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• main() : TOPPBase
• main_() : NucleicAcidSearchEngine , TOPPBase , TOPPGNPSExport , TOPPOpenPepXL , TOPPOpenPepXLLF , TOPPXFDR
• mainWindowNeedsUpdate() : TOPPASScene
• makeAutoRemoveTempDirectory_() : TOPPBase
• makeAxes_() : Spectrum3DOpenGLCanvas
• makeAxesTicks_() : Spectrum3DOpenGLCanvas
• makeConsensusFeature_() : QTClusterFinder
• makeDataAsStick_() : Spectrum3DOpenGLCanvas
• makeDataAsTopView_() : Spectrum3DOpenGLCanvas
• makeGridLines_() : Spectrum3DOpenGLCanvas
• makeGround_() : Spectrum3DOpenGLCanvas
• makePrecursorSelectionForKnownLCMSMap() : OfflinePrecursorIonSelection
• makeScanMap_() : PepXMLFile
• makeStream() : CompressedInputSource
• makeTempDirectory_() : TOPPBase
• manhattanDist_() : ConfidenceScoring
• map2csv() : QcMLFile
• map_() : PeakIntensityPredictor
• MapAlignmentAlgorithmIdentification() : MapAlignmentAlgorithmIdentification
• MapAlignmentAlgorithmKD() : MapAlignmentAlgorithmKD
• MapAlignmentAlgorithmPoseClustering() : MapAlignmentAlgorithmPoseClustering
• MapAlignmentAlgorithmSpectrumAlignment() : MapAlignmentAlgorithmSpectrumAlignment
• MapAlignmentAlgorithmTreeGuided() : MapAlignmentAlgorithmTreeGuided
• MapAlignmentEvaluationAlgorithm() : MapAlignmentEvaluationAlgorithm
• MapAlignmentEvaluationAlgorithmPrecision() : MapAlignmentEvaluationAlgorithmPrecision
• MapAlignmentEvaluationAlgorithmRecall() : MapAlignmentEvaluationAlgorithmRecall
• mapComponentsToConcentrations() : AbsoluteQuantitationStandards
• mapExperiment() : MRMMapping
• mapExperimentToTransitionList() : MRMFeatureFinderScoring
• mapFiles2Design_() : QuantitativeExperimentalDesign
• mapIndex() : KDTreeFeatureMaps
• mapPrecursorsToIdentifications() : IDMapper
• mapSearchEngineScoreToCvParam_() : MzTabFile
• mapSearchEngineToCvParam_() : MzTabFile
• mapSeeds2Features() : IsotopeWaveletTransform< PeakType >
• margin() : AxisWidget
• MarkerMower() : MarkerMower
• markUnreachable() : TOPPASMergerVertex , TOPPASSplitterVertex , TOPPASVertex
• marr_() : ContinuousWaveletTransformNumIntegration
• MascotGenericFile() : MascotGenericFile
• MascotInfile() : MascotInfile
• MascotRemoteQuery() : MascotRemoteQuery
• MascotXMLFile() : MascotXMLFile
• MascotXMLHandler() : MascotXMLHandler
• MassAnalyzer() : MassAnalyzer
• MassAnalyzerVisualizer() : MassAnalyzerVisualizer
• massCorrectionTerm() : PScore
• MassDecomposition() : MassDecomposition
• MassDecompositionAlgorithm() : MassDecompositionAlgorithm
• MassExplainer() : MassExplainer
• MassTrace() : MassTrace
• MasstraceCorrelator() : MasstraceCorrelator
• MassTraceDetection() : MassTraceDetection
• MassTraces() : FeatureFinderAlgorithmPickedHelperStructs::MassTraces
• Match() : TargetedSpectraExtractor::Match
• matchedCurrentChain() : XQuestScores
• MatchedIterator() : MatchedIterator< CONT_T, TRAIT, CONST_T >
• matchMasses_() : TOFCalibration
• matchMassTraces_() : MasstraceCorrelator
• matchModification_() : PepXMLFile , PepXMLFileMascot , ProtXMLFile
• matchOddsScore() : XQuestScores
• matchOddsScoreSimpleSpec() : XQuestScores
• matchSpectrum() : TargetedSpectraExtractor
• Matrix() : Matrix< Value >
• max_size() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConstRefVector< ContainerT >
