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CachedmzML() :
CachedmzML
CachedSwathFileConsumer() :
CachedSwathFileConsumer
calcCentroids() :
CentroidData
calcChargeStateIntensities_() :
ProtonDistributionModel
calcElutionFitScore() :
EmgScoring
calcFragmentIsotopeDist() :
IsotopeDistribution
calcFragmentIsotopeDist_() :
IsotopeDistribution
calcGridLines() :
AxisTickCalculator
calcIndSNScore() :
MRMScoring
calcIndXcorrIdCoelutionScore() :
MRMScoring
calcIndXcorrIdShape_score() :
MRMScoring
calcLibraryScore() :
MRMScoring
calcLogGridLines() :
AxisTickCalculator
calcMS1XcorrCoelutionScore() :
MRMScoring
calcMS1XcorrShape_score() :
MRMScoring
calcRTScore() :
MRMScoring
calcSNScore() :
MRMScoring
calculate_lda_prescore() :
OpenSwath_Scores
calculate_swath_lda_prescore() :
OpenSwath_Scores
calculateAddInfo_() :
PeakIntensityPredictor
calculateAvgWeight_() :
ElementDB
calculateBackwardPart_() :
HiddenMarkovModel
calculateBgEstimation_() :
MRMTransitionGroupPicker
calculateCalibCoeffs_() :
TOFCalibration
calculateChromatographicIdScores() :
OpenSwathScoring
calculateChromatographicScores() :
OpenSwathScoring
calculateCorrelation() :
TOPPMetaProSIP
calculateDecompositionWeightsIsotopicPatterns() :
MetaProSIPDecomposition
calculateDIAIdScores() :
OpenSwathScoring
calculateDIAScores() :
OpenSwathScoring
calculateEmissionProbabilities() :
HiddenMarkovModel
calculateFDRs_() :
FalseDiscoveryRate
calculateFitQuality_() :
ElutionModelFitter
calculateForwardPart_() :
HiddenMarkovModel
calculateGaussTable() :
SVMWrapper
calculateGB() :
AAIndex
calculateGlobalLR() :
TOPPMetaProSIP
calculateGridLines_() :
Spectrum3DOpenGLCanvas
calculateIntensityRankInMZWindow() :
PScore
calculateIsotopePatternsFor13CRange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor13CRangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateIsotopePatternsFor15NRange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor15NRangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateIsotopePatternsFor18ORange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor18ORangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateIsotopePatternsFor2HRange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor2HRangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateLibraryScores() :
OpenSwathScoring
calculateMonoWeight_() :
ElementDB
calculateMT_() :
RTSimulation
calculatePeakLevelSpectra() :
PScore
calculatePermutationPeptideScores_() :
AScore
calculatePrecursorDIAScores() :
OpenSwathScoring
calculateProteinProbabilities() :
PSProteinInference
calculateProtonDistribution_() :
ProtonDistributionModel
calculateProtonDistributionCharge1_() :
ProtonDistributionModel
calculateProtonDistributionCharge2_() :
ProtonDistributionModel
calculateProtonDistributionGreater2_() :
ProtonDistributionModel
calculateProtonDistributionIonPair_() :
ProtonDistributionModel
calculateRankMap() :
PScore
calculateXICs_() :
OfflinePrecursorIonSelection
,
PSLPFormulation
calcXcorrCoelutionScore() :
MRMScoring
calcXcorrCoelutionScore_weighted() :
MRMScoring
calcXcorrShape_score() :
MRMScoring
calcXcorrShape_score_weighted() :
