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
Aa |
AaBase |
AaModification |
AtomNumberInterface |
ExceptionInterrupted |
ExceptionNotFound |
ExceptionNotImplemented |
ExceptionNotPossible |
ExceptionNotRecognized | Excetion to use when an item type is not recognized
ExceptionOutOfRange |
FastaFileIndexerInterface |
FastaFileIndexer |
FastaHandlerInterface |
FastaOutputStream |
FastaReader |
FastaWriterInterface |
GrpExperiment |
GrpGroup |
GrpGroupingMonitorInterface |
GrpGroupingMonitor |
GrpMapPeptideToGroup |
GrpMapPeptideToSubGroupSet |
GrpPeptide |
GrpPeptideSet |
GrpProtein |
GrpSubGroup |
GrpSubGroupSet |
MassSpectrum | Class to represent a mass spectrum
MassSpectrumId |
PrecursorIonData |
QualifiedMassSpectrum | Class representing a fully specified mass spectrum
MsFileAccessor |
MsFileReader |
MzFormatEnumStr | Static functions to convert mz file formats
PwizMsFileReader |
TimsMsFileReader |
XyMsFileReader |
MsRunAlignment |
MsRunRetentionTimeSeamarkPoint |
MsRunRetentionTime |
PeptideMs2Point |
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)
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
MsRunReader | Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
MgfOutput |
MzxmlOutput |
Translater |
PwizMsRunReader |
TimsMsRunReader |
TimsMsRunReaderMs2 |
TimsMsRunReaderMs2Selected |
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 |
FilterOboPsiModSink |
FilterOboPsiModTermAccession |
FilterOboPsiModTermDiffMono |
FilterOboPsiModTermLabel |
FilterOboPsiModTermName |
OboPsiMod |
OboPsiModHandlerInterface |
OboPsiModTerm |
PappsoException |
Ion |
Peptide |
PeptideFragment |
PeptideFragmentIon |
PeptideFragmentIonListBase |
PeptideInterface |
PeptideNaturalIsotope |
PeptideNaturalIsotopeAverage |
PeptideNaturalIsotopeList |
SimplePeakIonMatch |
PeptideRawFragmentMasses |
PeptideStrParser |
PrecisionBase |
DaltonPrecision |
PpmPrecision |
ResPrecision |
PrecisionFactory |
MassDataCombinerInterface |
MassSpectrumCombiner |
MassSpectrumMinusCombiner |
MassSpectrumPlusCombiner |
MzIntegrationParams | Parameters definining how m/z !
SelectionPolygon |
SelectionPolygonSpec |
TraceCombiner |
TraceMinusCombiner |
TracePlusCombiner |
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
FilterLowPass | Remove datapoints higher than a given Y value (intensity)
FilterHighPass | Remove datapoints below a 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
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
XtandemError |
TandemWrapperRun |
WrapTandemInput |
WrapTandemResults |
XtandemPresetReader |
UiMonitorInterface |
UiMonitorText |
UiMonitorTextPercent |
UiMonitorVoid |
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 |
DeepProtEnumStr |
IonIsotopeRatioScore |
MorpheusScore |
PeakIonIsotopeMatch |
PeakIonMatch |
PeptideIsotopeSpectrumMatch |
PeptideSpectrumMatch |
XtandemHyperscore |
XtandemHyperscoreBis |
XtandemSpectrumProcess |
DataPoint |
LinearRegression |
MapTrace |
Trace | A simple container of DataPoint instances
Utils |
MzCalibrationInterface |
MzCalibrationModel1 |
MzCalibrationModel1Cached |
MzCalibrationStore |
TimsBinDec |
TimsData |
FrameIdDescr |
SpectrumDescr |
TimsFrame |
XicComputeStructure |
TimsFrameBase |
TimsFrameType1 |
TimsMs2CentroidFilter |
TimsDirectXicExtractor |
TimsXicExtractorInterface |
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 |
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 |
Ui |