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- c -
cacheChunk() :
FASTAContainer< TFI_File >
,
FASTAContainer< TFI_Vector >
CachedmzML() :
CachedmzML
CachedMzMLHandler() :
CachedMzMLHandler
CachedSwathFileConsumer() :
CachedSwathFileConsumer
calc_qfdr_() :
XFDRAlgorithm
calcChargeStateIntensities_() :
ProtonDistributionModel
calcElutionFitScore() :
EmgScoring
calcFragmentIsotopeDist() :
CoarseIsotopePatternGenerator
calcFragmentIsotopeDist_() :
CoarseIsotopePatternGenerator
calcGridLines() :
AxisTickCalculator
calcLibraryScore() :
MRMScoring
calcLogGridLines() :
AxisTickCalculator
calcMIPrecursorCombinedScore() :
MRMScoring
calcMIPrecursorContrastScore() :
MRMScoring
calcMIPrecursorScore() :
MRMScoring
calcMIScore() :
MRMScoring
calcMIWeightedScore() :
MRMScoring
calcRTScore() :
MRMScoring
calcSeparateMIContrastScore() :
MRMScoring
calcSeparateSNScore() :
MRMScoring
calcSeparateXcorrContrastCoelutionScore() :
MRMScoring
calcSeparateXcorrContrastShapeScore() :
MRMScoring
calcSNScore() :
MRMScoring
calculate_lda_prescore() :
OpenSwath_Scores
calculate_lda_single_transition() :
OpenSwath_Scores
calculate_swath_lda_prescore() :
OpenSwath_Scores
calculateAddInfo_() :
PeakIntensityPredictor
calculateAndAnnotateIndistProteins() :
IDBoostGraph
calculateAndAnnotateIndistProteins_() :
IDBoostGraph
calculateAndFilterFDR_() :
NucleicAcidSearchEngine
calculateAveragine() :
FLASHDeconvAlgorithm
calculateAvgWeight_() :
ElementDB
calculateBackwardPart_() :
HiddenMarkovModel
calculateBias() :
AbsoluteQuantitation
calculateBiasAndR() :
AbsoluteQuantitation
calculateCalibCoeffs_() :
TOFCalibration
calculateChromatographicIdScores() :
OpenSwathScoring
calculateChromatographicScores() :
OpenSwathScoring
calculateCorrectionFactor() :
DBSuitability_friend
calculateCorrectionFactor_() :
DBSuitability
calculateCoverages() :
IdentificationData
calculateDIAIdScores() :
OpenSwathScoring
calculateDIAScores() :
OpenSwathScoring
calculateEmissionProbabilities() :
HiddenMarkovModel
calculateEstimatedQVal_() :
FalseDiscoveryRate
calculateFDR_() :
FeatureFinderIdentificationAlgorithm
calculateFDRBasic_() :
FalseDiscoveryRate
calculateFDRs_() :
FalseDiscoveryRate
calculateFilterValuesMean() :
MRMFeatureFilter
calculateFilterValuesPercRSD() :
MRMFeatureFilter
calculateFilterValuesVar() :
MRMFeatureFilter
calculateFitQuality_() :
ElutionModelFitter
calculateFME_() :
FragmentMassError
calculateForwardPart_() :
HiddenMarkovModel
calculateGaussTable() :
SVMWrapper
calculateGB() :
AAIndex
calculateGridLines_() :
Plot3DOpenGLCanvas
calculateIntensityRankInMZWindow() :
PScore
calculateIonRatio() :
MRMFeatureFilter
calculateIsotopicPurities() :
IsotopeLabelingMDVs
calculateIsotopicPurity() :
IsotopeLabelingMDVs
calculateLibraryScores() :
OpenSwathScoring
calculateMap() :
QCBase::SpectraMap
calculateMDV() :
IsotopeLabelingMDVs
calculateMDVAccuracies() :
IsotopeLabelingMDVs
calculateMDVAccuracy() :
IsotopeLabelingMDVs
calculateMDVs() :
IsotopeLabelingMDVs
calculateMonoWeight_() :
ElementDB
calculateMT_() :
RTSimulation
calculateMZ_() :
FeatureFinderAlgorithmMetaboIdent
calculatePeakLevelSpectra() :
PScore
calculatePeakShapeMetrics() :
PeakIntegrator
calculatePeakShapeMetrics_() :
PeakIntegrator
calculatePermutationPeptideScores_() :
AScore
calculatePrecursorDIAScores() :
OpenSwathScoring
calculatePrecursorMass_() :
NucleicAcidSearchEngine
calculateProteinProbabilities() :
PSProteinInference
calculateProtonDistribution_() :
ProtonDistributionModel
calculateProtonDistributionCharge1_() :
ProtonDistributionModel
calculateProtonDistributionCharge2_() :
ProtonDistributionModel
calculateProtonDistributionGreater2_() :
ProtonDistributionModel
calculateProtonDistributionIonPair_() :
ProtonDistributionModel
calculateRankMap() :
PScore
calculateRatio() :
AbsoluteQuantitation
calculateResolution() :
MRMFeatureFilter
calculateRTDifference() :
MRMFeatureFilter
calculateSpectrum_() :
TheoreticalSpectrumGenerationDialog
calculateSuitability_() :
DBSuitability
calculateTheoreticalIsotopesNumber() :
EmpiricalFormula
calculateTIC() :