MRMScoring
calibrate() :
InternalCalibration
,
TOFCalibration
CalibrationData() :
CalibrationData
callback() :
OpenSwathOSWWriter
canModificationBeApplied_() :
SILACLabeler
canRun() :
JavaInfo
canvas() :
Spectrum1DWidget
,
Spectrum2DWidget
,
Spectrum3DWidget
,
SpectrumWidget
capacity() :
ConstRefVector< ContainerT >
cellClicked_() :
SpectraIdentificationViewWidget
cellindexAtClustercenter_() :
HashGrid< Cluster >
center() :
DIntervalBase< D >
centerOfBin() :
Histogram< ValueType, BinSizeType >
CentroidData() :
CentroidData
centroidDataModus() :
SuperHirnParameters
CentroidPeak() :
CentroidPeak
changedOutputFolder() :
TOPPASScene
changedParameter() :
TOPPASScene
changeElutionTimesByFactor() :
FeatureLCProfile
changeLabel() :
TOPPViewBase
changeLayerFilterState() :
SpectrumCanvas
changeLayerFlag() :
TOPPViewBase
changeLegendVisibility() :
SpectrumCanvas
,
SpectrumWidget
changeUnassigned() :
TOPPViewBase
changeVisibility() :
SpectrumCanvas
changeVisibleArea_() :
Spectrum1DCanvas
,
SpectrumCanvas
characters() :
ConsensusXMLFile
,
CVMappingFile
,
FeatureXMLFile
,
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_AC() :
SHFeature
check_elution_peak() :
ProcessData
check_elution_peak_belong() :
ProcessData
check_feature_list_empty() :
LCMS
check_LCMS_name() :
LCMS
check_match_by_id() :
SHFeature
check_MODIFICATION() :
MS2Info
check_MS2_empty() :
SHFeature
check_MZ_occurence() :
ProcessData
check_raw_spec_name_empty() :
LCMS
check_tree() :
KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
checkBelonging() :
BackgroundIntensityBin
checkCompliance() :
BinnedSpectrum
checkDefaults() :
Param
checkedToDouble_() :
EDTAFile
checkedToInt_() :
EDTAFile
checkExtraFeatures() :
PercolatorFeatureSetHelper
checkFeatureQuality_() :
FeatureFinderAlgorithmPicked
checkFormula_() :
Adduct
checkForRequiredUserParams_() :
PrecursorIonSelection
checkHits_() :
IDMapper
checkIds_() :
BaseGroupFinder
checkIfFeatureExtractionExists() :
FTPeakDetectController
checkIfIniParametersAreApplicable_() :
TOPPBase
checkIfWeAreDone() :
TOPPASScene
checkIsotopeBelongingAndAdjustMass() :
MSPeak
checkMassRanges_() :
OfflinePrecursorIonSelection
checkMassType_() :
IDMapper
checkMaximalRTSpan() :
EGHTraceFitter
,
GaussTraceFitter
,
TraceFitter
checkMinimalRTSpan() :
EGHTraceFitter
,
GaussTraceFitter
,
TraceFitter
checkName_() :
ControlledVocabulary
checkParam_() :
TOPPBase
checkParameters_() :
MapAlignmentAlgorithmIdentification
checkPositionForPlausibility_() :
IsotopeWaveletTransform< PeakType >
checkPPMTheoModel_() :
IsotopeWaveletTransform< PeakType >
checkPreferences_() :
TOPPViewBase
checkRDependencies() :
RIntegration
checkSize() :
SaveImageDialog
checkSolution_() :
FeatureDeconvolution
,
MetaboliteFeatureDeconvolution
checkSwathMap() :
OpenSwathHelper
checkSwathMapAndSelectTransitions() :
OpenSwathHelper
checkValidity_() :
TOPPASInputFileDialog
,
TOPPASIOMappingDialog
,
TOPPASOutputFilesDialog
chooseBestParameters_() :
SimpleSVM
chooseDecoys_() :
ConfidenceScoring
chooseElutionProfile_() :
RawMSSignalSimulation
chooseTraceFitter_() :
FeatureFinderAlgorithmPicked
