXIS
@ FLAT_ON_Y_AXIS
Definition integrationscopebase.h:53
pappso::FLAT_ON_ANY_AXIS
@ FLAT_ON_ANY_AXIS
Definition integrationscopebase.h:57

## 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,
};
pappso::QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexBegin
@ TimsFrameIonMobScanIndexBegin
Definition qualifiedmassspectrum.h:55
pappso::QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexEnd
@ TimsFrameIonMobScanIndexEnd
Definition qualifiedmassspectrum.h:56
pappso::MsRunReadConfigParameter::MzRangeBegin
@ MzRangeBegin
Definition msrunreadconfig.h:49
pappso::MsRunReadConfigParameter::TimsFrameIonMobOneOverK0Begin
@ TimsFrameIonMobOneOverK0Begin
Definition msrunreadconfig.h:44
pappso::MsRunReadConfigParameter::TimsFrameIonMobOneOverK0End
@ TimsFrameIonMobOneOverK0End
Definition msrunreadconfig.h:45
pappso::MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow
@ TimsFrameMzIndexMergeWindow
Definition msrunreadconfig.h:54
pappso::MsRunReadConfigParameter::MzRangeEnd
@ MzRangeEnd
Definition msrunreadconfig.h:50

## 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
};
pappso::MsRunXicExtractorFactoryType::diskbuffer
@ diskbuffer
Definition msrunxicextractorfactory.h:55
pappso::MsRunXicExtractorFactoryType::nose
@ nose
default factory
Definition msrunxicextractorfactory.h:47
pappso::MsRunXicExtractorFactoryType::disk
@ disk
Definition msrunxicextractorfactory.h:51
pappso::MsRunXicExtractorFactoryType::direct
@ direct
Definition msrunxicextractorfactory.h:48

## PeptideDirection

enum class pappso::PeptideDirection : std::int8_t

strong

Enumerator
Nter |
Cter |

Definition at line 46 of file peptide.h.

{
Nter = 0,
Cter = 1
};
pappso::PeptideDirection::Cter
@ Cter
Definition peptide.h:49
pappso::PeptideDirection::Nter
@ Nter
Definition peptide.h:48

## 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
};
pappso::PeptideIonCter::y
@ y
Definition peptide.h:87
pappso::PeptideIonCter::yp
@ yp
Definition peptide.h:91
pappso::PeptideIonCter::ystar
@ ystar
Definition peptide.h:88
pappso::PeptideIonCter::yo
@ yo
Definition peptide.h:89
pappso::PeptideIonCter::x
@ x
Definition peptide.h:92
pappso::PeptideIonCter::z
@ z
Definition peptide.h:90

## 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
};
pappso::masschroq::PeakQualityCategory::a
@ a
peak detected using a single direct MS2 observation
Definition types.h:46
pappso::masschroq::PeakQualityCategory::c
@ c
Definition types.h:54
pappso::masschroq::PeakQualityCategory::b
@ b
Definition types.h:52
pappso::PeptideIonNter::astar
@ astar
Definition peptide.h:78
pappso::PeptideIonNter::bp
@ bp
Definition peptide.h:80
pappso::PeptideIonNter::bstar
@ bstar
Definition peptide.h:75
pappso::PeptideIonNter::bo
@ bo
Definition peptide.h:76
pappso::PeptideIonNter::ao
@ ao
Definition peptide.h:79

## 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,
};
pappso::PointSpec::BOTTOM_RIGHT_POINT
@ BOTTOM_RIGHT_POINT
Definition selectionpolygon.h:28
pappso::PointSpec::TOP_LEFT_POINT
@ TOP_LEFT_POINT
Definition selectionpolygon.h:26
pappso::PointSpec::BOTTOM_LEFT_POINT
@ BOTTOM_LEFT_POINT
Definition selectionpolygon.h:29
pappso::PointSpec::ENUM_LAST
@ ENUM_LAST
Definition selectionpolygon.h:30
pappso::PointSpec::TOP_RIGHT_POINT
@ TOP_RIGHT_POINT
Definition selectionpolygon.h:27