Mobilogram
,
MSExperiment
,
MSSpectrum
calculateVariance_() :
FragmentMassError
calculateXICs_() :
OfflinePrecursorIonSelection
,
PSLPFormulation
calcXcorrCoelutionScore() :
MRMScoring
calcXcorrCoelutionWeightedScore() :
MRMScoring
calcXcorrContrastCoelutionScore() :
MRMScoring
calcXcorrContrastShapeScore() :
MRMScoring
calcXcorrPrecursorCoelutionScore() :
MRMScoring
calcXcorrPrecursorCombinedCoelutionScore() :
MRMScoring
calcXcorrPrecursorCombinedShapeScore() :
MRMScoring
calcXcorrPrecursorContrastCoelutionScore() :
MRMScoring
calcXcorrPrecursorContrastShapeScore() :
MRMScoring
calcXcorrPrecursorContrastSumFragCoelutionScore() :
MRMScoring
calcXcorrPrecursorContrastSumFragShapeScore() :
MRMScoring
calcXcorrPrecursorShapeScore() :
MRMScoring
calcXcorrShapeScore() :
MRMScoring
calcXcorrShapeWeightedScore() :
MRMScoring
CalibrantStats_() :
InternalCalibration::CalibrantStats_
calibrate() :
InternalCalibration
,
TOFCalibration
CalibrationData() :
CalibrationData
callSiriusQProcess() :
SiriusAdapterAlgorithm
callUpdateEntries() :
DataSelectionTabs
candidateEdges_() :
MetaboliteFeatureDeconvolution
canModificationBeApplied_() :
SILACLabeler
canRun() :
JavaInfo
,
PythonInfo
canvas() :
Plot1DWidget
,
Plot2DWidget
,
Plot3DWidget
,
PlotWidget
canvasPixelArea() :
PlotCanvas
capacity() :
ConstRefVector< ContainerT >
cbegin() :
ExposedVector< VectorElement >
,
Mobilogram
,
NASequence
cellindexAtClustercenter_() :
HashGrid< Cluster >
cend() :
ExposedVector< VectorElement >
,
Mobilogram
,
NASequence
center() :
DIntervalBase< D >
,
RangeBase
centerOfBin() :
Histogram< ValueType, BinSizeType >
changedOutputFolder() :
TOPPASScene
changedParameter() :
TOPPASScene
changeLabel() :
TOPPViewBase
changeLayerFilterState() :
PlotCanvas
changeLayerFlag() :
TOPPViewBase
changeLegendVisibility() :
PlotCanvas
,
PlotWidget
changeUnassigned() :
TOPPViewBase
changeVisibility() :
PlotCanvas
changeVisibleArea_() :
Plot1DCanvas
,
PlotCanvas
changeVisibleAreaCommon_() :
Plot1DCanvas
characters() :
CVMappingFile
,
ConsensusXMLHandler
,
FeatureXMLHandler
,
MascotXMLHandler
,
MzDataHandler
,
MzIdentMLHandler
,
MzMLHandler
,
MzQuantMLHandler
,
MzXMLHandler
,
PTMXMLHandler
,
SemanticValidator
,
ToolDescriptionHandler
,
TraMLHandler
,
UnimodXMLHandler
,
XMLHandler
,
OMSSAXMLFile
,
QcMLFile
,
XTandemXMLFile
charge() :
KDTreeFeatureMaps
ChargedIndexSet() :
IsotopeCluster::ChargedIndexSet
ChargePair() :
ChargePair
chargeTestworthy_() :
FeatureDeconvolution
,
MetaboliteFeatureDeconvolution
chauvenet() :
MRMRTNormalizer
chauvenet_probability() :
MRMRTNormalizer
check_() :
DataFilterDialog
,
TOPPASVertex::TOPPASFilenames
check_tree() :
KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
checkAndGetTermByName() :
ControlledVocabulary
checkAppliedProcessingSteps_() :
IdentificationData
CheckBox() :
TheoreticalSpectrumGenerationDialog::CheckBox
checkCompat_() :
BasicProteinInferenceAlgorithm
checkConditionISO_() :
MSstatsFile
checkConditionLFQ_() :
MSstatsFile
,
TriqlerFile
checkDatumRange() :
TransformationModel
checkDefaults() :
Param
checkDuplicated() :
ToolHandler
checked() :
Plot1DGoToDialog
,
Plot2DGoToDialog
checkedToDouble_() :
EDTAFile
checkedToInt_() :
EDTAFile
checkExtraFeatures() :
PercolatorFeatureSetHelper
checkFDInputReady_() :
FLASHDeconvTabWidget
checkFeatureQuality_() :
FeatureFinderAlgorithmPicked
checkFormula_() :
Adduct
checkForRequiredUserParams_() :
PrecursorIonSelection
checkForSignificantPeak_() :
MultiplexFiltering
checkHits_() :
IDMapper
checkIds_() :
BaseGroupFinder
checkIfIniParametersAreApplicable_() :
TOPPBase
checkIfWeAreDone() :
TOPPASScene
checkLOD() :
AbsoluteQuantitationMethod
checkLOQ() :
AbsoluteQuantitationMethod
checkMassRanges_() :
OfflinePrecursorIonSelection
checkMassType_() :
IDMapper
checkMaximalRTSpan() :
EGHTraceFitter
,
GaussTraceFitter
,
TraceFitter
checkMetaValue() :
MRMFeatureFilter
checkMinimalRTSpan() :
EGHTraceFitter
,
GaussTraceFitter
,
TraceFitter
checkName_() :
ControlledVocabulary
checkNumObservations_() :
FeatureFinderIdentificationAlgorithm
checkOldRunConsistency_() :