chop() :
String
,
StringUtils
Chromatogram() :
Chromatogram
chromatogram_flag_set() :
LayerData
chromatogramIdsMatch() :
MRMTransitionGroup< ChromatogramType, TransitionType >
ChromatogramMeta() :
ChromatogramMeta
ChromatogramPeak() :
ChromatogramPeak
ChromatogramSettings() :
ChromatogramSettings
ChromatogramTools() :
ChromatogramTools
classifyIsotopes_() :
CompNovoIonScoringBase
cleanDeconvPeaks() :
Deisotoper
cleanupTransitions_() :
TransitionTSVReader
clear() :
KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
,
CalibrationData
,
ConsensusFeature
,
ConsensusMap
,
ConstRefVector< ContainerT >
,
ConvexHull2D
,
DataFilters
,
Date
,
DateTime
,
DistanceMatrix< Value >
,
DPosition< D, TCoordinateType >
,
EnzymesDB
,
FeatureMap
,
HashGrid< Cluster >
,
HiddenMarkovModel
,
IMSAlphabet
,
DIntervalBase< D >
,
StringManager
,
IsotopeDistribution
,
KDTreeFeatureMaps
,
AveragePosition< D >
,
BasicStatistics< RealT >
,
Matrix< Value >
,
MetaInfo
,
MSChromatogram
,
MSExperiment
,
MSSpectrum
,
Param
,
ParamEditor
,
PeakIndex
,
SparseVector< Value >
,
StopWatch
,
TargetedExperiment
,
TOPPASResources
clear_() :
DataValue
,
ElementDB
,
MetaInfoVisualizer
,
ResidueDB
clear_feature_list() :
LCMS
clearCache() :
LogStreamBuf
clearEluents() :
Gradient
clearInitialTransitionProbabilities() :
HiddenMarkovModel
clearMetaDataArrays() :
MSExperiment
clearMetaInfo() :
MetaInfoInterface
clearMSLevels() :
PeakFileOptions
clearPercentages() :
Gradient
clearRanges() :
RangeManager< D >
clearResidues_() :
ResidueDB
clearResult() :
ProteinResolver
clearTags() :
Param
clearTimepoints() :
Gradient
clearTrainingEmissionProbabilities() :
HiddenMarkovModel
clearUniqueId() :
UniqueIdInterface
cleavageCorrectionTerm() :
PScore
CleavageModel_() :
EnzymaticDigestionLogModel::CleavageModel_
clicked() :
TOPPASVertex
clone() :
Digestion
,
Modification
,
SampleTreatment
,
Tagging
close() :
Bzip2Ifstream
,
GzipIfstream
closeByTab() :
TOPPASBase
,
TOPPViewBase
closeEvent() :
IDEvaluationBase
,
INIFileEditorWindow
,
SpectrumWidget
,
TOPPASBase
,
TOPPASWidget
,
TOPPViewBase
closeFile() :
TOPPASBase
,
TOPPViewBase
closeListEditor_() :
ParamEditorDelegate
cluster() :
ClusterHierarchical
,
GridBasedClustering< Metric >
,
MultiplexClustering
ClusterAnalyzer() :
ClusterAnalyzer
ClusteredMS2ConsensusSpectrum() :
ClusteredMS2ConsensusSpectrum
ClusterFunctor() :
ClusterFunctor
ClusterHierarchical() :
ClusterHierarchical
ClusteringGrid() :
ClusteringGrid
ClusterProxyKD() :
ClusterProxyKD
clusterSeeds_() :
IsotopeWaveletTransform< PeakType >
clusterSIPPeptides() :
MetaProSIPClustering
cmpOligos_() :
LibSVMEncoder
cohesion() :
ClusterAnalyzer
col() :
Matrix< Value >
colIndex() :
Matrix< Value >
collapseStringVector() :
TOPPViewIdentificationViewBehavior
collectDecompositionsRecursively_() :
IntegerMassDecomposer< ValueType, DecompositionValueType >
collectFragmentScansInArea() :
Spectrum2DCanvas
collectRatios_() :
IsobaricNormalizer
collectSetParameter() :
QcMLFile
colnames() :
CSVWriter
,
DataMatrix
,
IDataFrameWriter
color() :
MultiGradient
ColorSelector() :
ColorSelector
cols() :
Matrix< Value >
