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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() :
TOPPViewBase
,
TOPPViewBehaviorInterface
,
TOPPViewIdentificationViewBehavior
,
TOPPViewSpectraViewBehavior
activateAsPrecursorPeak() :
MSPeak
activateBehavior() :
TOPPViewBehaviorInterface
,
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
addBaseLine_() :
RawMSSignalSimulation
addBooleanComboBox_() :
BaseVisualizerGUI
addButton_() :
BaseVisualizerGUI
addChromatogram() :
MRMTransitionGroup< SpectrumType, TransitionType >
,
MSExperiment< PeakT, ChromatogramPeakT >
addCluster() :
ClusteringGrid
addColumn() :
LPWrapper
addComboBox_() :
BaseVisualizerGUI
addCompound() :
TargetedExperiment
addConfiguration() :
IncludeExcludeTarget
,
TraMLProduct
addConsensusMap() :
MSQuantifications
addContact() :
TargetedExperiment
addConvexHull() :
FeaFiModule< PeakType >
addCV() :
TargetedExperiment
addCVReference() :
CVMappings
addCVTerm() :
CVMappingRule
,
CVTermList
addData() :
TOPPViewBase
addData_() :
MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, addMassTraces >
,
MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, false >
,
MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, true >
addDataFile() :
TOPPViewBase
addDataProcessing() :
MSDataWritingConsumer
addDataProcessing_() :
SpectrumCanvas
,
TOPPBase
addDetectorNoise_() :
RawMSSignalSimulation
addDoubleLineEdit_() :
BaseVisualizerGUI
addEdge() :
TOPPASScene
addEluent() :
Gradient
addEluent_() :
GradientVisualizer
addEmptyLine_() :
TOPPBase
addEnzymeInfo() :
SequestInfile
addExcludeTarget() :
TargetedExperiment
addExternalType() :
ToolDescription
addFakeMSMSToFeature() :
FTPeakDetectController
addFeature() :
MRMFeature
,
MRMTransitionGroup< SpectrumType, TransitionType >
addFile() :
FileWatcher
addFilterResultPeak() :
MultiplexFilterResult
addHit() :
SpectrumIdentification
,
FoundProteinFunctor
addHoveringEdge() :
TOPPASScene
addIncludeTarget() :
TargetedExperiment
addInEdge() :
TOPPASVertex
addInstrument() :
TargetedExperiment
addIntensity() :
BackgroundIntensityBin
addIntermediateProduct() :
ReactionMonitoringTransition
addInterpretation() :
IncludeExcludeTarget
,
TraMLProduct
addIntLineEdit_() :
BaseVisualizerGUI
addIsotopeTrace() :
ConsensusIsotopePattern
addLabel_() :
BaseVisualizerGUI
addLabelAnnotation_() :
Spectrum1DCanvas
addLabelToProteinHits_() :
ICPLLabeler
addLayer() :
SpectrumCanvas
addLCelutionProfile() :
FTPeakDetectController
addLine() :
TextFile
addLineEdit_() :
BaseVisualizerGUI
addLineEditButton_() :
BaseVisualizerGUI
addListView_() :
BaseVisualizerGUI
addLossFormula() :
Residue
addLossName() :
Residue
addMappingRule() :
CVMappings
addMassTrace() :
FeatureHypothesis
addMaxInclusionListSizeConstraints_() :
PSLPFormulation
addModification() :
ModificationDefinitionsSet
addModification_() :
MRMAssay
,
TransitionTSVReader
addModificationsSequences_() :
MRMAssay
addModificationToPeptideHit_() :
ICPLLabeler
,
ITRAQLabeler
,
O18Labeler
,
SILACLabeler
addMS1elutionSignal() :
FeatureLCProfile
addMS1Map_() :
CachedSwathFileConsumer
,
RegularSwathFileConsumer
addMS2ConsensusSpectrum() :
ClusteredMS2ConsensusSpectrum
addMS2Feature() :
SHFeature
addMS2FeatureToMS1Feature() :
FTPeakDetectController
addMS2Fragment() :
MS2ConsensusSpectrum
addMSLevel() :
PeakFileOptions
addMSPeak() :
BackgroundIntensityBin
addNewState() :
HiddenMarkovModel
addNewSwathMap_() :
CachedSwathFileConsumer
,
RegularSwathFileConsumer
addNTermLossFormula() :
Residue
addNTermLossName() :
Residue
addOutEdge() :
TOPPASVertex
addOutsideMS1elutionSignal() :
FeatureLCProfile
addPeak_() :
PeakPickerCWT
addPeakAnnotation() :
Spectrum1DCanvas
addPeakAnnotations_() :
TOPPViewIdentificationViewBehavior
addPeakMSScan() :
BackgroundControl
addPeaks() :
TheoreticalSpectrumGenerator
addPeaks_() :
