Class Members - Functions

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AAIndex() : AAIndex
AASequence() : AASequence
AASequenceIdentity() : MRMDecoy
abort_() : FeatureFinderAlgorithmPicked
abortPipeline() : TOPPASBase , TOPPASScene
abortTOPPTool() : TOPPViewBase
aboutToBeDestroyed() : SpectrumWidget , TOPPASWidget
aboutToCloseId() : EnhancedTabBar , TOPPASTabBar
absolutePath() : File
AccurateMassSearchEngine() : AccurateMassSearchEngine
AccurateMassSearchResult() : AccurateMassSearchResult
acidic() : AAIndex
Acquisition() : Acquisition
AcquisitionInfo() : AcquisitionInfo
AcquisitionInfoVisualizer() : AcquisitionInfoVisualizer
AcquisitionVisualizer() : AcquisitionVisualizer
AcqusHandler() : AcqusHandler
actionModeChange() : Spectrum3DOpenGLCanvas , SpectrumCanvas
activate1DSpectrum() : TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
activateAsPrecursorPeak() : MSPeak
activateBehavior() : TOPPViewIdentificationViewBehavior , TOPPViewSpectraViewBehavior
activateLayer() : Spectrum1DCanvas , Spectrum2DCanvas , Spectrum3DCanvas , SpectrumCanvas
activatePrecalculationMode() : MultiGradient
activateSpectrum() : Spectrum1DCanvas
activeLayerIndex() : SpectrumCanvas
activeWindow_() : TOPPASBase
adaptPenScaling_() : Spectrum2DCanvas
add() : BigString , Compomer , DataFilters , AveragePosition< D > , MetaDataBrowser , QTCluster , TOPPASResources
add1DSignal_() : RawMSSignalSimulation
add2Buttons_() : BaseVisualizerGUI
add2DSignal_() : RawMSSignalSimulation
add_() : MetaInfoVisualizer
add_alignment_error() : LCMS
add_feature() : LCMS
add_LC_elution_peak() : LCMSCData
add_matched_feature() : SHFeature
add_modification() : MS2Info
add_MS2_info() : SHFeature
add_raw_peak_to_LC_MS_run() : FTPeakDetectController
add_raw_spec_name() : LCMS
add_raw_spec_name_map() : LCMS
add_scan_raw_data() : ProcessData
addAbundantImmoniumIons_() : TheoreticalSpectrumGenerator
addAnalysisResults() : PeptideHit
addBaseLine_() : RawMSSignalSimulation
addBooleanComboBox_() : BaseVisualizerGUI
addButton_() : BaseVisualizerGUI
addCheckboxItemToBottomRow_() : SpectraIdentificationViewWidget
addChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType > , MSExperiment
addChromatograms() : OpenSwathRetentionTimeNormalization , OpenSwathWorkflowSonar
addCluster() : ClusteringGrid
addClusterElements_() : QTClusterFinder
addColumn() : LPWrapper
addComboBox_() : BaseVisualizerGUI
addCOMETFeatures() : PercolatorFeatureSetHelper
addCommonPeaks_() : TheoreticalSpectrumGeneratorXLMS
addCompound() : TargetedExperiment
addCONCATSEFeatures() : PercolatorFeatureSetHelper
addConfiguration() : IncludeExcludeTarget , TraMLProduct
addConsensusFeature_() : FeatureGroupingAlgorithmKD
addConsensusMap() : MSQuantifications
addContact() : TargetedExperiment
addConvexHull() : FeaFiModule< PeakType >
addCV() : TargetedExperiment
addCVReference() : CVMappings
addCVTerm() : CVMappingRule , CVTermList , CVTermListInterface
addData() : TOPPViewBase
addData_() : MSExperiment::ContainerAdd_< ContainerValueType, addMassTraces > , MSExperiment::ContainerAdd_< ContainerValueType, false > , MSExperiment::ContainerAdd_< ContainerValueType, true >
addDataFile() : TOPPViewBase
addDataProcessing() : MSDataWritingConsumer
addDataProcessing_() : SpectrumCanvas , TOPPBase
addDetectorNoise_() : RawMSSignalSimulation
addDoubleItemToBottomRow_() : SpectraIdentificationViewWidget
addDoubleLineEdit_() : BaseVisualizerGUI
addEdge() : TOPPASScene
addEluent() : Gradient
addEluent_() : GradientVisualizer
addEmptyLine_() : TOPPBase