combineDecoyModifications_() :
MRMAssay
combineModifications_() :
MRMAssay
commitAndCloseComboBox_() :
ParamEditorDelegate
commitAndCloseLineEdit_() :
ParamEditorDelegate
commitAndCloseListEditor_() :
ParamEditorDelegate
Compare() :
MapAlignmentAlgorithmSpectrumAlignment::Compare
compare_AC() :
MS2Info
compare_feature_mass() :
LCMS
compareByFirst() :
SpectraMerger
compareChargeStates_() :
ConsensusIDAlgorithm
compareFeatureMassValuesAtPPMLevel() :
SHFeature
compareFiles() :
FuzzyStringComparator
compareIteratorToPeak() :
ProcessData
compareLines_() :
FuzzyStringComparator
compareMassValuesAtPPMLevel() :
SuperHirnUtil
compareMZ_() :
AScore
compareMZFeatureBeloning() :
MS1FeatureMerger
comparepeaks_() :
SpectrumCheapDPCorr
compareSpectra_() :
CompNovoIdentificationBase
compareStreams() :
FuzzyStringComparator
compareStrings() :
FuzzyStringComparator
compatible() :
MassDecomposition
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
compress() :
ConvexHull2D
CompressedInputSource() :
CompressedInputSource
compressSignals_() :
RawMSSignalSimulation
compressString() :
ZlibCompression
compressTrieDB() :
InspectOutfile
compute() :
AScore
,
FeatureDeconvolution
,
HyperScore
,
ILPDCWrapper
,
MassExplainer
,
CumulativeBinomial
,
MetaboliteFeatureDeconvolution
compute_CHRG() :
LCElutionPeak
compute_delta_area() :
LCElutionPeak
compute_F() :
SpectraSTSimilarityScore
computeApexSNR() :
ElutionPeakDetection
computeAveragineSimScore_() :
FeatureFindingMetabo
computeBestClusterForCenter_() :
FeatureGroupingAlgorithmKD
computeBinnedCoverage() :
MRMRTNormalizer
computeBoundaries_() :
EGHModel
computeCCs_() :
MapAlignmentAlgorithmKD
computeChiSquare() :
LinearRegression
computeClustering_() :
QTClusterFinder
computeConsensus() :
ConsensusFeature
computeConsensusStats_() :
LayerStatisticsDialog
computeCorrelation() :
ConsensusMapNormalizerAlgorithmThreshold
computeCosineSim_() :
AccurateMassSearchEngine
,
FeatureFindingMetabo
computeCoverage() :
ProteinIdentification
computeCumulativeScore_() :
AScore
computeDataProperties_() :
MzMLHandlerHelper
computeDechargeConsensus() :
ConsensusFeature
computeDeltaArea() :
MS1FeatureMerger
computeFeatureStats_() :
LayerStatisticsDialog
computeFileHash() :
FileHandler
computeFwhmArea() :
MassTrace
computeFwhmAreaSmooth() :
MassTrace
computeGoodness_() :
LinearRegression
computeHyperScore() :
MetaboliteSpectralMatching
computeIntensityHist() :
BackgroundIntensityBin
computeIntensityOfMSD_() :
ProteinResolver
computeIntensityProfile() :
FeatureFinderAlgorithmPickedHelperStructs::MassTraces
computeIsotopeDistributionSize_() :
IsotopeWavelet
computeIsotopePatternSimilarity_() :
AccurateMassSearchEngine
computeKernelMatrix() :
SVMWrapper
computeLabelingStatistics_() :
IsobaricQuantifier
computeLCElutionPeakParameters() :
LCElutionPeak
computeMassTraceNoise() :
ElutionPeakDetection
computeMassTraceSNR() :
ElutionPeakDetection
computeMaxLikelihood() :
PosteriorErrorProbabilityModel
computeMedian_() :
SignalToNoiseEstimatorMedianRapid
computeMedianIntensity_() :
MassTrace
computeMedians() :
ConsensusMapNormalizerAlgorithmMedian
computeMedians_() :
