All Classes

AArrayFilter AChart ACluster AdditionFilter AddRandomNoise AdminType ADynamicTimeWarp AElementFilter AffineAlignment AFragmentCommandTest AlignedPairVector Alignment Alignment Alignment2D AlignmentColumn AlignmentColumnComparator AlignmentFactory AlignmentFactory AlignmentMapChart AlignmentOutput AlignmentPane AlignmentPath2D AnchorDefinitionPane AnchorExporter AnchorImporter AnchorPairSet ANDIChromImporter ANDIMSExporter AnnotationsType AnnotationType APipeline ApplicationContextWorkerFactory Array1DVisualizer ArrayBhattacharryya ArrayCorr ArrayCos ArrayCosLp ArrayCov ArrayDot ArrayDotLp ArrayDotMap ArrayFactory ArrayHamming ArrayLp ArrayMerge ArrayRankCorr ArrayStatsMap ArrayStatsScanner ArrayTanimoto ArrayTools ArrayTools ArrayTools ArrayTools2 ArrayWeightedCosine AScanLineCache AttributeType AWorkerFactory BatchFilter BBHFinder BBHFinder BBHTools BeansXmlGenerator BHeatMapChart BidirectionalBestHit BinaryCluster BiPace BiPaceBidirectionalBestHit BiPaceResult BottomHatFilter BreakPoints CachedScanLineList Category Category CenterFinder CenterStarAlignment Chromatogram Chromatogram1D Chromatogram2D Chromatogram2DVisualizer ChromatogramFactory ChromatogramVisualizer ChromatogramWarp ChromatogramWarp2 ClassificationPerformancePostProcessor ClassificationPerformanceTest ClassificationPerformanceTest Clique Clique Clique CliqueFactory CliqueFinder CliqueStatistics CliqueTable CliqueTable ClusteringAlgorithm ColorRampReader ColumnWiseComparison CombinedDomainXYChart CompleteLinkageAlgorithm ConstraintFactory ContinuityArgmaxNodeBuilder ContinuousWaveletTransform CreateHorizontalTicVector Creator CSVAnchorReader CSVReader CSVWriter CvLookupType CvParamType CwtChartFactory CwtEicPeakFinder CwtEicPeakFinderCallable CwtPeakFinder CwtRunnable CwtTicPeakFinder CwtTicPeakFinderCallable Data2DNormalizer DataProcessingType DataProcessingType.Software DB4oServer DBMatch Default2DTWVisualizer Default2DVarLoader DefaultBinnedMSFeatureVector DefaultFeatureVector DefaultPairSet DefaultTaskResult DefaultVarLoader DefaultVarLoaderWorker DeltaMasses DenseArray DenseArrayProducer DenseArrayProducerWorker DescriptionType DigestionEnzyme DimensionReduce DistanceMatrix DTW DTW2DPeakAreaVisualizer DTW2DTicVisualizer DTWNew DtwPairwiseSimilarity DtwRecurrence DTWTest DtwTimePenalizedPairwiseSimilarity EditDistance EICHeatmapCoplot EICPeakFinder EIMSDBMetaboliteAssignment ElementNotFoundException Entity Entity EntityGroup EntityGroup EntityGroupBuilder EntityGroupClassificationResult EntityGroupClassificationResult EPlotRunner Eval Experiment1D Experiment2D ExperimentFactory ExpFilter FastBidirectionalBestHit FastBinnedMSFeatureVector FeatureMap FeatureMap.DataProcessing FeatureMap.DataProcessing.ProcessingAction FeatureMap.DataProcessing.Software FeatureMap.DataProcessing.UserParam FeatureMap.FeatureList FeatureMap.IdentificationRun FeatureMap.IdentificationRun.ProteinIdentification FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit FeatureMap.IdentificationRun.SearchParameters FeatureMap.IdentificationRun.SearchParameters.FixedModification FeatureMap.IdentificationRun.SearchParameters.VariableModification FeatureMap.UnassignedPeptideIdentification FeatureMap.UnassignedPeptideIdentification.PeptideHit FeatureType FeatureType.Convexhull FeatureType.Convexhull.Hullpoint