ConsensusMapMergerAlgorithm
,
IDMergerAlgorithm
checkOSWInputReady_() :
SwathTabWidget
checkParam_() :
TOPPBase
checkParameters_() :
MapAlignmentAlgorithmIdentification
checkParentMatches_() :
IdentificationData
checkPositionForPlausibility_() :
IsotopeWaveletTransform< PeakType >
checkPPMTheoModel_() :
IsotopeWaveletTransform< PeakType >
checkPreferences_() :
TOPPViewBase
checkPyProphetInput_() :
SwathTabWidget
checkRange() :
MRMFeatureFilter
checkSatellite() :
MultiplexFilteredPeak
checkScoreBetterThanThreshold_() :
DBSuitability
checkScoreTypes_() :
IdentificationData
checkSequenceUniqueness_() :
MzTab
checkSize() :
SaveImageDialog
checkSolution_() :
FeatureDeconvolution
,
MetaboliteFeatureDeconvolution
checkSwathMap() :
OpenSwathHelper
checkSwathMapAndSelectTransitions() :
OpenSwathHelper
checkTDAnnotation_() :
IDScoreGetterSetter
checkTransitions_() :
OSWData
checkUniqueIdentifiers_() :
XMLHandler
checkUnorderedContent_() :
MSstatsFile
,
TriqlerFile
checkValidity_() :
TOPPASInputFileDialog
,
TOPPASIOMappingDialog
,
TOPPASOutputFilesDialog
checkValidWeight() :
TransformationModel
chooseBestParameters_() :
SimpleSVM
chooseDecoys_() :
ConfidenceScoring
chooseElutionProfile_() :
RawMSSignalSimulation
chooseFilesDialog_() :
TOPPViewBase
chooseTraceFitter_() :
FeatureFinderAlgorithmPicked
chop() :
String
Chromatogram() :
Chromatogram
chromatogram_flag_set() :
LayerDataPeak
chromatogramIdsMatch() :
MRMTransitionGroup< ChromatogramType, TransitionType >
ChromatogramMeta() :
ChromatogramMeta
ChromatogramPeak() :
ChromatogramPeak
ChromatogramSettings() :
ChromatogramSettings
ChromatogramTools() :
ChromatogramTools
ChromeleonFile() :
ChromeleonFile
chromsDoubleClicked() :
SpectraTreeTab
chromsSelected() :
SpectraTreeTab
Chunk() :
MSSpectrum::Chunk
chunk_() :
FeatureFinderIdentificationAlgorithm
chunkAt() :
FASTAContainer< TFI_File >
,
FASTAContainer< TFI_Vector >
Chunks() :
MSSpectrum::Chunks
chunkSize() :
FASTAContainer< TFI_File >
,
FASTAContainer< TFI_Vector >
clampTo() :
RangeBase
,
RangeManager< RangeBases >
clampToUnsafe() :
RangeManager< RangeBases >
classifyFeatures_() :
FeatureFinderIdentificationAlgorithm
classifyIsotopes_() :
CompNovoIonScoringBase
cleanup() :
IdentificationData
cleanupTransitions_() :
TransitionTSVFile
clear() :
KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
,
Area< N_DIM >
,
CalibrationData
,
ConsensusFeature
,
ConsensusMap
,
ConstRefVector< ContainerT >
,
ConvexHull2D
,
CsvFile
,
DataFilters
,
DataTabBase
,
Date
,
DateTime
,
DBSuitability::SuitabilityData
,
DeconvolvedSpectrum
,
DIATreeTab
,
DistanceMatrix< Value >
,
DPosition< D, TCoordinateType >
,
FeatureMap
,
HashGrid< Cluster >
,
HiddenMarkovModel
,
IdentificationData
,
IMSAlphabet
,
DIntervalBase< D >
,
IsotopeDistribution
,
KDTreeFeatureMaps
,
AsymmetricStatistics< RealT >
,
AveragePosition< D >
,
BasicStatistics< RealT >
,
Matrix< Value >
,
MetaInfo
,
Mobilogram
,
MSChromatogram
,
MSExperiment
,
MSSpectrum
,
NASequence
,
OSWData
,
Param
,
ParamEditor
,
PeakIndex
,
QCBase::SpectraMap
,
RangeBase
,
RangeManager< RangeBases >
,
SpectraIDViewTab
,
SpectraTreeTab
,
StopWatch
,
TargetedExperiment
,
TOPPASResources
clear_() :
DataValue
,
ElementDB
,
MetaInfoVisualizer
,
ParamValue
,
PeakGroup
,
SimpleSVM
clearCache() :
LogStreamBuf
clearCurrentProcessingStep() :
IdentificationData
clearEluents() :
Gradient
clearInitialTransitionProbabilities() :
HiddenMarkovModel
clearMetaDataArrays() :
MSExperiment
clearMetaInfo() :
MetaInfoInterface
clearMSLevels() :
PeakFileOptions
clearPercentages() :
Gradient
clearPrimaryID() :
BaseFeature
clearProteins() :
OSWData
clearRanges() :
RangeManager< RangeBases >
clearResult() :
ProteinResolver
clearTags() :
Param
clearTimepoints() :
Gradient
clearTrainingEmissionProbabilities() :
HiddenMarkovModel
clearUniqueId() :
UniqueIdInterface
cleavageCorrectionTerm() :
PScore
CleavageModel_() :
EnzymaticDigestionLogModel::CleavageModel_
clicked() :
TOPPASVertex
clockTime() :
StopWatch::TimeDiff_
clone() :
Annotation1DCaret< DataPoint >
,
Annotation1DDistanceItem
,