• maxBound() : Histogram< ValueType, BinSizeType >
• maxLength() : TOPPASLogWindow
• MaxLikeliFitter1D() : MaxLikeliFitter1D
• maxPosition() : DIntervalBase< D >
• maxPositive() : DPosition< D, TCoordinateType >
• maxValue() : Histogram< ValueType, BinSizeType >
• maxX() : DIntervalBase< D >
• maxY() : DIntervalBase< D >
• mean() : BasicStatistics< RealT > , mean_and_stddev
• mean_and_stddev() : mean_and_stddev
• meanIntensity_() : MSstatsFile
• median() : CalibrationData
• MemUsage() : SysInfo::MemUsage
• merge() : IsotopeDistribution , Param , PeptideIndexing::FoundProteinFunctor , QcMLFile
• mergeable() : ProteinIdentification::SearchParameters
• mergeAllChannelFeatures_() : SILACLabeler
• mergeAllIDRuns() : ConsensusMapMergerAlgorithm
• mergeAlongTime() : FIAMSDataProcessor
• mergeAnnotatedSpectra() : OPXLSpectrumProcessingAlgorithms
• mergeConsensusMaps_() : QuantitativeExperimentalDesign
• mergeFailed() : TOPPASMergerVertex
• mergeFeatures() : MS1FeatureMerger
• mergeFeatures_() : ICPLLabeler , ITRAQLabeler , O18Labeler , SILACLabeler
• mergeIDFiles_() : QuantitativeExperimentalDesign
• mergeIntoLayer() : Spectrum2DCanvas
• mergeMS2Fragments() : ClusteredMS2ConsensusSpectrum
• mergeMULTISEPeptideIds() : PercolatorFeatureSetHelper
• mergeMULTISEProteinIds() : PercolatorFeatureSetHelper
• mergeOverlappingWindows_() : InclusionExclusionList
• mergePartitions() : SVMWrapper
• mergeProteinAccessions_() : BaseLabeler
• mergeProteinIdentificationsMaps_() : BaseLabeler
• mergeProteinIDRuns() : ConsensusMapMergerAlgorithm
• mergeProteinsAcrossFractionsAndReplicates() : ConsensusMapMergerAlgorithm
• mergeSpectra_() : SpectraMerger
• mergeSpectraBlockWise() : SpectraMerger
• mergeSpectraPrecursors() : SpectraMerger
• mergeVeto_() : GridBasedClustering< Metric >
• MessagePasserFactory() : MessagePasserFactory< Label >
• messageReady() : TOPPASScene
• MetaboliteFeatureDeconvolution() : MetaboliteFeatureDeconvolution
• MetaboliteSpectralMatching() : MetaboliteSpectralMatching
• MetaDataBrowser() : MetaDataBrowser
• metadataFileDialog() : TOPPViewBase
• MetaInfo() : MetaInfo
• MetaInfoDescription() : MetaInfoDescription
• MetaInfoDescriptionVisualizer() : MetaInfoDescriptionVisualizer
• MetaInfoInterface() : MetaInfoInterface
• MetaInfoInterfaceUtils() : MetaInfoInterfaceUtils
• MetaInfoRegistry() : MetaInfoRegistry
• MetaInfoVisualizer() : MetaInfoVisualizer
• metaPasses_() : DataFilters
• metaRegistry() : MetaInfoInterface
• MetaStatsValue_() : LayerStatisticsDialog::MetaStatsValue_
• metaValueExists() : MetaInfoInterface
• minBound() : Histogram< ValueType, BinSizeType >
• MinimumDistance() : MinimumDistance
• minNegative() : DPosition< D, TCoordinateType >
• minPosition() : DIntervalBase< D >
• minPositive() : DPosition< D, TCoordinateType >
• minValue() : Histogram< ValueType, BinSizeType >
• minX() : DIntervalBase< D >
• minY() : DIntervalBase< D >
• mirrorModeActive() : Spectrum1DCanvas
• MissedCleavages() : MissedCleavages
• MissingInformation() : MissingInformation
• MockFeature() : MockFeature
• MockMRMFeature() : MockMRMFeature
• MockSignalToNoise() : MockSignalToNoise
• MockTransitionGroup() : MockTransitionGroup
• ModelDescription() : ModelDescription< D >
