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Namespace List
Here is a list of all namespaces with brief descriptions:

pappso | Tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge
specglob |
AminoAcidModel |
ExperimentalSpectrum |
ExperimentalSpectrumDataPoint |
PeptideModel |
PeptideSpectrum |
PeptideSpectrumDataPoint |
PostTreatment |
ScoreValues |
SpectralAlignment |
SpectralAlignmentDataPoint |
TheoreticalPeakDataPoint |
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 |
AaStringCodec |
AaStringCodeMassMatching |
aaCodeAndMassRange |
AtomNumberInterface |
BaseColorMapPlotWidget |
BasePlotContext |
BasePlotWidget |
BaseTracePlotWidget |
CodeToMass |
ColorMapPlotConfig |
CosineSimilarity |
DaltonPrecision |
DataPoint |
DeepProtEnumStr |
DriftSpecMassSpecColorMapPlotWidget |
DriftSpecTracePlotWidget |
Enzyme |
EnzymeProductInterface |
ExceptionInterrupted |
ExceptionNotFound |
ExceptionNotImplemented |
ExceptionNotPossible |
ExceptionNotRecognized | Excetion to use when an item type is not recognized
ExceptionOutOfRange |
FastaFileIndexer |
FastaFileIndexerInterface |
FastaHandlerInterface |
FastaOutputStream |
FastaReader |
FastaWriterInterface |
FilterCeilingAmplitudePercentage | Redefines the ceiling intensity of the Trace
FilterChargeDeconvolution |
DataPointInfo |
FilterComplementIonEnhancer | Try to detect complementary ions and assign maximum intensity of both elements
FilterFloorAmplitudePercentage | Redefines the floor intensity of the Trace
FilterFloorY | Apply std::floor (round to lowest integer) to all Y values
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
FilterHighPass | Remove datapoints below a given Y value (intensity)
FilterHighPassPercentage | Remove datapoints below a given intensity percentage (ratio) of the maximum intensity
FilterInterface | Generic interface to apply a filter on a 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
FilterLowPass | Remove datapoints higher than a given Y value (intensity)
FilterMorphoAntiSpike | Anti spike filter set to zero alone values inside the window
FilterMorphoBackground | Compute background of a trace compute background noise on a trace
FilterMorphoMax | Transform the trace into its maximum over a window
FilterMorphoMaxMin | Transform the trace with the maximum of the minimum equivalent of the erode filter for pictures
FilterMorphoMean | Mean filter apply mean of y values inside the window : this results in a kind of smoothing
FilterMorphoMedian | Median filter apply median of y values inside the 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
FilterMorphoSum | Test purpose
FilterMorphoWindowBase | Base class that apply a signal treatment based on a window
FilterMzExclusion |
FilterNameInterface | Interface that allows to build filter objects from strings
FilterNormalizeIntensities | Sets the maximum intensity of the trace to the provided value
FilterOboPsiModSink |
FilterOboPsiModTermAccession |
FilterOboPsiModTermDiffMono |
FilterOboPsiModTermLabel |
FilterOboPsiModTermName |
FilterPeakDelta |
FilterQuantileBasedRemoveY | Removes a value found by quantile to all Y values
FilterRemoveC13 |
FilterRemoveY | Removes a value to all Y values
FilterResampleKeepGreater |
FilterResampleKeepPointInPolygon |
FilterResampleKeepSmaller |
FilterResampleKeepXRange |
FilterResampleRemoveXRange |
FilterRescaleY | Rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored
FilterRoundY | Apply std::round (round to nearest integer) to all Y values
FilterSavitzkyGolay | Uses Savitsky-Golay filter on trace
FilterScaleFactorY | Rescales Y values given a tranformation factor
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 |
FrameIdDescr |
GrpExperiment |
GrpGroup |
GrpGroupingMonitor |
GrpGroupingMonitorInterface |
GrpMapPeptideToGroup |
GrpMapPeptideToSubGroupSet |
GrpPeptide |
GrpPeptideSet |
GrpProtein |
GrpSubGroup |
GrpSubGroupSet |
HttpButton |
Ion |
IonIsotopeRatioScore |
IonMobilityGrid |
LinearRegression |
MapTrace |
MassDataCombinerInterface |
MassSpecTracePlotContext |
MassSpecTracePlotWidget |
MassSpectrum | Class to represent a mass spectrum
MassSpectrumCombiner |
MassSpectrumFilterGreatestItensities |
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
MassSpectrumFilterResampleKeepMzRange |
MassSpectrumFilterResampleRemoveMzRange |
MassSpectrumId |
MassSpectrumMinusCombiner |
MassSpectrumPlusCombiner |
MassSpectrumWidget |
MgfOutput |
MorpheusScore |
MsFileAccessor |
MsFileReader |
MsRunAlignment |
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
MsRunReaderQualifiedSpectrumList | Store all qualified spectrum into a vector
MsRunReaderRetentionTimeLine | Collect retention times along MS run
MsRunReaderScanNumberMultiMap | Multimap to find quickly spectrum index from scan number
MsRunReaderTicChromatogram | Calculate a TIC chromatogram
MsRunRetentionTime |
PeptideMs2Point |
MsRunRetentionTimeSeamarkPoint |
MsRunSimpleStatistics | Example of interface to count MS levels of all spectrum in an MSrun
MsRunSlice |
MsRunXicExtractor |
MsRunXicExtractorPoints |
MsRunXicExtractorReadPoints | Class to read retention time points of MsRun
MsRunXicExtractorDisk |
MsRunXicExtractorDiskBuffer |
MsRunXicExtractorFactory | Factory to build different kinds of XIC extractors
MsRunXicExtractorInterface |
MzCalibrationInterface |
MzCalibrationModel1 |
MzCalibrationModel1Cached |
MzCalibrationStore |
MzFormatEnumStr | Static functions to convert mz file formats
MzIntegrationParams | Parameters definining how m/z !