Annotation1DItem
,
Annotation1DPeakItem< DataPoint >
,
Annotation1DTextItem
,
Annotation1DVerticalLineItem
,
Digestion
,
DimBase
,
DimIM
,
DimINT
,
DimMZ
,
DimRT
,
Modification
,
SampleTreatment
,
Tagging
cloneWith() :
Area< N_DIM >
close() :
Bzip2Ifstream
,
GzipIfstream
,
HDF5Connector
closeByTab() :
TOPPASBase
,
TOPPViewBase
closeEditor_() :
ParamEditorDelegate
closeEvent() :
INIFileEditorWindow
,
ListFilterDialog
,
PlotWidget
,
TOPPASBase
,
TOPPASWidget
,
TOPPViewBase
closeFile() :
TOPPASBase
closeRequested() :
EnhancedTabBar
closeTab() :
TOPPViewBase
cluster() :
ClusterHierarchical
,
GridBasedClustering< Metric >
,
MultiplexClustering
ClusterAnalyzer() :
ClusterAnalyzer
ClusterFunctor() :
ClusterFunctor
ClusterHierarchical() :
ClusterHierarchical
clusterIndistProteinsAndPeptides() :
IDBoostGraph
clusterIndistProteinsAndPeptidesAndExtendGraph() :
IDBoostGraph
ClusteringGrid() :
ClusteringGrid
ClusterProxyKD() :
ClusterProxyKD
clusterSeeds_() :
IsotopeWaveletTransform< PeakType >
CMMzTabStream() :
MzTab::CMMzTabStream
cmpOligos_() :
LibSVMEncoder
CoarseIsotopePatternGenerator() :
CoarseIsotopePatternGenerator
cohesion() :
ClusterAnalyzer
col() :
Matrix< Value >
colIndex() :
Matrix< Value >
collapseFramesToSingle() :
IMDataConverter
collapseStringVector() :
TVIdentificationViewController
collectDecompositionsRecursively_() :
IntegerMassDecomposer< ValueType, DecompositionValueType >
collectFragmentScansInArea_() :
Plot2DCanvas
collectPrecursorCandidates() :
OPXLHelper
collectQCData() :
QcMLFile
collectRatios_() :
IsobaricNormalizer
collectSetParameter() :
QcMLFile
colnames() :
CSVWriter
,
DataMatrix
,
IDataFrameWriter
color() :
MultiGradient
Colorizer() :
Colorizer
ColorSelector() :
ColorSelector
colorStream_() :
Colorizer
cols() :
Matrix< Value >
columnExists() :
SqliteConnector
ColumnHeader() :
ConsensusMap::ColumnHeader
combineMods() :
ResidueModification
combinePrecursorPurities() :
PrecursorPurity
combineTopRanksFromPairs() :
OPXLHelper
Command() :
Command
commitAndCloseEditor_() :
ParamEditorDelegate
commitAndCloseLineEdit_() :
ParamEditorDelegate
Compare() :
MapAlignmentAlgorithmSpectrumAlignment::Compare
compare_() :
Contaminants
compareChargeStates_() :
ConsensusIDAlgorithm
compareFiles() :
FuzzyStringComparator
compareIDsSmallerScores_() :
IDConflictResolverAlgorithm
compareLines_() :
FuzzyStringComparator
compareMZ_() :
AScore
comparepeaks_() :
SpectrumCheapDPCorr
compareSpectra_() :
CompNovoIdentificationBase
compareStreams() :
FuzzyStringComparator
compareStrings() :
FuzzyStringComparator
compatible() :
MassDecomposition
compatible_() :
PrecursorCorrection
compatibleIDs_() :
StablePairFinder
ComplementFilter() :
ComplementFilter
ComplementMarker() :
ComplementMarker
CompleteLinkage() :
CompleteLinkage
CompNovoIdentification() :
CompNovoIdentification
CompNovoIdentificationBase() :
CompNovoIdentificationBase
CompNovoIdentificationCID() :
CompNovoIdentificationCID
CompNovoIonScoring() :
CompNovoIonScoring
CompNovoIonScoringBase() :
CompNovoIonScoringBase
CompNovoIonScoringCID() :
CompNovoIonScoringCID
Compomer() :
Compomer
compomerValid_() :
MassExplainer
Compound() :
Compound
CompoundSpectrumPair() :
MetaboTargetedAssay::CompoundSpectrumPair
CompoundTargetDecoyPair() :
MetaboTargetedAssay::CompoundTargetDecoyPair
compress() :
ConvexHull2D
CompressedInputSource() :
CompressedInputSource
compressSignals_() :
RawMSSignalSimulation
compressString() :
ZlibCompression
compressTrie() :
ACTrie
compressTrieDB() :
InspectOutfile
compute() :
AScore
,
Contaminants
,
DBSuitability
,
FeatureDeconvolution
,
FeatureSummary
,
FragmentMassError
,
FWHM
,
HyperScore
,
IdentificationSummary
,
ILPDCWrapper
,
MassExplainer
,
MetaboliteFeatureDeconvolution
,
MissedCleavages
,
MorpheusScore
,
Ms2IdentificationRate
,
Ms2SpectrumStats
,
MzCalibration
,
PeptideMass
,
PSMExplainedIonCurrent
,
RTAlignment
,
SpectrumCount
,
TIC
compute_F() :
SpectraSTSimilarityScore
compute_z() :
EmgGradientDescent
,
EmgGradientDescent_friend
computeApexSNR() :
ElutionPeakDetection
computeAveragineSimScore_() :