PILISModel
addPeptide() :
TargetedExperiment
addPeptideEvidence() :
PeptideHit
addPoint() :
ConvexHull2D
addPoints() :
ConvexHull2D
addPrecursorAcquisitionNumberConstraint_() :
PSLPFormulation
addPrecursorChromatogram() :
MRMTransitionGroup< SpectrumType, 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
addResidue() :
ResidueDB
addResidue_() :
ResidueDB
addResidueSet() :
Residue
addRow() :
LPWrapper
addRTBinCapacityConstraint_() :
PSLPFormulation
addRunAttachment() :
QcMLFile
addRunQualityParameter() :
QcMLFile
addScore() :
MRMFeature
addSearchFile() :
IDEvaluationBase
addSeparator_() :
BaseVisualizerGUI
addSetAttachment() :
QcMLFile
addSetQualityParameter() :
QcMLFile
addShotNoise_() :
RawMSSignalSimulation
addSingleChargedIons_() :
CompNovoIonScoringBase
addSoftware() :
TargetedExperiment
addSourceFile() :
TargetedExperiment
addSpectrum() :
MSExperiment< PeakT, ChromatogramPeakT >
addSpectrumIdentification() :
Identification
addSpectrumMetaData_() :
MzMLHandler< MapType >
addStepSizeConstraint_() :
PSLPFormulation
addSuccessorState() :
HMMState
addSynonym() :
Residue
,
ResidueModification
addSynonymTransition() :
HiddenMarkovModel
addTab() :
EnhancedTabBar
,
TOPPASTabBar
addTag() :
Param
addTags() :
Param
addTargetCVTerm() :
TargetedExperiment
addText_() :
TOPPBase
addTextEdit_() :
BaseVisualizerGUI
addTheoreticalSpectrumLayer_() :
TOPPViewIdentificationViewBehavior
addTimepoint() :
Gradient
addTimepoint_() :
GradientVisualizer
addToCache_() :
LogStreamBuf
addToGroup() :
FeatureGroupingAlgorithmUnlabeled
addTOPPASFile() :
TOPPASBase
addTransition() :
MRMTransitionGroup< SpectrumType, 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
adjustBuffer_() :
SpectrumCanvas
adjustCorrectToMS1Precursor() :
ProcessData
advanceFollowUp() :
IsobaricChannelExtractor::PuritySate_
affineGapalign_() :
MapAlignmentAlgorithmSpectrumAlignment
align() :
MapAlignmentAlgorithmPoseClustering
alignCompactFeatureMaps() :
MapAlignmentAlgorithm
alignConsensusMaps() :
MapAlignmentAlgorithm
,
MapAlignmentAlgorithmIdentification
alignFeatureMaps() :
MapAlignmentAlgorithm
,
MapAlignmentAlgorithmIdentification
alignMaps() :
MapAlignmentAlgorithmIdentification
alignPeakMaps() :
MapAlignmentAlgorithm
,
MapAlignmentAlgorithmIdentification
,
MapAlignmentAlgorithmSpectrumAlignment
alignPeptideIdentifications() :
MapAlignmentAlgorithm
,
MapAlignmentAlgorithmIdentification
aliphatic() :
AAIndex
allInputsReady() :
TOPPASMergerVertex
,
TOPPASVertex
AminoAcidModification() :
PepXMLFile::AminoAcidModification
AnalysisSummary() :
MSQuantifications::AnalysisSummary
analyzeHeader_() :
QuantitativeExperimentalDesign
analyzeLCElutionPeak() :
LCElutionPeak
annotate() :
IDMapper
annotate_() :
AccurateMassSearchEngine
annotateIon() :
MRMIonSeries
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
appendASCII() :
StringManager
appendChromatogram() :
IChromatogramsWriter
appendConsumer() :
MSDataChainingConsumer
appendSpectrum() :
ISpectraWriter
apply() :
ComplementFilter
,
ComplementMarker
,
ConsensusIDAlgorithm
,
DeNovoPostScoring
,
FalseDiscoveryRate
,
FilterFunctor
,
GoodDiffFilter
,
IDDecoyProbability
,
IntensityBalanceFilter
,
IsotopeDiffFilter
,
IsotopeMarker
,
NeutralLossDiffFilter
,
NeutralLossMarker
,
PeakMarker
,
PILISCrossValidation
,
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
applyVariableModifications() :
ModifiedPeptideGenerator
areaBegin() :
MSExperiment< PeakT, ChromatogramPeakT >
areaBeginConst() :
MSExperiment< PeakT, ChromatogramPeakT >
areaEnd() :
MSExperiment< PeakT, ChromatogramPeakT >
areaEndConst() :
MSExperiment< PeakT, ChromatogramPeakT >
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 >
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
OpenMS / TOPP release 2.0.0
Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11