Class Members - Functions

- r -

random() : String , StringUtils
RangeManager() : RangeManager< D >
rankWeightedPermutationPeptideScores_() : AScore
ransac() : RANSAC< TModelType >
RANSACParam() : RANSACParam
raster() : LinearResampler , LinearResamplerAlign
raster_align() : LinearResamplerAlign
raster_interpolate() : LinearResamplerAlign
rasterExperiment() : LinearResampler
Ratio() : ConsensusFeature::Ratio
RawData() : RawData
RawMSSignalSimulation() : RawMSSignalSimulation
RawTandemMSSignalSimulation() : RawTandemMSSignalSimulation
rbegin() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace , SparseVector< Value >
rdbuf() : LogStream
ReactionMonitoringTransition() : ReactionMonitoringTransition
read() : Bzip2Ifstream , CsiFingerIdMzTabWriter , GzipIfstream , SiriusMzTabWriter
readable() : File
readBytes() : Bzip2InputStream , GzipInputStream
readChromatogram_() : CachedmzML
readChromatogramFast() : CachedmzML
readConsoleSize_() : ConsoleUtils
readEnzymesFromFile_() : EnzymesDB
readExperiment() : MzMLSqliteHandler
readFromFile_() : ElementDB
readFromOBOFile() : CrossLinksDB , ModificationsDB
readFromUnimodXMLFile() : ModificationsDB
readMappingFile_() : OMSSAXMLFile
readMemdump() : CachedmzML
readMzIdentMLFile() : MzIdentMLDOMHandler
readNext() : FASTAFile
readNextLine_() : FuzzyStringComparator
readOutHeader() : InspectOutfile , SequestOutfile
readPQPInput_() : TransitionPQPReader
readProblem() : LPWrapper
readQuantData() : PeptideAndProteinQuant
readResiduesFromFile_() : ResidueDB
readResponseHeader() : MascotRemoteQuery
readRTMZCharge_() : PepXMLFile
readSpectra() : SpectrumLookup , SpectrumMetaDataLookup
readSpectrum_() : CachedmzML
readSpectrumFast() : CachedmzML
readStart() : FASTAFile
readSwathWindows() : SwathWindowLoader
readUnstructuredTSVInput_() : TransitionTSVReader
readyReadSlot() : MascotRemoteQuery
RealMassDecomposer() : RealMassDecomposer
reannotateTransitions() : MRMAssay
recalculateAxes() : SpectrumCanvas
recalculateAxes_() : Spectrum1DWidget , Spectrum2DWidget , Spectrum3DWidget , SpectrumWidget
recalculateCurrentLayerDotGradient() : Spectrum2DCanvas
recalculateDotGradient_() : Spectrum2DCanvas , Spectrum3DOpenGLCanvas
recalculatePeakBorders_() : MRMTransitionGroupPicker
recalculateRanges_() : SpectrumCanvas
recalculateSnapFactor_() : Spectrum1DCanvas , Spectrum2DCanvas , SpectrumCanvas
recomputeConsensus_() : BaseLabeler
recurseAndGenerateVariableModifiedPeptides_() : ModifiedPeptideGenerator
reduce() : DistanceMatrix< Value >
reducePermuts_() : CompNovoIdentification , CompNovoIdentificationCID
refreshModificationList() : ModifierRep
refreshParameters() : TOPPASBase , TOPPASScene , TOPPASToolVertex
refreshPipelineParameters() : TOPPASBase
registerAt() : LogStreamNotifier
registerChannelsInOutputMap_() : IsobaricChannelExtractor
registerChildren() : BaseGroupFinder , BaseLabeler , BaseModel< D > , BaseSuperimposer , BinnedSpectrumCompareFunctor , ClusterFunctor , FeatureFinderAlgorithm , FeatureGroupingAlgorithm , FilterFunctor , Fitter1D , MapAlignmentEvaluationAlgorithm , PeakSpectrumCompareFunctor , PepIterator , ProgressLogger::ProgressLoggerImpl
registerDoubleList_() : TOPPBase
registerDoubleOption_() : TOPPBase
registeredProducts() : Factory< FactoryProduct >
registerExperiment() : MSQuantifications
registerFactory() : SingletonRegistry
registerFlag_() : TOPPBase
registerFullParam_() : TOPPBase
registerInputFile_() : TOPPBase
registerInputFileList_() : TOPPBase
registerIntList_() : TOPPBase
registerIntOption_() : TOPPBase
registerName() : MetaInfoRegistry
registerOptionsAndFlags_() : TOPPBase , RNPxlSearch , SimpleSearchEngine , TOPPMetaProSIP , TOPPOpenPepXL , TOPPOpenPepXLLF , TOPPRNPxl
registerOutputFile_() : TOPPBase
registerOutputFileList_() : TOPPBase
registerParamSubsectionsAsTOPPSubsections_() : TOPPBase