• Modification() : Modification , Peptide::Modification
• modificationCorrectionTerm() : PScore
• ModificationDefinition() : ModificationDefinition
• ModificationDefinitionsSet() : ModificationDefinitionsSet
• ModificationsDB() : ModificationsDB
• modificationStatus_() : SpectrumCanvas
• ModificationVisualizer() : ModificationVisualizer
• modified() : ParamEditorDelegate , ParamEditor
• ModifyMultiIndexAddProcessingStep() : IdentificationData::ModifyMultiIndexAddProcessingStep< ElementType >
• ModifyMultiIndexAddScore() : IdentificationData::ModifyMultiIndexAddScore< ElementType >
• ModifyMultiIndexRemoveParentMatches() : IdentificationData::ModifyMultiIndexRemoveParentMatches< ElementType >
• modifyStrings() : SVOutStream
• MoleculeParentMatch() : MoleculeParentMatch
• MoleculeQueryMatch() : MoleculeQueryMatch
• monitorFileChanged_() : FileWatcher
• MorphologicalFilter() : MorphologicalFilter
• mouseDoubleClickEvent() : EnhancedTabBar , MultiGradientSelector , Spectrum2DCanvas , TOPPASEdge , TOPPASInputFileListVertex , TOPPASSplitterVertex , TOPPASTabBar , TOPPASToolVertex , TOPPASVertex
• mouseMoveEvent() : HistogramWidget , MultiGradientSelector , Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DOpenGLCanvas , TOPPASTreeView , TOPPASVertex
• mousePressEvent() : ColorSelector , HistogramWidget , MultiGradientSelector , Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DOpenGLCanvas , TOPPASTreeView , TOPPASVertex
• mouseReleaseEvent() : HistogramWidget , MultiGradientSelector , Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DOpenGLCanvas , TOPPASVertex
• move() : Annotation1DCaret , Annotation1DDistanceItem , Annotation1DItem , Annotation1DPeakItem , Annotation1DTextItem
• moveCurrentItem() : TOPPASInputFilesDialog
• moveNewEdgeTo_() : TOPPASVertex
• movePepIDsAndRefProteinsToResultFaster_() : IDMergerAlgorithm
• moveSelectedItems() : TOPPASScene
• mQ_() : TOFCalibration
• mQAv_() : TOFCalibration
• MRMAssay() : MRMAssay
• MRMBatchFeatureSelector() : MRMBatchFeatureSelector
• MRMDecoy() : MRMDecoy
• MRMFeature() : MRMFeature
• MRMFeatureFilter() : MRMFeatureFilter
• MRMFeatureFinderScoring() : MRMFeatureFinderScoring
• MRMFeatureOpenMS() : MRMFeatureOpenMS
• MRMFeaturePicker() : MRMFeaturePicker
• MRMFeaturePickerFile() : MRMFeaturePickerFile
• MRMFeatureQC() : MRMFeatureQC
• MRMFeatureQCFile() : MRMFeatureQCFile
• MRMFeatureSelector() : MRMFeatureSelector
• MRMFeatureSelector_test() : MRMFeatureSelector_test
• MRMFragmentSelection() : MRMFragmentSelection
• MRMIonSeries() : MRMIonSeries
• MRMMapping() : MRMMapping
• MRMTransitionGroup() : MRMTransitionGroup< ChromatogramType, TransitionType >
• MRMTransitionGroupPicker() : MRMTransitionGroupPicker
• MS1Extraction_() : OpenSwathWorkflowBase
• ms1FeatureClustering() : SuperHirnParameters
• MS1FeatureMerger() : MS1FeatureMerger
• MS2ConsensusSpectrum() : MS2ConsensusSpectrum
• MS2Feature() : MS2Feature
• MS2File() : MS2File
• MS2Fragment() : MS2Fragment
• Ms2IdentificationRate() : Ms2IdentificationRate
• MS2Info() : MS2Info
• Ms2SpectrumStats() : Ms2SpectrumStats
• MSChromatogram() : MSChromatogram
• MSDataAggregatingConsumer() : MSDataAggregatingConsumer
• MSDataCachedConsumer() : MSDataCachedConsumer
• MSDataChainingConsumer() : MSDataChainingConsumer