MapAlignmentAlgorithmIdentification
computeMetaAverages_() :
LayerStatisticsDialog
computeMetaDataArrayStats_() :
LayerStatisticsDialog
computeMinSpacing() :
IsotopeWaveletTransform< PeakType >
computeMonoisotopicConsensus() :
ConsensusFeature
computeMS2SpectrumParameters() :
MS2ConsensusSpectrum
computeNewMS1FeatureParameters() :
MS1FeatureMerger
computeNoiseInWindows_() :
SignalToNoiseEstimatorMedianRapid
computeNormalizationFactors_() :
IsobaricNormalizer
computeOLSCoeff_() :
FeatureFindingMetabo
computePeakArea() :
MassTrace
computePeakStats_() :
LayerStatisticsDialog
computePermutations_() :
AScore
computePrecursorPurity_() :
IsobaricChannelExtractor
computeProbability() :
PosteriorErrorProbabilityModel
computePScore() :
PScore
computeQuality_() :
MRMTransitionGroupPicker
,
QTCluster
computeRegression() :
LinearRegression
,
QuadraticRegression
computeRegressionWeighted() :
LinearRegression
,
QuadraticRegression
computeSelection() :
Spectrum3DOpenGLCanvas
computeSingleScanPrecursorPurity_() :
IsobaricChannelExtractor
computeSiteDeterminingIons_() :
AScore
computeSlice_() :
ILPDCWrapper
computeSliceOld_() :
ILPDCWrapper
computeSmoothedPeakArea() :
MassTrace
computeSonarScores() :
SONARScoring
computeSonarWindows_() :
OpenSwathWorkflowSonar
computeStats_() :
IsobaricIsotopeCorrector
computeSTN_() :
SignalToNoiseEstimator< Container >
,
SignalToNoiseEstimatorMeanIterative< Container >
,
SignalToNoiseEstimatorMedian< Container >
computeTheoretical() :
TraceFitter
computeTransformations_() :
MapAlignmentAlgorithmIdentification
computeWeightedChiSquare() :
LinearRegression
computeXCorr_() :
SONARScoring
concatenate() :
ListUtils
,
String
concatMULTISEPeptideIds() :
PercolatorFeatureSetHelper
condensIsotopePattern() :
ConsensusIsotopePattern
ConfidenceScoring() :
ConfidenceScoring
configure() :
LogConfigHandler
ConnectedComponent() :
ConnectedComponent
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
ConsensusIsotopePattern() :
ConsensusIsotopePattern
ConsensusMap() :
ConsensusMap
ConsensusMapNormalizerAlgorithmMedian() :
ConsensusMapNormalizerAlgorithmMedian
ConsensusMapNormalizerAlgorithmQuantile() :
ConsensusMapNormalizerAlgorithmQuantile
ConsensusMapNormalizerAlgorithmThreshold() :
ConsensusMapNormalizerAlgorithmThreshold
ConsensusXMLFile() :
ConsensusXMLFile
ConsoleUtils() :
ConsoleUtils
ConstIterator() :
AASequence::ConstIterator
,
HashGrid< Cluster >::ConstIterator
ConstRefVector() :
ConstRefVector< ContainerT >
ConstRefVectorConstIterator() :
ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >
ConstRefVectorIterator() :
ConstRefVector< ContainerT >::ConstRefVectorIterator< ValueT >
constructClusteredConsenusSpectraFragments() :
ClusteredMS2ConsensusSpectrum
constructConsusPattern() :
ConsensusIsotopePattern
constructHeader_() :
IBSpectraFile
constructMS1FeatureFromMS2Feature() :
FTPeakDetectController
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
,
ListUtils
containsInvalidReferences() :
TargetedExperiment
containsMS1Scans() :
TOPPViewBase
containsMSLevel() :
PeakFileOptions
containsTag() :
MassDecomposition
contextMenuEvent() :