## 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
};
pappso::ProjectParamCategory::identification
@ identification
concerning identification
Definition projectparameters.h:47
pappso::ProjectParamCategory::instrument
@ instrument
information about instrument
Definition projectparameters.h:50
pappso::ProjectParamCategory::undefined
@ undefined
undefined
Definition projectparameters.h:45
pappso::ProjectParamCategory::general
@ general
concerning the whole process
Definition projectparameters.h:46
pappso::ProjectParamCategory::quantification
@ quantification
quantification
Definition projectparameters.h:49
pappso::ProjectParamCategory::filter
@ filter
concerning filters (psm, peptide, protein validation)
Definition projectparameters.h:48

## 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
};
pappso::QualifiedMassSpectrumParameter::IsolationMzWidth
@ IsolationMzWidth
m/z isolation window width (left + right)
Definition qualifiedmassspectrum.h:59
pappso::QualifiedMassSpectrumParameter::TimsIonMobScanIndex
@ TimsIonMobScanIndex
Definition qualifiedmassspectrum.h:54
pappso::QualifiedMassSpectrumParameter::ScanNumber
@ ScanNumber
Definition qualifiedmassspectrum.h:68
pappso::QualifiedMassSpectrumParameter::TimsFrameMzIndexBegin
@ TimsFrameMzIndexBegin
Bruker's timsTOF mz index frame start range.
Definition qualifiedmassspectrum.h:65
pappso::QualifiedMassSpectrumParameter::CollisionEnergy
@ CollisionEnergy
Bruker's timsTOF collision energy.
Definition qualifiedmassspectrum.h:61
pappso::QualifiedMassSpectrumParameter::IonMobOneOverK0Begin
@ IonMobOneOverK0Begin
1/K0 range's begin value
Definition qualifiedmassspectrum.h:51
pappso::QualifiedMassSpectrumParameter::IonMobOneOverK0End
@ IonMobOneOverK0End
1/K0 range's end value
Definition qualifiedmassspectrum.h:52
pappso::QualifiedMassSpectrumParameter::IsolationMz
@ IsolationMz
Isolation m/z value.
Definition qualifiedmassspectrum.h:58
pappso::QualifiedMassSpectrumParameter::TimsFrameScansCount
@ TimsFrameScansCount
Bruker's timsTOF frame's total ion mobility slots.
Definition qualifiedmassspectrum.h:63
pappso::QualifiedMassSpectrumParameter::TimsFrameMzIndexEnd
@ TimsFrameMzIndexEnd
Bruker's timsTOF mz index frame end range.
Definition qualifiedmassspectrum.h:66
pappso::QualifiedMassSpectrumParameter::BrukerPrecursorIndex
@ BrukerPrecursorIndex
Bruker's timsTOF precursor index.
Definition qualifiedmassspectrum.h:62
pappso::QualifiedMassSpectrumParameter::IonMobOneOverK0
@ IonMobOneOverK0
1/kO value
Definition qualifiedmassspectrum.h:50

## RangeType

enum class pappso::RangeType

strong

Enumerator
outermost |
innermost |

Definition at line 72 of file baseplotwidget.h.

{
outermost = 1,
innermost = 2,
};
pappso::RangeType::innermost
@ innermost
Definition baseplotwidget.h:75
pappso::RangeType::outermost
@ outermost
Definition baseplotwidget.h:74

## 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
};
pappso::RawFragmentationMode::full
@ full
Definition peptiderawfragmentmasses.h:44
pappso::RawFragmentationMode::proline_effect
@ proline_effect
Definition peptiderawfragmentmasses.h:45