FeatureType.Convexhull.Hullpoint.Hposition FeatureType.Model FeatureType.Model.Param FeatureType.PeptideIdentification FeatureType.PeptideIdentification.PeptideHit FeatureType.Position FeatureType.Quality FeatureType.Subordinate FeatureVectorDtwSimilarity FeatureVectorFactory FeatureVectorList FiFoQueue FileCopy FileInputOutputPane FilePipeline FilterButtonActionListener FirstDerivativeFilter FsaTxtDataSource GaussianDifferenceSimilarity GCGCToGCMSConverter GenerateTicChart GradientPaintScale GradientVisualizer Group HeatMapChart IAggregatePredicateFactory IAlignment IAnchor IArrayD2Byte IArrayD2Double IArraySimilarity IBaselineEstimator IBidirectionalBestHit IChromatogram IChromatogram1D IChromatogram2D IClique ICliqueMemberCriterion ICliqueUpdater ICluster IClusteringAlgorithm IDBQuery Ident2DTWVisualizer IdentityNodeBuilder IDtwSimilarityFunction IDynamicTimeWarp IExperiment IExperiment1D IExperiment2D IFeatureVector IFeatureVectorComparator IFeatureVectorComparator IFileFragmentModifier ImagePanel ImageTools IMatchPredicate IMetabolite ImpaxsExecution IMutableFeatureVector InstrumentDescriptionType InstrumentDescriptionType.AnalyzerList IOptimizationFunction IPairwiseFeatureVectorSequenceOperation IPeakExporter IPeakFinder IPeakGroup1DProvider IPeakIdentification IPeakIntegration IPeakIntegrator IPeakListProvider IPeakNormalizer IPeakPicking IPipeline IPostProcessor IPostProcessor IRecurrence IRegionGrowing IRetentionInfo IRetentionInfo2D IRidgeCost IScalarArraySimilarity IScalarSimilarity IScan IScan1D IScan1DProvider IScan2D IScan2DProvider IScanLine IScanProvider ITask ITaskResult ITreatmentGroup IVisualization IWarpInput IWavelet JFreeChartTools JFreeChartViewer JoinScans LineVectorRenderer LocalHostLauncher LocalHostMaltcmsProcess LoessMinimaBaselineEstimator LogDeltaEvaluation LogFilter MAggregatePredicate MAggregatePredicateFactory Main Maltcms MaltcmsAnnotation MaltcmsAnnotationFactory MaltcmsConfigurableRunnable MaltcmsFeatureVector MaltcmsTaskResult MaltcmsTools MaltcmsWorkflow MappedPointsType MassFilter MassSpectrumPlot MassSpectrumVisualization MassType MatchPredicate MaxSortPeakPicking MeanStdDevNormalizationFilter MeanVarProducer MeanVarVis MedianBaselineFilter Metabolite Metabolite2D MetaboliteBrowser MetaboliteListCellRenderer MetaboliteListSelectionListener MetabolitePredicate MetaboliteQueryAction MetaboliteQueryDB MetaboliteQueryPanel MetaboliteSearchPreferences MetaboliteSimilarity MetaboliteView MetaboliteViewModel MexicanHatWavelet MexicanHatWaveletFilter MinimumFilter MinMaxMassFinderWorker MinMaxNormalizationFilter MissingPeak2D MNumRangePredicate ModulationExtractor ModulationTimeEstimator ModulationTimeEstimatorTask MovingAverageFilter MovingMedianFilter MSimilarityPredicate MSPeaklistAlignment MSPExporter MSPFormatMetaboliteParser MSScanVisualizer MStringContainsPredicate MStringMatchPredicate MultipleAlignment MultipleAlignmentColumnEvaluation MultipleAlignmentRowEvaluation MultipleAlignmentWriter MultiplicationFilter MyWorkflow MzData MzData.Description MzData.SpectrumList MzData.SpectrumList.Spectrum MZDataDataSource MZIDistributionVisualizer MziDtwWorkerFactory MZIDynamicTimeWarp MZIWarpInput MZMLDataSource MZXMLDataSource MZXMLSaxDataSource MZXMLStaxDataSource NeighborJoinAlgorithm NetcdfDataSource NewDistanceMatrix NodeBuilder