registerProduct() : Factory< FactoryProduct >
registerProtein_() : ProtXMLFile
registerRun() : QcMLFile
registerSet() : QcMLFile
registerStream() : StreamHandler
registerStringList_() : TOPPBase
registerStringOption_() : TOPPBase
registerSubsection_() : TOPPBase
registerTOPPSubsection_() : TOPPBase
registry() : MetaInfo
RegularSwathFileConsumer() : RegularSwathFileConsumer
reindexingNodes_() : ProteinResolver
released() : TOPPASVertex
remove() : DataFilters , File , LogStream , MultiGradient , Param , String , StringUtils
remove_() : MetaInfoVisualizer
remove_background_peak() : LCElutionPeak
remove_chromatogram_flag() : LayerData
remove_feature() : LCMS
remove_feature_by_ID() : LCMS
remove_feature_from_list() : LCMS
remove_overlapping_features() : MRMTransitionGroupPicker
remove_raw_spec_name() : LCMS
removeAdduct() : Compomer
removeAll() : Param , TOPPASInputFilesDialog
removeAllAttachments() : QcMLFile
removeAllClusters() : ClusteringGrid
removeAllMS2Information() : SHFeature
removeAttachment() : QcMLFile
removeCluster() : ClusteringGrid
removeCurrentRow() : ListTable
removeData_() : GradientVisualizer
removeDecoyHits() : IDFilter
removeDir() : File
removeDirRecursively() : File
removeDuplicatePeptideHits() : IDFilter
removeEmptyIdentifications() : IDFilter
removeExtension() : File
removeFile() : FileWatcher
removeHitsMatchingProteins() : IDFilter
removeHostName_() : MascotRemoteQuery
removeId() : EnhancedTabBar , TOPPASTabBar
removeInEdge() : TOPPASVertex
removeLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
removeMatchingItems() : IDFilter
removeMetaValue() : MetaInfoInterface
removeMS2Feature() : SHFeature
removeNoise() : CentroidData
removeOutEdge() : TOPPASVertex
removeOutlierFragments() : ClusteredMS2ConsensusSpectrum
removeOutliersIterative() : MRMRTNormalizer
removeOutliersRANSAC() : MRMRTNormalizer
removeOverlappingPeaks_() : PeakPickerMRM
removePeakAnnotationsFromPeptideHit() : LayerData
removePeptidesWithMatchingModifications() : IDFilter
removePeptidesWithMatchingSequences() : IDFilter
removePhosphositesFromSequence_() : AScore
removeQualityParameter() : QcMLFile
removeSelected() : TOPPASInputFilesDialog , TOPPASScene
removeSelectedItems() : Annotations1DContainer
removeSmallClustersY() : GridBasedClustering< Metric >
removeTempDirectory_() : TOPPBase
removeTemporaryAnnotations_() : TOPPViewIdentificationViewBehavior
removeTheoreticalSpectrumLayer_() : TOPPViewIdentificationViewBehavior
removeTreatment() : Sample
removeUnreferencedProteins() : IDFilter
removeValue() : MetaInfo
removeWhitespaces() : String , StringUtils
removeZeroedElements_() : EmpiricalFormula
renameOutput_() : TOPPASToolVertex
rend() : KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc > , ConsensusFeature , ConstRefVector< ContainerT > , IsotopeDistribution , MassTrace , SparseVector< Value >
renderForImage() : Spectrum1DWidget
renormalize() : IsotopeDistribution
replace() : DataFilters
replaceCVTerm() : CVTermList , CVTermListInterface
replaceCVTerms() : CVTermList , CVTermListInterface
replyFinished() : NetworkGetRequest
reportFailure_() : FuzzyStringComparator
reportSuccess_() : FuzzyStringComparator
requestClipboardContent() : TOPPASScene
requestVisibleArea1D() : SpectraIdentificationViewWidget
RequiredParameterNotGiven() : RequiredParameterNotGiven
rerunTOPPTool() : TOPPViewBase
resample() : ConsensusMapNormalizerAlgorithmQuantile
resampleChromatogram_() : MRMTransitionGroupPicker
rescaleFragmentFeature_() : PercolatorFeatureSetHelper
rescore() : PrecursorIonSelection
rescore_() : PrecursorIonSelection
reserve() : ConstRefVector< ContainerT > , MSExperiment
reserveSpaceChromatograms() : MSExperiment
reserveSpaceSpectra() : MSExperiment