## 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)
};
pappso::SelectionDrawingLines::VERTICAL_LINES
@ VERTICAL_LINES
Definition baseplotwidget.h:67
pappso::SelectionDrawingLines::FULL_POLYGON
@ FULL_POLYGON
Definition baseplotwidget.h:69
pappso::SelectionDrawingLines::TOP_LINE
@ TOP_LINE
Definition baseplotwidget.h:59
pappso::SelectionDrawingLines::BOTTOM_LINE
@ BOTTOM_LINE
Definition baseplotwidget.h:60
pappso::SelectionDrawingLines::HORIZONTAL_LINES
@ HORIZONTAL_LINES
Definition baseplotwidget.h:62

## 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
};
pappso::XicCoordParam::TimsTofIonMobilityScanNumberStart
@ TimsTofIonMobilityScanNumberStart
Definition xiccoord.h:52
pappso::XicCoordParam::TimsTofIonMobilityScanNumberStop
@ TimsTofIonMobilityScanNumberStop
Definition xiccoord.h:54

## 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;
}
pappso::combinations_cache
uint64_t combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:44
CACHE_ARRAY_SIZE
#define CACHE_ARRAY_SIZE
Definition peptidenaturalisotope.cpp:42

References CACHE_ARRAY_SIZE, and combinations_cache.

Referenced by isotopem_ratio().

## DIFFC12C13()

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

Referenced by pappso::FilterChargeDeconvolution::FilterChargeDeconvolution(), pappso::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(); });
}
pappso::TracePeak
Definition tracepeak.h:40
pappso::PeptideIonNter::a
@ a
Definition peptide.h:77
pappso::PeptideIonNter::b
@ b
Definition peptide.h:74

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;
});
}
pappso::PeakIonIsotopeMatch
Definition peakionisotopematch.h:47
pappso::PeakIonIsotopeMatch::getPeptideNaturalIsotopeAverageSp
virtual const PeptideNaturalIsotopeAverageSp & getPeptideNaturalIsotopeAverageSp() const
Definition peakionisotopematch.cpp:85
pappso::PeakIonMatch::getPeptideFragmentIonSp
virtual const PeptideFragmentIonSp & getPeptideFragmentIonSp() const
Definition peakionmatch.cpp:68
pappso::PeakIonMatch::getPeptideIonType
Enums::PeptideIon getPeptideIonType() const
Definition peakionmatch.cpp:86
pappso::PeakIonMatch::getCharge
unsigned int getCharge() const
Definition peakionmatch.cpp:80
pappso::PeptideFragmentIon::size
virtual unsigned int size() const override
Definition peptidefragmention.cpp:538
pappso::PeptideNaturalIsotopeAverage::getIsotopeNumber
unsigned int getIsotopeNumber() const
Definition peptidenaturalisotopeaverage.cpp:210
pappso::peptideIonTypeIsComplement
bool peptideIonTypeIsComplement(Enums::PeptideIon ion_type_ref, Enums::PeptideIon ion_type)
tells if an ion type is the complement ion of the other
Definition peptide.cpp:70

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;
});
}
pappso::DataPoint
Definition datapoint.h:22
pappso::DataPoint::y
pappso_double y
Definition datapoint.h:25

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;
});
}
pappso::DataPoint::x
pappso_double x
Definition datapoint.h:24

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;
}
pappso::Trace
A simple container of DataPoint instances.
Definition trace.h:152
pappso::Trace::maxYDataPoint
const DataPoint & maxYDataPoint() const
Definition trace.cpp:966

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;
}
pappso::MzIntegrationParams::BinningType::NONE
@ NONE
< no binning
Definition mzintegrationparams.h:111
pappso::binningTypeMap
std::map< MzIntegrationParams::BinningType, QString > binningTypeMap
Map relating the BinningType to a textual representation.
Definition mzintegrationparams.cpp:62

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;
}
pappso::PeptideNaturalIsotopeAverage
Definition peptidenaturalisotopeaverage.h:43
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:60
pappso::PeptideNaturalIsotopeAverageSp
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp
Definition peptidenaturalisotopeaverage.h:40