NormalizationFilter ObiWarplmataExporter ObjectFactory ObjectFactory ObjectFactory ObjectFactory OneAffineAlignment OneByOneRegionGrowing OneWayPeakAnova OptimalAlignmentVector PairwiseAlignment PairwiseAlignmentMatrixVisualizer PairwiseAlignmentVisualizer PairwiseDistanceCalculator PairwiseDistanceResult PairwiseDistances PairwiseDistanceWorker PairwiseFeatureSequenceSimilarity PairwiseFeatureSimilarity PairwisePeakListSimilarities PairwiseSimilarityWorker ParamType PartitionCalculator PartitionedArray PathTools PathTools.Direction PathWarp Peak Peak Peak1D Peak1DBidiBestHitsCriterion Peak1DCliqueStatistics Peak1DGroup Peak1DSimilarityCalculator Peak2D Peak2D Peak2DClique Peak2DClique Peak2DCliqueStatistics Peak2DSimilarityCalculator PeakAnnotation PeakArea2D PeakAreaTableExporter PeakCliqueAlignment PeakComparator PeakComparator PeakExporter PeakFactory PeakFactory PeakFileFragmentComparator PeakFileFragmentComparator PeakFinderUtils PeakIdentification PeakIntegration PeakIntegration PeakList PeakList1DProvider PeakList2DProvider PeakListBinaryType PeakListBinaryType.Data PeakNormalization PeakPositionsResultSet PeakRTFeatureVector PeakRTFeatureVector PeakRTFeatureVectorComparator PeakRTFeatureVectorComparator PeakSeparator PeakSimilarityCalculator PeakSimilarityVisualizer PeakSimilarityVisualizer PeakType PerformanceMetrics PerformanceMetrics PersonType PipelineWizard PlotRunner PointMapType PointType PointType.Dimension PrecursorType PreprocessingPane ProductSimilarity ProfileChromatogram1D ProgressiveTreeAlignment PublicMemberGetters Quad QuadTree QuadTreeNode QuadTreeNodeDepthFirstVisitor QuadTreeNodeVisitor QualityControl QuantileSnrPeakFinder QueryCallable QueryDB QueryResultListCellRenderer Rank Rank.ResponseComparator RankComparator RankSorter RawMSQuery ReBuild Reliability ResourceType ResourceType Result RetentionIndexCalculator RetentionIndexPeakAnnotation RetentionInfo Ridge RidgeCost0 RidgeCost1 RidgeCost2 RingBuffer RTGroupCorrectionWarp RTUnit SavitzkyGolayFilter Scan1D Scan2D ScanLineCache ScanLineCacheFactory ScanLineCacheOld ScanlineFilterTicWarp ScanlineHorizontalTicWarp ScanlineMaxMSWarp ScanlineMeanMSWarp ScanlineTicWarp ScoreDistributionVisualizer SeededRegionGrowing SimilarityTools SimplePeakPicking SingleLinkageAlgorithm SoftwareType SortedJavArrays SourceFileType Sparse SparseArray SparseScanLineCache SparseTools SpectrumDescType SpectrumDescType.PrecursorList SpectrumSettingsType SpectrumSettingsType.AcqSpecification SpectrumSettingsType.AcqSpecification.Acquisition SpectrumSettingsType.SpectrumInstrument SpectrumType SpiderWebChart SqrtFilter Standardizer StatsWriter SupDataBinaryType SupDataType SupDescType SymbolConvert SymbolicRepresentationAlignment TabbedPanel Task TestCallable TestConfigurableCallable TestRunnable ThreePredecessorsOptimization ThreePredecessorsOptimization.State TicAreaNormalizer TicDtwWorkerFactory TICDynamicTimeWarp TICHeatmapCoplot TICPeakFinder TICPeakListImporter TICWarpInput TiledArray TopHatFilter TreatmentGroup1D TreatmentGroup2D TwoFeatureVectorOperation UPGMAAlgorithm UserParam UserParamType UserParamType VariableDataExporter VariableSelectionPanel VBetaFamilyComparison Visualization2D VisualizationPane WarpMap2D WorkerFactory XLSIOProvider XmlAlignmentWriter XYBPlot XYChart XYZChart ZipResourceExtractor