EnhancedTabBar
,
MultiGradientSelector
,
Spectrum1DCanvas
,
Spectrum2DCanvas
,
Spectrum3DCanvas
,
TOPPASEdge
,
TOPPASLogWindow
,
TOPPASScene
,
TOPPASTabBar
,
TOPPASVertex
ContinuousWaveletTransform() :
ContinuousWaveletTransform
ContinuousWaveletTransformNumIntegration() :
ContinuousWaveletTransformNumIntegration
ControlledVocabulary() :
ControlledVocabulary
ConversionError() :
ConversionError
convert() :
StringManager
,
MapConversion
,
TransitionHelper
convert_ms_peaks() :
ProcessData
convert_to_LC_elution_peak() :
ProcessData
convertChromatogramsToSpectra() :
ChromatogramTools
convertData_() :
SimpleSVM
convertModificationSet_() :
XTandemInfile
convertPeptideIdScores_() :
PrecursorIonSelection
convertPeptideToAASequence() :
OpenSwathDataAccessHelper
convertPQPToTargetedExperiment() :
TransitionPQPReader
convertSeedList() :
SeedListGenerator
convertSpectraToChromatograms() :
ChromatogramTools
convertTargetedCompound() :
OpenSwathDataAccessHelper
convertTargetedExp() :
OpenSwathDataAccessHelper
convertTargetedExperimentToPQP() :
TransitionPQPReader
convertTargetedExperimentToTSV() :
TransitionTSVReader
convertToOpenMSChromatogram() :
OpenSwathDataAccessHelper
convertToOpenMSChromatogramFilter() :
OpenSwathDataAccessHelper
convertToOpenMSSpectrum() :
OpenSwathDataAccessHelper
convertToSpectrumPtr() :
OpenSwathDataAccessHelper
convertTransition_() :
TransitionTSVReader
convertTSVToTargetedExperiment() :
TransitionTSVReader
ConvexHull2D() :
ConvexHull2D
convolve_() :
IsotopeDistribution
convolvePow_() :
IsotopeDistribution
convolveSquare_() :
IsotopeDistribution
copy() :
Param
copy_() :
HiddenMarkovModel
,
TOPPASOutputFileListVertex
copyBatchTransitions_() :
OpenSwathWorkflow
copyLayer() :
TOPPViewBase
copySelected() :
TOPPASScene
correctAreaToObeyMinMaxRanges_() :
SpectrumWidget
correctIsotopicImpurities() :
IsobaricIsotopeCorrector
correctMZ() :
SwathMapMassCorrection
correlate_() :
PeakPickerCWT
correlateXICsToMono() :
MetaProSIPXICExtraction
count() :
squared_difference_counted< _Tp, _Dist >
,
mean_and_stddev
count_within_range() :
KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >
countFreeIDs() :
DocumentIDTagger
countHits() :
IDFilter
countIntensities_() :
SvmTheoreticalSpectrumGeneratorTrainer
countIonizedResidues_() :
IonizationSimulation
countMissedCleavages_() :
EnzymaticDigestion
countMissedCleavagesTryptic_() :
CompNovoIdentificationBase
countPeptides_() :
PeptideAndProteinQuant
countScansInSwath_() :
SwathFile
countTargetDecoy() :
ProteinResolver
countTreatments() :
Sample
create() :
AverageLinkage
,
BiGaussFitter1D
,
BiGaussModel
,
BinnedSharedPeakCount
,
BinnedSpectralContrastAngle
,
BinnedSumAgreeingIntensities
,
ComplementFilter
,
ComplementMarker
,
CompleteLinkage
,
EGHFitter1D
,
EGHModel
,
EmgFitter1D
,
EmgModel
,
ExtendedIsotopeFitter1D
,
ExtendedIsotopeModel
,
Factory< FactoryProduct >
,
FastaIterator
,
FastaIteratorIntern
,
FeatureFinderAlgorithmIsotopeWavelet
,
FeatureFinderAlgorithmMRM
,
FeatureFinderAlgorithmPicked
,
FeatureFinderAlgorithmSH
,
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 >
,
QTClusterFinder
,