FeatureFindingMetabo
computeBaseProbability_() :
AScore
computeBestClusterForCenter_() :
FeatureGroupingAlgorithmKD
computeBinnedCoverage() :
MRMRTNormalizer
computeBoundaries_() :
EGHModel
computeCCs_() :
MapAlignmentAlgorithmKD
computeChiSquare() :
LinearRegression
computeClustering_() :
QTClusterFinder
computeConnectedComponents() :
IDBoostGraph
computeConsensus() :
ConsensusFeature
computeCorrelation() :
ConsensusMapNormalizerAlgorithmThreshold
computeCosineSim_() :
AccurateMassSearchEngine
,
FeatureFindingMetabo
computeCoverage() :
ProteinIdentification
computeCoverageFromEvidenceMapping_() :
ProteinIdentification
computeCumulativeScore_() :
AScore
computeDataProperties_() :
MzMLHandlerHelper
computeDechargeConsensus() :
ConsensusFeature
computeDeltaScores() :
OPXLHelper
computeFileHash() :
FileHandler
computeFwhmArea() :
MassTrace
computeFwhmAreaSmooth() :
MassTrace
computeGoodness_() :
LinearRegression
computeHyperScore() :
MetaboliteSpectralMatching
computeHyperScore_() :
MetaboliteSpectralMatching
computeInitialMean() :
EmgGradientDescent
,
EmgGradientDescent_friend
computeIntensityOfMSD_() :
ProteinResolver
computeIntensityProfile() :
FeatureFinderAlgorithmPickedHelperStructs::MassTraces
computeIsotopeDistributionSize_() :
IsotopeWavelet
computeIsotopePatternSimilarity_() :
AccurateMassSearchEngine
computeKernelMatrix() :
SVMWrapper
computeLabelingStatistics_() :
IsobaricQuantifier
computeLLAndIncorrectPosteriorsFromLogDensities() :
PosteriorErrorProbabilityModel
computeLogLikelihood() :
PosteriorErrorProbabilityModel
computeMassTraceNoise() :
ElutionPeakDetection
computeMassTraceSNR() :
ElutionPeakDetection
computeMedian_() :
SignalToNoiseEstimatorMedianRapid
computeMedianIntensity_() :
MassTrace
computeMedians() :
ConsensusMapNormalizerAlgorithmMedian
computeMedians_() :
MapAlignmentAlgorithmIdentification
computeMinSpacing() :
IsotopeWaveletTransform< PeakType >
computeModifications() :
ProteinIdentification
computeMonoisotopicConsensus() :
ConsensusFeature
computeMuMaxDistance() :
EmgGradientDescent
,
EmgGradientDescent_friend
computeNoiseInWindows_() :
SignalToNoiseEstimatorMedianRapid
computeNormalizationFactors_() :
IsobaricNormalizer
computePeakArea() :
MassTrace
computePermutations_() :
AScore
computePointY() :
LinearRegression
computePrecursorError() :
OPXLHelper
computePrecursorId() :
OpenSwathHelper
computePrecursorPurities() :
PrecursorPurity
computePrecursorPurity() :
PrecursorPurity
computePrecursorPurity_() :
IsobaricChannelExtractor
computeProbability() :
PosteriorErrorProbabilityModel
computePScore() :
PScore
computeQuality_() :
MRMTransitionGroupPicker
,
QTCluster
computeRegression() :
LinearRegression
,
QuadraticRegression
computeRegressionWeighted() :
LinearRegression
,
QuadraticRegression
computeScore_() :
MRMFeatureSelector
,
MRMFeatureSelector_test
computeSelection_() :
Plot3DOpenGLCanvas
computeSingleScanPrecursorPurity_() :
IsobaricChannelExtractor
computeSiteDeterminingIons_() :
AScore
computeSlice_() :
ILPDCWrapper
computeSliceOld_() :
ILPDCWrapper
computeSmoothedPeakArea() :
MassTrace
computeSonarScores() :
SONARScoring
computeSonarWindows_() :
OpenSwathWorkflowSonar
computeStatistics_() :
LayerStatistics
,
LayerStatisticsConsensusMap
,
LayerStatisticsFeatureMap
,
LayerStatisticsIdent
,
LayerStatisticsPeakMap
computeStats_() :
IsobaricIsotopeCorrector
computeSTN_() :
SignalToNoiseEstimator< Container >
,
SignalToNoiseEstimatorMeanIterative< Container >
,
SignalToNoiseEstimatorMedian< Container >
computeTheoretical() :
TraceFitter
computeTrafosByOriginalRT() :
MapAlignmentAlgorithmTreeGuided
computeTransformations_() :
MapAlignmentAlgorithmIdentification
computeTransformedFeatureMaps() :
MapAlignmentAlgorithmTreeGuided
computeTransitionGroupId() :
OpenSwathHelper
computeWeightedChiSquare() :
LinearRegression
computeWithDetail() :
HyperScore
computeXCorr_() :
SONARScoring
concatenate() :
ListUtils
,
String
concatMULTISEPeptideIds() :
PercolatorFeatureSetHelper
ConfidenceScoring() :
ConfidenceScoring
configure() :
LogConfigHandler
connectEdgeSignals() :
