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Class List
Here are the classes, structs, unions and interfaces with brief descriptions:

pappso | Tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge
masschroq |
AlignmentMethod |
JsonInput |
PrecursorParser |
MbrPeptideMeasurements |
MsRun |
MsRunGroup |
MsRunPeptideList |
CborOutputStream |
Peptide |
AlignedPeakPositionElement | Internal structure to compute consensus retention times
MsRunXicCoordCharge | Internal structure to store msrun + charge + intensity + xic coordinate
PeptideBase |
PeptideLabel |
PeptideMeasurements |
PeptideMeasurementsBase |
Measurement |
PeptideObservation |
Observation |
Precursor | A Precursor object represents the parent/precursor of the MS level 2 scan with number _scan_num in the mzxml file
Protein |
QuantificationMethod |
Utils |
cbor |
mzcbor |
BinaryDataArray |
ConvertToMzml |
CvParam |
CvParamMap |
MzcborBuildIndexReader |
MzcborIndexReader |
MzcborReaderBase | Base class to initialize mzCBOR file parsing
MzcborSpectrumCollectionReader |
MzmlConvert |
IsolationWindow |
SelectedIon |
Precursor |
Scan |
Spectrum |
psm |
CborScanMapBase |
PsmFeatures |
PsmFeaturesScan |
PsmIonSeries | Computes spectrum isotope match for each PSM and stores ion series in "props"
PsmIonSeriesScan |
PsmNewEval |
PsmSpecGlob |
PsmSpecGlobScan |
PsmSpecPeptidOms |
PsmSpecPeptidOmsScan |
MzIdentMlReader |
CvParam |
Modification |
MzidDBSequence |
MzidSearchDatabase |
MzidSpectraData |
MzidPeptideEvidence |
UserParam |
SpectrumIdentificationItem |
SpectrumIdentificationResult |
PsmCbor2Json |
PsmCborUtils | Utilities to help managing data in PSM CBOR data file
PsmProteinRef |
PsmFileAppend |
SampleStorage |
PsmFile |
PsmFileReaderBase |
PsmProteinRef |
PsmFileScanProcess | Basic PSM file reader to process scan (parallelized scan processing)
PsmFileScanProcessAndCopy | Basic PSM file reader to process scan (parallelized scan processing) and write a new resulting PSM file
PsmProtein |
PsmProteinMap | Store PsmProtein in a map with accession as key
SageFileReader |
SageReader |
SageModification |
FastaSeq |
SageTsvHandler |
Line |
Psm |
Scan |
Sample |
CborStreamReader | Simple override of the raw QCborStreamReader This adds convenient functions to put CBOR data into C++ structures
CborStreamReaderInterface | Base class to start a CBOR reader
CborStreamWriter | Overrides QCborStreamWriter base class to provide convenient functions
JsonStreamWriter | Helper class to write json text using CBOR data structures
specglob |
ExperimentalSpectrumDataPoint |
ExperimentalSpectrum |
AminoAcidModel |
TheoreticalPeakDataPoint |
PeptideModel |
PeptideSpectrumDataPoint |
PeptideSpectrum |
PostTreatment |
ScoreValues |
SpectralAlignmentDataPoint |
SpectralAlignment |
specpeptidoms |
CorrectionTree |
Location |
LocationSaver |
AminoAcidModel |
PeptideModel | Modelize peptide sequence to facilitate rendering in bracket or proforma
ScenarioCell |
Scenario |
ScoreValues |
KeyCell |
Alignment |
SemiGlobalAlignment |
SpOMSAa |
SpOMSProtein |
AaPosition |
SpOMSSpectrum |
specself |
SelfSpectrum |
SelfSpectrumDataPoint |
spectree |
Bucket |
BucketClustering |
ItemCart | Container for spectree items
SpecTree |
SpecTreeNode |
MapSimilarityCountElement |
MapSimilarityCount |
SpecXtractInterface | Yield similarities between pairs of ItemCart