MzRange |
MzxmlOutput |
Translater |
OboChooserWidget |
OboListModel |
OboPsiModHandler |
OboListProxyModel |
OboListWidget |
OboPsiMod |
OboPsiModHandlerInterface |
OboPsiModTerm |
OboTermForm |
PappsoException |
PeakIonIsotopeMatch |
PeakIonMatch |
Peptide |
PeptideBuilder | Builds a peptide shared pointer from peptide string and adds fixed modifications
PeptideFixedModificationBuilder |
PeptideFragment |
PeptideFragmentIon |
PeptideFragmentIonListBase |
PeptideInterface |
PeptideIsotopeSpectrumMatch |
PeptideMethioninRemove | Potential remove Nter Methionin
PeptideModificatorBase |
PeptideModificatorInterface |
PeptideModificatorPipeline |
PeptideModificatorTee |
PeptideNaturalIsotope |
PeptideNaturalIsotopeAverage |
PeptideNaturalIsotopeList |
PeptideProFormaParser |
PeptideRawFragmentMasses |
PeptideSemiEnzyme | Cut a regular peptide obtained with an enzyme at any position from Nter or Cter
PeptideSinkInterface |
PeptideSizeFilter | Filter peptide string by size
PeptideSpectrumMatch |
PeptideSpSinkInterface |
PeptideStrParser |
PeptideVariableModificationBuilder | Modify a peptide shared pointer with a variable modification on one AA
PeptideVariableModificationReplacement |
PpmPrecision |
PrecisionBase |
PrecisionFactory |
PrecisionWidget |
PrecursorIonData |
Protein |
ProteinIntegerCode |
PsmFeatures |
PwizMsFileReader |
PwizMsRunReader |
QCPSpectrum |
QCPXic |
QualifiedMassSpectrum | Class representing a fully specified mass spectrum
QualifiedXic |
ResPrecision |
SavGolParams | Parameters for the Savitzky-Golay filter
SelectionPolygon |
SelectionPolygonSpec |
SimplePeakIonMatch |
SpectrumCollectionHandlerInterface | Interface to collect spectrums from the MsRunReader class
SwitchWidget |
TandemWrapperRun |
TicXicChromDriftSpecColorMapPlotWidget |
TicXicChromMassSpecColorMapPlotWidget |
TicXicChromTracePlotWidget |
TimsBinDec |
TimsData |
SpectrumDescr |
TimsDirectXicExtractor |
TimsFrame |
XicComputeStructure |
TimsFrameBase |
TimsFrameRawDataChunck |
TimsFrameRecord |
TimsFramesMsRunReader |
TimsFrameType1 |
TimsMs2CentroidFilter |
TimsMsFileReader |
TimsMsRunReader |
TimsMsRunReaderMs2 |
TimsMsRunReaderMs2Selected |
TimsXicExtractorInterface |
Trace | A simple container of DataPoint instances
TraceCombiner |
TraceDetectionInterface |
TraceDetectionMoulon |
TraceDetectionSinkInterface |
TraceDetectionZivy |
TraceMinusCombiner |
TracePeak |
TracePeakList |
TracePlusCombiner |
UiMonitorInterface |
UiMonitorText |
UiMonitorTextPercent |
UiMonitorVoid |
Utils |
WrapTandemInput |
WrapTandemResults |
Xic |
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
XicPeptideFragmentIon |
XicPeptideFragmentIonNaturalIsotope |
XicPeptideInterface |
XicWidget |
XmlStreamReaderInterface | Convenient xml reader helper
XtandemError |
XtandemHyperscore |
XtandemHyperscoreBis |
XtandemPresetReader |
XtandemSpectrumProcess |
XyMsFileReader |
XyMsRunReader |
Ui |