TOPPASScene
connectMergerVertexSignals() :
TOPPASScene
connectOutputVertexSignals() :
TOPPASScene
connectToolVertexSignals() :
TOPPASScene
connectVertexSignals() :
TOPPASScene
connectVisualizer_() :
MetaDataBrowser
ConsensusFeature() :
ConsensusFeature
ConsensusIDAlgorithm() :
ConsensusIDAlgorithm
ConsensusIDAlgorithmAverage() :
ConsensusIDAlgorithmAverage
ConsensusIDAlgorithmBest() :
ConsensusIDAlgorithmBest
ConsensusIDAlgorithmIdentity() :
ConsensusIDAlgorithmIdentity
ConsensusIDAlgorithmPEPIons() :
ConsensusIDAlgorithmPEPIons
ConsensusIDAlgorithmPEPMatrix() :
ConsensusIDAlgorithmPEPMatrix
ConsensusIDAlgorithmRanks() :
ConsensusIDAlgorithmRanks
ConsensusIDAlgorithmSimilarity() :
ConsensusIDAlgorithmSimilarity
ConsensusIDAlgorithmWorst() :
ConsensusIDAlgorithmWorst
ConsensusMap() :
ConsensusMap
ConsensusMapMergerAlgorithm() :
ConsensusMapMergerAlgorithm
ConsensusMapNormalizerAlgorithmMedian() :
ConsensusMapNormalizerAlgorithmMedian
ConsensusMapNormalizerAlgorithmQuantile() :
ConsensusMapNormalizerAlgorithmQuantile
ConsensusMapNormalizerAlgorithmThreshold() :
ConsensusMapNormalizerAlgorithmThreshold
ConsensusXMLFile() :
ConsensusXMLFile
ConsensusXMLHandler() :
ConsensusXMLHandler
ConsoleUtils() :
ConsoleUtils
ConstIterator() :
AASequence::ConstIterator
,
HashGrid< Cluster >::ConstIterator
,
NASequence::ConstIterator
ConstRefVector() :
ConstRefVector< ContainerT >
ConstRefVectorConstIterator() :
ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
ConstRefVectorIterator() :
ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
constructFile_() :
MSstatsFile
,
TriqlerFile
constructHeader_() :
IBSpectraFile
constructTargetDecoyMassMapping() :
MetaboTargetedTargetDecoy
constructTargTransList_() :
MRMFeatureSelector
,
MRMFeatureSelector_test
constructTransitionsList() :
TargetedSpectraExtractor
constructTransitionsMap_() :
MetaboTargetedTargetDecoy
consumeChromatogram() :
FullSwathFileConsumer
,
IMSDataConsumer
,
MSDataAggregatingConsumer
,
MSDataCachedConsumer
,
MSDataChainingConsumer
,
MSDataSqlConsumer
,
MSDataStoringConsumer
,
MSDataTransformingConsumer
,
MSDataWritingConsumer
,
NoopMSDataConsumer
,
NoopMSDataWritingConsumer
consumeCVTerms() :
CVTermList
,
CVTermListInterface
consumeMS1Spectrum_() :
CachedSwathFileConsumer
,
FullSwathFileConsumer
,
MzMLSwathFileConsumer
,
RegularSwathFileConsumer
consumeSpectrum() :
FullSwathFileConsumer
,
IMSDataConsumer
,
MSDataAggregatingConsumer
,
MSDataCachedConsumer
,
MSDataChainingConsumer
,
MSDataSqlConsumer
,
MSDataStoringConsumer
,
MSDataTransformingConsumer
,
MSDataWritingConsumer
,
NoopMSDataConsumer
,
NoopMSDataWritingConsumer
consumeSwathSpectrum_() :
CachedSwathFileConsumer
,
FullSwathFileConsumer
,
MzMLSwathFileConsumer
,
RegularSwathFileConsumer
Contact() :
Contact
ContactPerson() :
ContactPerson
ContactPersonVisualizer() :
ContactPersonVisualizer
contains() :
EmpiricalFormula
,
FileTypeList
,
ListUtils
,
RangeBase
containsAll() :
RangeManager< RangeBases >
containsIMData() :
MSSpectrum
containsIntensity() :
RangeIntensity
containsInvalidReferences() :
TargetedExperiment
containsMobility() :
RangeMobility
containsMSLevel() :
PeakFileOptions
containsMZ() :
RangeMZ
containsRT() :
RangeRT
containsScanOfLevel() :
MSExperiment
containsTag() :
MassDecomposition
Contaminants() :
Contaminants
contextMenuEvent() :
EnhancedTabBar
,
LayerListView
,
LogWindow
,
MultiGradientSelector
,
Plot1DCanvas
,
Plot2DCanvas
,
Plot3DCanvas
,
TOPPASEdge
,
TOPPASScene
,
TOPPASVertex
ContinuousWaveletTransform() :
ContinuousWaveletTransform
ContinuousWaveletTransformNumIntegration() :
ContinuousWaveletTransformNumIntegration
ControlledVocabulary() :
ControlledVocabulary
ConversionError() :
ConversionError
convert() :
StringManager
,
MapConversion
,
TransitionHelper
convertChromatogramsToSpectra() :
ChromatogramTools
convertData_() :
SimpleSVM
convertModificationSet_() :
XTandemInfile
convertPeptideIdScores_() :
PrecursorIonSelection
convertPeptideToAASequence() :
OpenSwathDataAccessHelper
convertPQPToTargetedExperiment() :
TransitionPQPFile
convertPtr() :