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;
}
pappso::RegisterFunc
std::function< void(QJSEngine *)> RegisterFunc
Definition jsclassregistrar.h:50
pappso::NamespaceClassnamePairAsKey
std::pair< QString, QString > NamespaceClassnamePairAsKey
Definition jsclassregistrar.h:49
pappso::AreNamespaceClassnamePairsEqual
Definition jsclassregistrar.h:65
pappso::NamespaceClassnameAsKeyHash
Definition jsclassregistrar.h:54

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;
}
pappso::peptideIonIsNter
bool peptideIonIsNter(Enums::PeptideIon ion_type)
tells if an ion is Nter
Definition peptide.cpp:87

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;
}
pappso::Trace::append
size_t append(const DataPoint &data_point)
appends a datapoint and return new size
Definition trace.cpp:657

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));
}
pappso::Combinations
uint64_t Combinations(unsigned int n, unsigned int k)
Definition peptidenaturalisotope.cpp:47

References Combinations().

Referenced by isotopem_ratio_cache().

## isotopem_ratio_cache()

pappso_double pappso::isotopem_ratio_cache | ( | 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);
}
pappso::Enums::Isotope::S36
@ S36
Definition types.h:139
pappso::Enums::Isotope::C13
@ C13
Definition types.h:128
pappso::Enums::Isotope::N15
@ N15
Definition types.h:135
pappso::Enums::Isotope::S33
@ S33
Definition types.h:137
pappso::Enums::Isotope::O18
@ O18
Definition types.h:133
pappso::Enums::Isotope::O17
@ O17
Definition types.h:132
pappso::Enums::Isotope::S34
@ S34
Definition types.h:138
pappso::Enums::Isotope::H2
@ H2
Definition types.h:130
pappso::ratioO17_cache
pappso_double ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:90
pappso::ABUNDANCES36
const pappso_double ABUNDANCES36(0.00010999120070394368536836893213148869108408689498901367187500)
pappso::ratioS34_cache
pappso_double ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:88
pappso::ABUNDANCEN15
const pappso_double ABUNDANCEN15(0.00364198543205827118818262988497735932469367980957031250000000)
pappso::ratioC13_cache
pappso_double ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:85
pappso::isotopem_ratio
pappso_double isotopem_ratio(pappso_double abundance, unsigned int total, unsigned int heavy)
Definition peptidenaturalisotope.cpp:79
pappso::ratioH2_cache
pappso_double ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:92
pappso::ABUNDANCEC13
const pappso_double ABUNDANCEC13(0.01078805814953308406245469086570665240287780761718750000000000)
pappso::ABUNDANCEO17
const pappso_double ABUNDANCEO17(0.00038099847600609595965615028489992255344986915588378906250000)
pappso::ABUNDANCEH2
const pappso_double ABUNDANCEH2(0.00011570983569203332000374651045149221317842602729797363281250)
pappso::ratioO18_cache
pappso_double ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:91
pappso::ABUNDANCES34
const pappso_double ABUNDANCES34(0.04252059835213182203972337447339668869972229003906250000000000)
pappso::ratioS36_cache
pappso_double ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:87
pappso::ABUNDANCEO18
const pappso_double ABUNDANCEO18(0.00205139179443282221315669744399201590567827224731445312500000)
pappso::ABUNDANCES33
const pappso_double ABUNDANCES33(0.00751939844812414937003097747947322204709053039550781250000000)
pappso::ratioN15_cache
pappso_double ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:86
pappso::ratioS33_cache
pappso_double ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
Definition peptidenaturalisotope.cpp:89

References ABUNDANCEC13(), ABUNDANCEH2(), ABUNDANCEN15(), ABUNDANCEO17(), ABUNDANCEO18(), ABUNDANCES33(), ABUNDANCES34(), ABUNDANCES36(), 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);
}
pappso::ExceptionOutOfRange
Definition exceptionoutofrange.h:32
pappso::sumYTrace
double sumYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
calculate the sum of y value of a trace
Definition trace.cpp:226