SILACLabeler
,
SimplePairFinder
,
SingleLinkage
,
SpectraSTSimilarityScore
,
SpectrumAlignmentScore
,
SpectrumCheapDPCorr
,
SpectrumPrecursorComparator
,
StablePairFinder
,
SteinScottImproveScore
,
TICFilter
,
TrypticIterator
,
VersionInfo::VersionDetails
,
ZhangSimilarityScore
createAdduct_() :
MassExplainer
createAndSolveCombinedLPFeatureBased_() :
PSLPFormulation
createAndSolveCombinedLPForKnownLCMSMapFeatureBased() :
PSLPFormulation
createAndSolveILP_() :
PSLPFormulation
createAndSolveILPForInclusionListCreation() :
PSLPFormulation
createAndSolveILPForKnownLCMSMapFeatureBased() :
PSLPFormulation
createBinnedPeptideRIAData_() :
MetaProSIPReporting
createCompound_() :
TransitionTSVReader
createCompoundReferenceMap_() :
TargetedExperiment
createConsensIsotopPattern() :
LCElutionPeak
createContaminants_() :
RawMSSignalSimulation
createCSVReport() :
MetaProSIPReporting
createDirs() :
TOPPASToolVertex
createEditor() :
ListEditorDelegate
,
ParamEditorDelegate
createExperiment() :
RTSimulation
createFeatureElutionProfiles() :
SuperHirnParameters
createFeatureMap_() :
MSSim
createFlankingAAXMLString_() :
IdXMLFile
createHRData() :
FeatureFinderAlgorithmIsotopeWavelet
createIfNotExists_() :
CVTermListInterface
,
MetaInfoInterface
createINI_() :
ToolsDialog
createIntensityDistribution_() :
Spectrum1DWidget
,
Spectrum2DWidget
,
Spectrum3DWidget
,
SpectrumWidget
createMemdumpIndex() :
CachedmzML
createMetaDistribution_() :
Spectrum1DWidget
,
Spectrum2DWidget
,
Spectrum3DWidget
,
SpectrumWidget
createModel() :
ModelDescription< D >
createMRMFeature() :
MRMTransitionGroupPicker
createMZFeatureClusters() :
MS1FeatureMerger
createNewRow() :
ListTable
createOutputDir() :
TOPPASOutputFileListVertex
createPeptide_() :
TransitionTSVReader
createPeptideCentricCSVReport() :
MetaProSIPReporting
createPeptideReferenceMap_() :
TargetedExperiment
,
LightTargetedExperiment
createPositionXMLString_() :
IdXMLFile
createProtein_() :
TransitionTSVReader
createProteinReferenceMap_() :
TargetedExperiment
createProteinSequenceBasedLPInclusionList() :
OfflinePrecursorIonSelection
createProteinToPeptideLinks_() :
MzTabFile
createQualityReport() :
MetaProSIPReporting
createRandomPartitions() :
SVMWrapper
createResources() :
TOPPASScene
createSpec_() :
MSExperiment
createStream_() :
StreamHandler
createTables() :
MzMLSqliteHandler
createTheoreticalSpectra_() :
AScore
createTOPPToolsTreeWidget() :
TOPPASBase
createTransition_() :
TransitionTSVReader
cropFeature_() :
FeatureFinderAlgorithmPicked
CrossLinksDB() :
CrossLinksDB
CsvFile() :
CsvFile
CSVWriter() :
CSVWriter
CubicSpline2d() :
CubicSpline2d
curPos() :
Bzip2InputStream
,
GzipInputStream
currentChanged_() :
EnhancedTabBar
,
TOPPASTabBar
currentIdChanged() :
EnhancedTabBar
,
TOPPASTabBar
currentLayerParametersChanged_() :
Spectrum2DCanvas
currentLayerParamtersChanged_() :
Spectrum1DCanvas
,
Spectrum3DCanvas
currentPeakData_() :
SpectrumCanvas
curve() :
ROCCurve
cut() :
ClusterAnalyzer
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
OpenMS / TOPP release 2.3.0
Documentation generated on Tue Jan 9 2018 18:22:39 using doxygen 1.8.13