StringManager
convertSeedList() :
SeedListGenerator
convertSpectraToChromatograms() :
ChromatogramTools
convertTargetedCompound() :
OpenSwathDataAccessHelper
convertTargetedExp() :
OpenSwathDataAccessHelper
convertTargetedExperimentToPQP() :
TransitionPQPFile
convertTargetedExperimentToTSV() :
TransitionTSVFile
convertToChromatogramPtr() :
OpenSwathDataAccessHelper
convertToFeatureMap() :
FIAMSDataProcessor
convertToOpenMSChromatogram() :
OpenSwathDataAccessHelper
convertToOpenMSChromatogramFilter() :
OpenSwathDataAccessHelper
convertToOpenMSSpectrum() :
OpenSwathDataAccessHelper
convertToSpectrumPtr() :
OpenSwathDataAccessHelper
convertTransition_() :
TransitionTSVFile
convertTSVToTargetedExperiment() :
TransitionTSVFile
ConvexHull2D() :
ConvexHull2D
convolve() :
CoarseIsotopePatternGenerator
convolvePow_() :
CoarseIsotopePatternGenerator
convolveSquare_() :
CoarseIsotopePatternGenerator
copy() :
Param
copy_() :
HiddenMarkovModel
,
TOPPASOutputFileListVertex
copyBatchTransitions_() :
OpenSwathWorkflow
copyDirRecursively() :
File
copyLayer() :
TOPPViewBase
copyMetaDataOnly() :
ProteinIdentification
copySearchParams_() :
IDMergerAlgorithm
copySelected() :
TOPPASScene
copySubset() :
Param
correctGravityAxisOfVisibleArea_() :
Plot1DCanvas
correctIM() :
SwathMapMassCorrection
correctIsotopicImpurities() :
IsobaricIsotopeCorrector
correctMass_() :
CoarseIsotopePatternGenerator
correctMZ() :
SwathMapMassCorrection
correctPeptideIntensities_() :
FeatureFinderMultiplexAlgorithm
correctToHighestIntensityMS1Peak() :
PrecursorCorrection
correctToNearestFeature() :
PrecursorCorrection
correctToNearestMS1Peak() :
PrecursorCorrection
correlate_() :
PeakPickerCWT
count() :
squared_difference_counted< _Tp, _Dist >
,
ROCCurve
,
mean_and_stddev
count_within_range() :
KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
countDecoys() :
DecoyHelper
countEnzymatic_() :
PercolatorInfile
countFreeIDs() :
DocumentIDTagger
countHits() :
IDFilter
countIntensities_() :
SvmTheoreticalSpectrumGeneratorTrainer
countInternalCleavageSites() :
EnzymaticDigestion
countIonizedResidues_() :
IonizationSimulation
countLabelsAndTransitionTypes() :
MRMFeatureFilter
countMissedCleavages_() :
EnzymaticDigestion
countMissedCleavagesTryptic_() :
CompNovoIdentificationBase
countPeptides_() :
PeptideAndProteinQuant
countScansInSwath_() :
SwathFile
countTableRows() :
SqliteConnector
countTargetDecoy() :
ProteinResolver
countTreatments() :
Sample
crbegin() :
Mobilogram
create() :
AverageLinkage
,
BiGaussFitter1D
,
BiGaussModel
,
BinnedSharedPeakCount
,
BinnedSpectralContrastAngle
,
BinnedSumAgreeingIntensities
,
ComplementFilter
,
ComplementMarker
,
CompleteLinkage
,
EGHFitter1D
,
EGHModel
,
EmgFitter1D
,
EmgModel
,
ExtendedIsotopeFitter1D
,
ExtendedIsotopeModel
,
Factory< FactoryProduct >
,
FeatureFinderAlgorithmIsotopeWavelet
,
FeatureFinderAlgorithmMRM
,
FeatureFinderAlgorithmPicked
,
FeatureGroupingAlgorithmKD
,
FeatureGroupingAlgorithmLabeled
,
FeatureGroupingAlgorithmQT
,
FeatureGroupingAlgorithmUnlabeled
,
GaussFitter1D
,
GaussModel
,
GoodDiffFilter
,
GUIProgressLoggerImpl
,
ICPLLabeler
,
IntensityBalanceFilter
,
IsotopeDiffFilter
,
IsotopeFitter1D
,
IsotopeMarker
,
IsotopeModel
,
ITRAQLabeler
,
LabeledPairFinder
,
LabelFreeLabeler
,
ListUtils
,
MapAlignmentEvaluationAlgorithmPrecision
,
MapAlignmentEvaluationAlgorithmRecall
,
NeutralLossDiffFilter
,
NeutralLossMarker
,
O18Labeler
,
PeakAlignment
,
PoseClusteringAffineSuperimposer
,
PoseClusteringShiftSuperimposer
,
ProductModel< 2 >
,
ProteinIdentification::Mapping
,
QTClusterFinder
,
SILACLabeler
,
SimplePairFinder
,
SingleLinkage
,
SpectraSTSimilarityScore
,
SpectrumAlignmentScore
,
SpectrumCheapDPCorr
,
SpectrumPrecursorComparator
,
StablePairFinder
,
SteinScottImproveScore
,
TICFilter
,
VersionInfo::VersionDetails
,
ZhangSimilarityScore
create_() :
DimMapper< N_DIM >
createAdduct_() :
MassExplainer
createAndSolveCombinedLPFeatureBased_() :
PSLPFormulation
createAndSolveCombinedLPForKnownLCMSMapFeatureBased() :
PSLPFormulation
createAndSolveILP_() :
PSLPFormulation