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));
}
pappso::MzIntegrationParams::InitializationResult
InitializationResult
Definition mzintegrationparams.h:124

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);
}
pappso::Peptide::m_aaVec
std::vector< Aa > m_aaVec
Definition peptide.h:266

## 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);
}
pappso::Peptide::getCterModification
AaModificationP getCterModification() const
Definition peptide.cpp:680
pappso::Peptide::getCleavageCterModification
AaModificationP getCleavageCterModification() const
Definition peptide.cpp:643
pappso::Peptide::getNterModification
AaModificationP getNterModification() const
Definition peptide.cpp:686
pappso::Peptide::getCleavageNterModification
AaModificationP getCleavageNterModification() const
Definition peptide.cpp:638

## 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;
}
pappso::PappsoException
Definition pappsoexception.h:41

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;
}
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition massspectrum.h:70
pappso::MsRunSlice::setSpectrum
void setSpectrum(std::size_t i, const MassSpectrum &spectrum)
set the mass spectrum for a given index (retention time)
Definition msrunslice.cpp:93
pappso::MsRunSlice::setSliceNumber
void setSliceNumber(unsigned int slice_number)
Definition msrunslice.cpp:63
pappso::MsRunSlice::setSize
void setSize(std::size_t size)
set number of spectrum (mz/intensity) stored in this slice
Definition msrunslice.cpp:81
pappso::MsRunSlice::size
std::size_t size() const
Definition msrunslice.cpp:75

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;
}
pappso::Enums::PeptideIon::y
@ y
Cter amino ions.
Definition types.h:295
pappso::Enums::PeptideIon::ystar
@ ystar
Cter amino ions + NH3 loss.
Definition types.h:296
pappso::Enums::PeptideIon::yo
@ yo
Cter amino ions + H2O loss.
Definition types.h:297
pappso::Enums::PeptideIon::bstar
@ bstar
Nter acylium ions + NH3 loss.
Definition types.h:288
pappso::Enums::PeptideIon::b
@ b
Nter acylium ions.
Definition types.h:287
pappso::Enums::PeptideIon::ao
@ ao
Nter aldimine ions + H2O loss.
Definition types.h:292

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);
}
}
pappso::getNameSpaceClassNameJsConstructorRegistrarMap
std::unordered_map< NamespaceClassnamePairAsKey, RegisterFunc, NamespaceClassnameAsKeyHash, AreNamespaceClassnamePairsEqual > & getNameSpaceClassNameJsConstructorRegistrarMap()
Definition jsclassregistrar.cpp:10

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;
}
pappso::CubicSplineModel::derivative
double derivative(const double x_value) const
Definition cubicsplinemodel.cpp:197
pappso::CubicSplineModel::evalSplineAt
double evalSplineAt(double x_value) const
Definition cubicsplinemodel.cpp:169

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"}}
pappso::MzIntegrationParams::BinningType::DATA_BASED
@ DATA_BASED
binning based on mass spectral data
Definition mzintegrationparams.h:114
pappso::MzIntegrationParams::BinningType::ARBITRARY
@ ARBITRARY
binning based on arbitrary bin size value
Definition mzintegrationparams.h:117

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"}}
pappso::Enums::DataKind::dt
@ dt
Drift time.
Definition types.h:252
pappso::Enums::DataKind::mz
@ mz
m/z
Definition types.h:253
pappso::Enums::DataKind::rt
@ rt
Retention time.
Definition types.h:251
pappso::Enums::DataKind::unset
@ unset
not set
Definition types.h:250

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"}}
pappso::Enums::PrecisionUnit::none
@ none
Definition types.h:97
pappso::Enums::PrecisionUnit::mz
@ mz
Definition types.h:101
pappso::Enums::PrecisionUnit::res
@ res
Definition types.h:100
pappso::Enums::PrecisionUnit::ppm
@ ppm
Definition types.h:99
pappso::Enums::PrecisionUnit::dalton
@ dalton
Definition types.h:98

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().