addEntry_() : SpectrumLookup
addEnzyme() : EnzymesDB
addEnzyme_() : EnzymesDB
addEnzymeInfo() : SequestInfile
addExcludeTarget() : TargetedExperiment
addExternalType() : ToolDescription
addFakeMSMSToFeature() : FTPeakDetectController
addFeature() : KDTreeFeatureMaps , MRMFeature , MRMTransitionGroup< ChromatogramType, TransitionType >
addFile() : FileWatcher
addFilterResultPeak() : MultiplexFilterResult
addFragmentAnnotations_() : TOPPViewIdentificationViewBehavior
addHit() : SpectrumIdentification
addHoveringEdge() : TOPPASScene
addIncludeTarget() : TargetedExperiment
addInEdge() : TOPPASVertex
addInstrument() : TargetedExperiment
addIntensity() : BackgroundIntensityBin
addIntermediateProduct() : ReactionMonitoringTransition
addInterpretation() : IncludeExcludeTarget , TraMLProduct
addIntItemToBottomRow_() : SpectraIdentificationViewWidget
addIntLineEdit_() : BaseVisualizerGUI
addIonMatchStatistics() : SpectrumAnnotator
addIsotopeCluster_() : TheoreticalSpectrumGenerator
addIsotopeTrace() : ConsensusIsotopePattern
addLabel_() : BaseVisualizerGUI
addLabelAnnotation_() : Spectrum1DCanvas
addLabelToProteinHits_() : ICPLLabeler
addLayer() : SpectrumCanvas
addLCelutionProfile() : FTPeakDetectController
addLine() : TextFile
addLineEdit_() : BaseVisualizerGUI
addLineEditButton_() : BaseVisualizerGUI
addListView_() : BaseVisualizerGUI
addLosses_() : TheoreticalSpectrumGenerator
addLossFormula() : Residue
addLossName() : Residue
addMappingRule() : CVMappings
addMaps() : KDTreeFeatureMaps
addMASCOTFeatures() : PercolatorFeatureSetHelper
addMassTrace() : FeatureHypothesis
addMatches_() : ModificationDefinitionsSet
addMaxInclusionListSizeConstraints_() : PSLPFormulation
addMetaValues_() : XQuestResultXMLHandler
addMissingRTsToPeptideIDs() : SpectrumMetaDataLookup
addMissingSpectrumReferences() : SpectrumMetaDataLookup
addModification() : ModificationDefinitionsSet , ModificationsDB
addModification_() : TransitionTSVReader
addModificationsSequences_() : MRMAssay
addModificationToPeptideHit_() : ICPLLabeler , ITRAQLabeler , O18Labeler , SILACLabeler
addMS1elutionSignal() : FeatureLCProfile
addMS1Map_() : CachedSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
addMS2ConsensusSpectrum() : ClusteredMS2ConsensusSpectrum
addMS2Feature() : SHFeature
addMS2FeatureToMS1Feature() : FTPeakDetectController
addMS2Fragment() : MS2ConsensusSpectrum
addMSGFFeatures() : PercolatorFeatureSetHelper
addMSLevel() : PeakFileOptions
addMSPeak() : BackgroundIntensityBin
addMULTISEFeatures() : PercolatorFeatureSetHelper
addNewState() : HiddenMarkovModel
addNewSwathMap_() : CachedSwathFileConsumer , MzMLSwathFileConsumer , RegularSwathFileConsumer
addNTermLossFormula() : Residue
addNTermLossName() : Residue
addOutEdge() : TOPPASVertex
addOutsideMS1elutionSignal() : FeatureLCProfile
addPeak_() : PeakPickerCWT , TheoreticalSpectrumGeneratorXLMS
addPeakAnnotation() : Spectrum1DCanvas
addPeakAnnotations_() : TOPPViewIdentificationViewBehavior
addPeakMSScan() : BackgroundControl
addPeaks_() : TheoreticalSpectrumGenerator
addPeptide() : TargetedExperiment
addPeptideEvidence() : PeptideHit
addPoint() : ConvexHull2D
addPoints() : ConvexHull2D
addPrecursorAcquisitionNumberConstraint_() : PSLPFormulation
addPrecursorChromatogram() : MRMTransitionGroup< ChromatogramType, TransitionType >
addPrecursorCVTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
addPrecursorFeature() : MRMFeature
addPrecursorLabels1D_() : TOPPViewIdentificationViewBehavior
addPrecursorPeaks_() : TheoreticalSpectrumGenerator