SpecXtractMap | Store all similarities in vectors an map : very costly for memory and CPU
Aa |
AaBase |
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
AaModification |
CodeToMass |
AaStringCodec | Code and decode amino acid string sequence to unique integer
AaStringCodeMassMatching | Convert a list of mass to amino acid string codes
aaCodeAndMassRange |
AtomNumberInterface |
IsotopeCount |
ChemicalFormula |
ExceptionInterrupted |
ExceptionNotFound |
ExceptionNotImplemented |
ExceptionNotPossible |
ExceptionNotRecognized | Excetion to use when an item type is not recognized
ExceptionOutOfRange |
FastaFileIndexerInterface |
FastaFileIndexer |
FastaHandlerInterface |
FastaSeqHandler |
FastaOutputStream |
FastaReader |
FastaWriterInterface |
GrpExperiment |
GrpGroup |
GrpGroupingMonitorInterface |
GrpGroupingMonitor |
GrpMapPeptideToGroup |
GrpMapPeptideToSubGroupSet |
GrpPeptide |
GrpPeptideSet |
GrpProtein |
GrpSubGroup |
GrpSubGroupSet |
DataPointJs |
NamespaceClassnameAsKeyHash |
AreNamespaceClassnamePairsEqual |
MassSpectrumJs | JavaScript wrapper around MassSpectrum
QPointFJs |
TraceJs |
MassSpectrum | Class to represent a mass spectrum
MassSpectrumId |
PrecursorIonData |
QualifiedMassSpectrum | Class representing a fully specified mass spectrum
BafAsciiFileReader |
MsFileAccessor |
MsFileReader |
MzcborMsFileReader |
MsDataFormatEnumStr | Static functions to convert mz file formats
PwizMsFileReader |
TimsMsFileReader |
XyMsFileReader |
MsRunRetentionTimeSeamarkPoint |
MsRunRetentionTime |
PeptideMs2Point |
MassSpectrumLineData |
BafAsciiMsRunReader |
MsRunDataSetTree |
MsRunDataSetTreeNode |
MsRunDataSetTreeNodeVisitorInterface |
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)
MsRunReadConfig |
MsRunReader | Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
MgfOutput |
MzxmlOutput |
Translater |
MzcborMsRunReader |
PwizMsRunReader |
TimsFramesMsRunReader |
TimsMsRunReader |
TimsMsRunReaderBase |
TimsMsRunReaderDia |
TimsMsRunReaderMs2 |
TimsMsRunReaderMs2Selected |
SpectrumCollectionHandlerInterface | Interface to collect spectrums from the MsRunReader class
MsRunSimpleStatistics | Example of interface to count MS levels of all spectrum in an MSrun
MsRunReaderScanNumberMultiMap | Multimap to find quickly spectrum index from scan number
MsRunReaderRetentionTimeLine | Collect retention times along MS run
MsRunReaderTicChromatogram | Calculate a TIC chromatogram
MsRunQualifiedSpectrumLoader | Load all qualified spectrum into a vector
IonMobilityGrid |
XicCoord | Coordinates of the XIC to extract and the resulting XIC after extraction
XicCoordTims | Coordinates of the XIC to extract and the resulting XIC after extraction
XyMsRunReader |
MzRange |
FilterOboPsiModMap |
FilterOboPsiModSink |
FilterOboPsiModTermAccession |
FilterOboPsiModTermDiffMono |
FilterOboPsiModTermLabel |
FilterOboPsiModTermName |
OboPsiMod |
OboPsiModHandlerInterface |
OboPsiModTerm |
OboPsiMs |
OboUnimod |
PappsoException |
Ion |
Peptide |
PeptideFragment |
PeptideFragmentIon |
PeptideFragmentIonListBase |
PeptideInterface |
PeptideNaturalIsotope |
PeptideNaturalIsotopeAverage |
PeptideNaturalIsotopeList |
PeptideProFormaParser |
SimplePeakIonMatch |
PeptideRawFragmentMasses |
PeptideStrParser |
PrecisionBase |
DaltonPrecision |
PpmPrecision |
ResPrecision |