createAndSolveILPForInclusionListCreation() :
PSLPFormulation
createAndSolveILPForKnownLCMSMapFeatureBased() :
PSLPFormulation
createAssayLibrary_() :
FeatureFinderIdentificationAlgorithm
createBFPeptideProbabilisticAdderFactor() :
MessagePasserFactory< Label >
createChargeFactor() :
MessagePasserFactory< Label >
createCompound_() :
TransitionTSVFile
createCompoundReferenceMap_() :
TargetedExperiment
createConsensusFeature_() :
QTClusterFinder
createConsensusMapCache() :
MasstraceCorrelator
createContaminants_() :
RawMSSignalSimulation
createDirs() :
TOPPASToolVertex
createEditor() :
ListEditorDelegate
,
ParamEditorDelegate
createExperiment() :
RTSimulation
createFeatureMap_() :
MSSim
createFlankingAAXMLString_() :
IdXMLFile
createHRData() :
FeatureFinderAlgorithmIsotopeWavelet
createIfNotExists_() :
CVTermListInterface
,
MetaInfoInterface
createIndices_() :
MzMLSqliteHandler
createINI_() :
ToolsDialog
createMemdumpIndex() :
CachedMzMLHandler
createMMSpawns_() :
ACTrie
createMMSubSpawns_() :
ACTrie
createModel() :
ModelDescription< D >
createMRMFeature() :
MRMTransitionGroupPicker
createNewRow() :
ListTable
createOutputDir() :
TOPPASOutputFileListVertex
createPeptide_() :
TransitionTSVFile
createPeptideEvidenceFactor() :
MessagePasserFactory< Label >
createPeptideProbabilisticAdderFactor() :
MessagePasserFactory< Label >
createPeptideReferenceMap_() :
TargetedExperiment
,
LightTargetedExperiment
createPositionXMLString_() :
IdXMLFile
createProtein_() :
TransitionTSVFile
createProteinFactor() :
MessagePasserFactory< Label >
createProteinReferenceMap_() :
TargetedExperiment
createProteinSequenceBasedLPInclusionList() :
OfflinePrecursorIonSelection
createProteinToPeptideIDMap_() :
SpectraIDViewTab
createProteinToPeptideLinks_() :
MzTabFile
createPseudoSpectra() :
MasstraceCorrelator
createRandomPartitions() :
SVMWrapper
createRegularizingSumEvidenceFactor() :
MessagePasserFactory< Label >
createReplicateFactor() :
MessagePasserFactory< Label >
createResidueModificationToResidueMap_() :
ModifiedPeptideGenerator
createResources() :
TOPPASScene
createSpawns_() :
ACTrie
createSpec_() :
MSExperiment
createStream_() :
StreamHandler
createSubSpawns_() :
ACTrie
createSumEvidenceFactor() :
MessagePasserFactory< Label >
createSumFactor() :
MessagePasserFactory< Label >
createTable_() :
OMSFileStore
createTableAppliedProcessingStep_() :
OMSFileStore
createTableBaseFeature_() :
OMSFileStore
createTableCVTerm_() :
OMSFileStore
createTableDataValue_DataType_() :
OMSFileStore
createTableIdentifiedMolecule_() :
OMSFileStore
createTableMetaInfo_() :
OMSFileStore
createTableMoleculeType_() :
OMSFileStore
createTableParentMatches_() :
OMSFileStore
createTables() :
MzMLSqliteHandler
createTheoreticalSpectra_() :
AScore
createToolsList_() :
ToolsDialog
createTOPPToolsTreeWidget() :
TOPPASBase
createTransition_() :
TransitionTSVFile
createUnknownFromMassString() :
ResidueModification
crend() :
Mobilogram
cropFeature_() :
FeatureFinderAlgorithmPicked
CrossLinksDB() :
CrossLinksDB
CsvFile() :
CsvFile
CSVWriter() :
CSVWriter
CubicSpline2d() :
CubicSpline2d
curPos() :
Bzip2InputStream
,
GzipInputStream
currentCellChanged_() :
SpectraIDViewTab
currentChanged_() :
EnhancedTabBar
currentIdChanged() :
EnhancedTabBar
currentLayerParametersChanged_() :
Plot2DCanvas
currentLayerParamtersChanged_() :
Plot1DCanvas
,
Plot3DCanvas
currentRowChangedAction_() :
LayerListView
currentSpectraSelectionChanged_() :
SpectraIDViewTab
currentTabChanged() :
DataSelectionTabs
curve() :
ROCCurve
customContextMenuRequested_() :
FilterList
cut() :
ClusterAnalyzer
cutForTime() :
FIAMSDataProcessor
cutoffNeg() :
ROCCurve
cutoffPos() :
ROCCurve
CV() :
CV
CVMappingFile() :
CVMappingFile
CVMappingRule() :
CVMappingRule
CVMappings() :
CVMappings
CVMappingTerm() :
CVMappingTerm
cvParam_() :
MzDataHandler
CVReference() :
CVReference
cvStringToEnum_() :
XMLHandler
CVTerm() :
ControlledVocabulary::CVTerm
,
CVTerm
CVTermList() :
CVTermList
CVTermListInterface() :
CVTermListInterface
Generated on Fri Jul 14 2023 13:07:39 for OpenMS by
1.9.1