addPredecessorState() : HMMState
addPredictionTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
addProductCVTerm() : IncludeExcludeTarget , ReactionMonitoringTransition
addProtein() : TargetedExperiment
addProteinCoverageConstraint_() : PSLPFormulation
addProteinGroups_() : IdXMLFile
addProteinToILP_() : PSLPFormulation
addPublication() : TargetedExperiment
addRatio() : ConsensusFeature
addRecentFile_() : TOPPViewBase
addReferenceFormat() : SpectrumLookup
addResidue() : ResidueDB
addResidue_() : ResidueDB
addResidueSet() : Residue
addRow() : LPWrapper
addRTBinCapacityConstraint_() : PSLPFormulation
addRTFitData() : MapAlignmentAlgorithmKD
addRunAttachment() : QcMLFile
addRunQualityParameter() : QcMLFile
addScore() : MRMFeature
addSearchFile() : IDEvaluationBase
addSection() : Param
addSeparator_() : BaseVisualizerGUI
addSetAttachment() : QcMLFile
addSetQualityParameter() : QcMLFile
addShotNoise_() : RawMSSignalSimulation
addSingleChargedIons_() : CompNovoIonScoringBase
addSoftware() : TargetedExperiment
addSourceFile() : TargetedExperiment
addSpectrum() : MSExperiment
addSpectrumIdentification() : Identification
addSpectrumMetaData_() : MzMLHandler
addStepSizeConstraint_() : PSLPFormulation
addSuccessorState() : HMMState
addSynonym() : Enzyme , Residue , ResidueModification
addSynonymTransition() : HiddenMarkovModel
addTab() : EnhancedTabBar , TOPPASTabBar
addTag() : Param
addTags() : Param
addTargetCVTerm() : TargetedExperiment
addText_() : TOPPBase
addTextEdit_() : BaseVisualizerGUI
addTextItemToBottomRow_() : SpectraIdentificationViewWidget
addTheoreticalSpectrumLayer_() : TOPPViewIdentificationViewBehavior
addTimepoint() : Gradient
addTimepoint_() : GradientVisualizer
addToCache_() : LogStreamBuf
addToGroup() : FeatureGroupingAlgorithmUnlabeled
addTOPPASFile() : TOPPASBase
addTransition() : MRMTransitionGroup< ChromatogramType, TransitionType > , TargetedExperiment
addTreatment() : Sample
Adduct() : Adduct
AdductInfo() : AdductInfo
addUpSpectra() : SpectrumAddition
addUserLabelAnnotation_() : Spectrum1DCanvas
addUserPeakAnnotation_() : Spectrum1DCanvas
addValue() : BilinearInterpolation< Key, Value > , LinearInterpolation< Key, Value >
addVertex() : TOPPASScene
addVSpacer_() : BaseVisualizerGUI
addWhiteNoise_() : RawMSSignalSimulation
addXLinkIonPeaks_() : TheoreticalSpectrumGeneratorXLMS
addXTANDEMFeatures() : PercolatorFeatureSetHelper
adjustBuffer_() : SpectrumCanvas
adjustCorrectToMS1Precursor() : ProcessData
advanceFollowUp() : IsobaricChannelExtractor::PuritySate_
affineGapalign_() : MapAlignmentAlgorithmSpectrumAlignment
after() : SysInfo::MemUsage
align() : MapAlignmentAlgorithmIdentification , MapAlignmentAlgorithmPoseClustering , MapAlignmentAlgorithmSpectrumAlignment
aliphatic() : AAIndex
allInputsReady() : TOPPASVertex
AminoAcidModification() : PepXMLFile::AminoAcidModification
AnalysisSummary() : MSQuantifications::AnalysisSummary
analyzeHeader_() : QuantitativeExperimentalDesign
analyzeLCElutionPeak() : LCElutionPeak
annotate() : IDMapper , RNPxlReport
annotate_() : AccurateMassSearchEngine
annotateIon() : MRMIonSeries
annotateMatches() : SpectrumAnnotator
annotateMS1FromMassFingerprinting_() : TOPPViewBase
annotateSwathMapsFromFile() : SwathWindowLoader
annotateTransition() : MRMIonSeries
annotateTransitionCV() : MRMIonSeries
annotateWithID() : TOPPViewBase
Annotation1DCaret() : Annotation1DCaret
Annotation1DDistanceItem() : Annotation1DDistanceItem
Annotation1DItem() : Annotation1DItem
Annotation1DPeakItem() : Annotation1DPeakItem
Annotation1DTextItem() : Annotation1DTextItem