PrecisionFactory |
IntegrationScope |
IntegrationScopeBase |
IntegrationScopeSpec |
IntegrationScopeRect |
IntegrationScopeRhomb |
MassDataCombinerInterface |
MassSpectrumCombiner |
MassSpectrumMinusCombiner |
MassSpectrumPlusCombiner |
MzIntegrationParams | Parameters definining how m/z integrations must be performed
SelectionPolygon |
SelectionPolygonSpec |
TraceCombiner |
TraceMinusCombiner |
TracePlusCombiner |
CosineSimilarity |
CubicSplineModel |
HighResPeakPicker |
Parameters |
PeakRange |
LocalSignalToNoiseEstimator |
Parameters |
GaussianEstimateParams |
TraceDetectionSinkInterface |
TraceDetectionInterface |
TraceDetectionMoulon |
TraceDetectionZivy |
TracePeak |
TracePeakList |
FilterCeilingAmplitudePercentage | Redefines the ceiling intensity of the Trace
FilterChargeDeconvolution |
DataPointInfo |
FilterComplementIonEnhancer | Try to detect complementary ions and assign maximum intensity of both elements
FilterMzExclusion |
FilterFloorAmplitudePercentage | Redefines the floor intensity of the Trace
FilterInterface | Generic interface to apply a filter on a trace
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
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
FilterLowIntensitySignalRemoval | Redefines the floor intensity of the Trace
FilterMorphoWindowBase | Base class that apply a signal treatment based on a window
FilterMorphoSum | Test purpose
FilterMorphoMax | Transform the trace into its maximum over a window
FilterMorphoMin | Transform the trace into its minimum over a window
FilterMorphoMinMax | Transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures
FilterMorphoMaxMin | Transform the trace with the maximum of the minimum equivalent of the erode filter for pictures
FilterMorphoAntiSpike | Anti spike filter set to zero alone values inside the window
FilterMorphoMedian | Median filter apply median of y values inside the window
FilterMorphoMean | Mean filter apply mean of y values inside the window : this results in a kind of smoothing
FilterMorphoBackground | Compute background of a trace compute background noise on a trace
FilterNameInterface | Interface that allows to build filter objects from strings
FilterNormalizeIntensities | Sets the maximum intensity of the trace to the provided value
FilterLowPass | Remove datapoints higher or equal to a given Y value (intensity)
FilterHighPass | Remove datapoints below or equal to the given Y value (intensity)
FilterHighPassPercentage | Remove datapoints below a given intensity percentage (ratio) of the maximum intensity
FilterGreatestY | Keep N datapoints form the greatest intensities to the lowest
FilterGreatestYperWindow | Keep N datapoints form the greatest intensities to the lowest within a mass range in dalton
MassSpectrumFilterGreatestItensities |
FilterFloorY | Apply std::floor (round to lowest integer) to all Y values
FilterRoundY | Apply std::round (round to nearest integer) to all Y values
FilterRescaleY | Rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored
FilterScaleFactorY | Rescales Y values given a tranformation factor
FilterRemoveY | Removes a value to all Y values
FilterQuantileBasedRemoveY | Removes a value found by quantile to all Y values
FilterPeakDelta |
FilterRemoveC13 |
FilterResampleKeepSmaller |
FilterResampleKeepGreater |
FilterResampleRemoveXRange |