• MSDataSqlConsumer() : MSDataSqlConsumer
• MSDataStoringConsumer() : MSDataStoringConsumer
• MSDataTransformingConsumer() : MSDataTransformingConsumer
• MSDataWritingConsumer() : MSDataWritingConsumer
• MSExperiment() : MSExperiment
• MSFileSectionEntry() : ExperimentalDesign::MSFileSectionEntry
• msFilter_() : MapAlignmentAlgorithmSpectrumAlignment
• MsInspectFile() : MsInspectFile
• MSNumpressCoder() : MSNumpressCoder
• MSPeak() : MSPeak
• MSPFile() : MSPFile
• MSPGenericFile() : MSPGenericFile
• MSPGenericFile_friend() : MSPGenericFile_friend
• MSQuantifications() : MSQuantifications
• MSSim() : MSSim
• MSSpectrum() : MSSpectrum
• MSstatsFile() : MSstatsFile
• MSstatsLine_() : MSstatsFile::MSstatsLine_
• MSstatsTMTLine_() : MSstatsFile::MSstatsTMTLine_
• MultiGradient() : MultiGradient
• MultiGradientSelector() : MultiGradientSelector
• MultiplexClustering() : MultiplexClustering
• MultiplexDeltaMasses() : MultiplexDeltaMasses
• MultiplexDeltaMassesGenerator() : MultiplexDeltaMassesGenerator
• MultiplexDistance() : MultiplexClustering::MultiplexDistance
• MultiplexFilteredMSExperiment() : MultiplexFilteredMSExperiment
• MultiplexFilteredPeak() : MultiplexFilteredPeak
• MultiplexFiltering() : MultiplexFiltering
• MultiplexFilteringCentroided() : MultiplexFilteringCentroided
• MultiplexFilteringProfile() : MultiplexFilteringProfile
• MultiplexIsotopicPeakPattern() : MultiplexIsotopicPeakPattern
• MultiplexSatelliteCentroided() : MultiplexSatelliteCentroided
• MultiplexSatelliteProfile() : MultiplexSatelliteProfile
• myLog2_() : IsotopeWavelet
• myPow() : IsotopeWavelet
• myPow2_() : IsotopeWavelet
• mz() : KDTreeFeatureMaps
• MZBegin() : IsotopeWaveletTransform< PeakType >::TransSpectrum , MSSpectrum
• MzCalibration() : MzCalibration
• MzDataFile() : MzDataFile
• MzDataHandler() : MzDataHandler
• MzDataValidator() : MzDataValidator
• MZEnd() : IsotopeWaveletTransform< PeakType >::TransSpectrum , MSChromatogram , MSSpectrum
• MzIdentMLDOMHandler() : MzIdentMLDOMHandler
• MzIdentMLFile() : MzIdentMLFile
• MzIdentMLHandler() : MzIdentMLHandler
• MzIdentMLValidator() : MzIdentMLValidator
• MzMLFile() : MzMLFile
• MzMLHandler() : MzMLHandler
• MzMLSpectrumDecoder() : MzMLSpectrumDecoder
• MzMLSqliteHandler() : MzMLSqliteHandler
• MzMLSqliteSwathHandler() : MzMLSqliteSwathHandler
• MzMLSwathFileConsumer() : MzMLSwathFileConsumer
• MzMLValidator() : MzMLValidator
• MzQuantMLFile() : MzQuantMLFile
• MzQuantMLHandler() : MzQuantMLHandler
• MzQuantMLValidator() : MzQuantMLValidator
• MzTab() : MzTab
• MzTabBoolean() : MzTabBoolean
• MzTabDouble() : MzTabDouble
• MzTabDoubleList() : MzTabDoubleList
• MzTabFile() : MzTabFile
• MzTabInteger() : MzTabInteger
• MzTabIntegerList() : MzTabIntegerList
• MzTabMetaData() : MzTabMetaData
• MzTabModification() : MzTabModification
• MzTabNullAbleBase() : MzTabNullAbleBase
• MzTabNullNaNAndInfAbleBase() : MzTabNullNaNAndInfAbleBase
• MzTabParameter() : MzTabParameter
• MzTabProteinSectionRow() : MzTabProteinSectionRow
• MzTabSpectraRef() : MzTabSpectraRef
• MzTabString() : MzTabString
• MzTabStringList() : MzTabStringList
• mzToXAxis() : SpectrumCanvas
• MZTrafoModel() : MZTrafoModel
• MzXMLFile() : MzXMLFile
• MzXMLHandler() : MzXMLHandler