reset() : squared_difference_counted< _Tp, _Dist > , FuzzyStringComparator::StreamElement_ , XMLHandler , IsobaricQuantifierStatistics , Histogram< ValueType, BinSizeType > , MSExperiment , PrecursorIonSelection , StopWatch , SysInfo::MemUsage , TOPPASOutputFileListVertex , TOPPASToolVertex , TOPPASVertex
resetAlignment() : Spectrum1DCanvas , Spectrum1DWidget
resetDownstream() : TOPPASScene
resetErrors() : XMLValidator
resetInterpretations() : TraMLProduct
resetMembers_() : FeatureXMLFile , ProtXMLFile
resetPeakGroupIter() : CentroidData
resetProcessesQueue() : TOPPASScene
resetTranslation() : Spectrum3DOpenGLCanvas
resetZoom() : IDEvaluationBase , SpectrumCanvas , TOPPViewBase
residualOutlierCandidate_() : MRMRTNormalizer
Residue() : Residue
ResidueDB() : ResidueDB
ResidueModification() : ResidueModification
residuesMatch_() : ModificationsDB
residueTypeToIonLetter_() : TheoreticalSpectrumGenerator , TheoreticalSpectrumGeneratorXLMS
ResidueTypeToString_() : SvmTheoreticalSpectrumGenerator
resize() : ConstRefVector< ContainerT > , DistanceMatrix< Value > , Matrix< Value > , MSExperiment , SparseVector< Value >
resizeEvent() : HistogramWidget , Spectrum3DCanvas , SpectrumCanvas , TOPPASWidget
resizeGL() : Spectrum3DOpenGLCanvas
resolveAutoMode_() : AccurateMassSearchEngine
resolveConnectedComponent() : PeptideProteinResolution
resolveConsensus() : ProteinResolver
resolveGraph() : PeptideProteinResolution
resolveID() : ProteinResolver
resolveMisassignedNTermMods_() : PercolatorOutfile
resolveMixedSequenceGroups_() : TransitionTSVReader
resolveUniqueIdConflicts() : UniqueIdIndexer< RandomAccessContainer >
restoreRotationAndZoom() : Spectrum3DOpenGLCanvas
restrictTransitions() : MRMAssay
RetentionTime() : RetentionTime
retrieveSwathMaps() : FullSwathFileConsumer
return_chromatogram() : ChromatogramExtractor
reverse() : String , StringUtils
ReverseComparator() : ReverseComparator< Cmp >
reverseComparator() : ReverseComparator< Cmp >
ReverseComparator() : ReverseComparator< Cmp >
reversePeptide() : MRMDecoy
rhop() : SparseVector< Value >::SparseVectorConstReverseIterator , SparseVector< Value >::SparseVectorReverseIterator
RichPeak2D() : RichPeak2D
rip() : IDRipper
rm_fit() : RansacModel< ModelT >
rm_fit_impl() : RansacModelLinear , RansacModelQuadratic
rm_inliers() : RansacModel< ModelT >
rm_inliers_impl() : RansacModelLinear , RansacModelQuadratic
rm_rsq() : RansacModel< ModelT >
rm_rsq_impl() : RansacModelLinear , RansacModelQuadratic
rm_rss() : RansacModel< ModelT >
rm_rss_impl() : RansacModelLinear , RansacModelQuadratic
RNPxlSearch() : RNPxlSearch
ROCCurve() : ROCCurve
roundBasedMode() : TOPPASMergerVertex
row() : Matrix< Value >
rowCount() : CsvFile
rowIndex() : Matrix< Value >
rows() : Matrix< Value >
rt() : KDTreeFeatureMaps
RTBegin() : MSChromatogram , MSExperiment
RTEnd() : MSChromatogram , MSExperiment
RtIterator() : RtIterator< FeaFiModuleType >
RTNormalization() : OpenSwathRetentionTimeNormalization
RTSimulation() : RTSimulation
run() : AccurateMassSearchEngine , BaseGroupFinder , BaseSuperimposer , FeatureFinder , FeatureFinderAlgorithm , FeatureFinderAlgorithmIsotopeWavelet , FeatureFinderAlgorithmMRM , FeatureFinderAlgorithmPicked , FeatureFinderAlgorithmSH , FeatureFindingMetabo , LabeledPairFinder , MascotRemoteQuery , MassTraceDetection , MetaboliteSpectralMatching , NetworkGetRequest , PeptideIndexing , PoseClusteringAffineSuperimposer , PoseClusteringShiftSuperimposer , QTClusterFinder , SimplePairFinder , StablePairFinder , TOPPASInputFileListVertex , TOPPASMergerVertex , TOPPASOutputFileListVertex , TOPPASSplitterVertex , TOPPASToolVertex , TOPPASVertex , UpdateCheck
run_() : MassTraceDetection , QTClusterFinder
run_internal_() : QTClusterFinder
runClustering_() : FeatureGroupingAlgorithmKD
runNextProcess() : TOPPASScene
runPipeline() : TOPPASBase , TOPPASScene
runScript() : RWrapper
runTOPPTool_() : TOPPViewBase