FilterResampleKeepXRange |
FilterResampleKeepPointInPolygon |
MassSpectrumFilterResampleRemoveMzRange |
MassSpectrumFilterResampleKeepMzRange |
FilterSuite | Apply a suite of filters from a vector
FilterSuiteString |
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:
FilterTriangle |
SavGolParams | Parameters for the Savitzky-Golay filter
FilterSavitzkyGolay | Uses Savitsky-Golay filter on trace
ProjectParam |
ProjectParameters |
XtandemError |
TandemWrapperRun |
WrapTandemInput |
WrapTandemResults |
XtandemPresetReader |
UiMonitorInterface |
UiMonitorText |
UiMonitorTextPercent |
UiMonitorVoid |
MzIdentMlWriter |
XmlStreamReaderInterface | Convenient xml reader helper
Enzyme |
EnzymeProductInterface |
PeptideModificatorInterface |
PeptideSinkInterface |
PeptideSpSinkInterface |
PeptideBuilder | Builds a peptide shared pointer from peptide string and adds fixed modifications
PeptideFixedModificationBuilder |
PeptideMethioninRemove | Potential remove Nter Methionin
PeptideModificatorBase |
PeptideModificatorPipeline |
PeptideModificatorTee |
PeptideSemiEnzyme | Cut a regular peptide obtained with an enzyme at any position from Nter or Cter
PeptideSizeFilter | Filter peptide string by size
PeptideVariableModificationBuilder | Modify a peptide shared pointer with a variable modification on one AA
PeptideVariableModificationReplacement |
Protein |
ProteinIntegerCode |
ProteinPresenceAbsenceMatrix |
DeepProtEnumStr |
IonIsotopeRatioScore |
PsmFeatures |
MorpheusScore |
PeakIonIsotopeMatch |
PeakIonMatch |
PeptideIsotopeSpectrumMatch |
PeptideSpectrumMatch |
XtandemHyperscore |
XtandemHyperscoreBis |
XtandemSpectrumProcess |
DataPoint |
LinearRegression |
MapTrace |
Trace | A simple container of DataPoint instances
Utils |
TimsFrameMobilityTraces |
MzCalibrationInterface |
MzCalibrationModel1 |
MzCalibrationModel1Cached |
MzCalibrationStore |
TimsBinDec |
FrameIdDescr |
TimsData |
TimsDataFastMap | Replacement for std::map
TimsDataFastMapElement |
TimsDdaPrecursors |
SpectrumDescr |
TimsDiaSlices |
MsMsWindow |
MsMsWindowGroup |
MsMsWindowGroupList |
FrameSliceRange |
TimsFrame |
XicComputeStructure |
TimsFrameBase |
TofIndexIntensityPair |
TimsFrameRawDataChunck |
TimsFrameRecord |
TimsFrameType1 |
TimsMs2CentroidFilter |
TimsDirectXicExtractor |
TimsXicExtractorInterface |
QualifiedXic |
Xic |
XicPeptideFragmentIon |
XicPeptideFragmentIonNaturalIsotope |
XicPeptideInterface |
MsRunXicExtractorFactory | Factory to build different kinds of XIC extractors
MsRunXicExtractorInterface |
MsRunSlice |
MsRunXicExtractor |
MsRunXicExtractorPoints |
MsRunXicExtractorReadPoints | Class to read retention time points of MsRun
MsRunXicExtractorDisk |
MsRunXicExtractorDiskBuffer |
HttpButton |
MassSpectrumWidget |
QCPSpectrum |
OboChooserWidget |
OboListModel |
OboPsiModHandler |
OboListProxyModel |
OboListWidget |
OboTermForm |
BaseColorMapPlotWidget |
BasePlotContext |
BasePlotWidget |
BaseTracePlotWidget |
ColorMapPlotConfig |
DriftSpecMassSpecColorMapPlotWidget |
DriftSpecTracePlotWidget |
MassSpecTracePlotContext |
MassSpecTracePlotWidget |
TicXicChromDriftSpecColorMapPlotWidget |
TicXicChromMassSpecColorMapPlotWidget |
TicXicChromTracePlotWidget |
PrecisionWidget |
SwitchWidget |
QCPXic |
XicWidget |
ContainsAny |
GraphicDeviceWidget |
InHousePolynomialSolverResult |
ProteinPeptideList |