Annotations1DContainer() : Annotations1DContainer
AnnotationStatistics() : AnnotationStatistics
annotationToCV_() : MRMIonSeries
annotationToCVTermList_() : MRMIonSeries
append() : ToolDescription , TOPPASVertex::TOPPASFilenames
appendASCII() : StringManager
appendChromatogram() : IChromatogramsWriter
appendConsumer() : MSDataChainingConsumer
appendSpectrum() : ISpectraWriter
apply() : ComplementFilter , ComplementMarker , ConsensusIDAlgorithm , DeNovoPostScoring , FalseDiscoveryRate , FilterFunctor , GoodDiffFilter , IDDecoyProbability , IntensityBalanceFilter , IsotopeDiffFilter , IsotopeMarker , NeutralLossDiffFilter , NeutralLossMarker , PeakMarker , TICFilter , TransformationDescription
apply_() : ConsensusIDAlgorithm , ConsensusIDAlgorithmIdentity , ConsensusIDAlgorithmSimilarity , IDDecoyProbability
applyAtMostOneVariableModification_() : ModifiedPeptideGenerator
applyDesign2Quantifier() : QuantitativeExperimentalDesign
applyDesign2Resolver() : QuantitativeExperimentalDesign
applyDilation_() : MorphologicalFilter
applyDilationSimple_() : MorphologicalFilter
applyErosion_() : MorphologicalFilter
applyErosionSimple_() : MorphologicalFilter
applyFixedModifications() : ModifiedPeptideGenerator
applyLabelToProteinHit_() : SILACLabeler
applyLogTransformation() : Histogram< ValueType, BinSizeType >
applyMemberFunction() : ConsensusMap , Feature , FeatureMap
applyToBaseFeature_() : MapAlignmentTransformer
applyToConsensusFeature_() : MapAlignmentTransformer
applyTOFConversion_() : TOFCalibration
applyToFeature_() : MapAlignmentTransformer
applyTransformation() : InternalCalibration
applyTransformation_() : InternalCalibration
applyTransformations() : KDTreeFeatureMaps
applyVariableModifications() : ModifiedPeptideGenerator
areaBegin() : MSExperiment
areaBeginConst() : MSExperiment
areaEnd() : MSExperiment
areaEndConst() : MSExperiment
AreaIterator() : AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
asBool_() : XMLHandler
AScore() : AScore
asDateTime_() : XMLHandler
asDouble_() : XMLHandler
asFloat_() : XMLHandler
asInt_() : XMLHandler
askForOutputDir() : TOPPASScene
asMass() : AccurateMassSearchEngine::CompareEntryAndMass_
asMutable() : FeatureHandle
Assay() : MSQuantifications::Assay
assembleInclusionListForProteinBasedLP_() : PSLPFormulation
assign() : ConstRefVector< ContainerT > , DIntervalBase< D >
assignDeltaScore_() : PercolatorFeatureSetHelper
assignRanks() : PeptideIdentification , ProteinIdentification
assignUIDs() : MSQuantifications
associateMS2FeatureToMS1Feature() : FTPeakDetectController
asUInt_() : XMLHandler
AsymmetricStatistics() : AsymmetricStatistics< RealT >
at() : SparseVector< Value >
attachLayer() : SpectraIdentificationViewWidget
Attachment() : QcMLFile::Attachment
attributeAsDouble_() : XMLHandler
attributeAsDoubleList_() : XMLHandler
attributeAsInt_() : XMLHandler
attributeAsIntList_() : XMLHandler
attributeAsString_() : XMLHandler
attributeAsStringList_() : XMLHandler
AUC() : ROCCurve
autoUpdateProjections() : Spectrum2DWidget
average() : SpectraMerger
averageCentroidSpectra_() : SpectraMerger
averageCoefficients_() : TOFCalibration
averageErrors_() : TOFCalibration
AverageLinkage() : AverageLinkage
averagePopulationAberration() : ClusterAnalyzer
AveragePosition() : AveragePosition< D >
averageProfileSpectra_() : SpectraMerger
averageSilhouetteWidth() : ClusterAnalyzer
averagineSimilarityFilter_() : MultiplexFiltering
AxisPainter() : AxisPainter
AxisTickCalculator() : AxisTickCalculator
AxisWidget() : AxisWidget