Hierarchy For All Packages

Package Hierarchies:

maltcms.commands, maltcms.commands.distances, maltcms.commands.distances.dtw, maltcms.commands.distances.dtwng, maltcms.commands.filters, maltcms.commands.filters.array, maltcms.commands.filters.array.wavelet, maltcms.commands.fragments.alignment, maltcms.commands.fragments.alignment.peakCliqueAlignment, maltcms.commands.fragments.assignment, maltcms.commands.fragments.cluster, maltcms.commands.fragments.cluster.pairwiseDistanceCalculator, maltcms.commands.fragments.io, maltcms.commands.fragments.peakfinding, maltcms.commands.fragments.peakfinding.cwtEicPeakFinder, maltcms.commands.fragments.peakfinding.ticPeakFinder, maltcms.commands.fragments.preprocessing, maltcms.commands.fragments.preprocessing.defaultVarLoader, maltcms.commands.fragments.preprocessing.denseArrayProducer, maltcms.commands.fragments.spectratyping, maltcms.commands.fragments.visualization, maltcms.commands.fragments.warp, maltcms.commands.fragments2d.peakfinding, maltcms.commands.fragments2d.peakfinding.bbh, maltcms.commands.fragments2d.peakfinding.output, maltcms.commands.fragments2d.peakfinding.picking, maltcms.commands.fragments2d.peakfinding.srg, maltcms.commands.fragments2d.preprocessing, maltcms.commands.fragments2d.preprocessing.default2dVarLoader, maltcms.commands.fragments2d.testing, maltcms.commands.fragments2d.tools, maltcms.commands.fragments2d.visualization, maltcms.commands.fragments2d.warp, maltcms.commands.fragments2d.warp.visualization, maltcms.commands.scanners, maltcms.datastructures, maltcms.datastructures.alignment, maltcms.datastructures.array, maltcms.datastructures.caches, maltcms.datastructures.cluster, maltcms.datastructures.constraint, maltcms.datastructures.feature, maltcms.datastructures.fragments, maltcms.datastructures.ms, maltcms.datastructures.peak, maltcms.datastructures.peak.annotations, maltcms.datastructures.peak.normalization, maltcms.datastructures.quadTree, maltcms.datastructures.rank, maltcms.datastructures.ridge, maltcms.datastructures.warp, maltcms.db, maltcms.db.connection, maltcms.db.predicates, maltcms.db.predicates.metabolite, maltcms.db.ui, maltcms.experimental.bipace, maltcms.experimental.bipace.api, maltcms.experimental.bipace.datastructures.api, maltcms.experimental.bipace.datastructures.spi, maltcms.experimental.bipace.peakCliqueAlignment, maltcms.experimental.bipace.peakCliqueAlignment.io, maltcms.experimental.bipace.spi, maltcms.experimental.operations, maltcms.experimental.ui, maltcms.io, maltcms.io.andims, maltcms.io.csv, maltcms.io.misc, maltcms.io.xml.bindings.alignment, maltcms.io.xml.bindings.annotation, maltcms.io.xml.bindings.openms.featurexml, maltcms.io.xml.mzData, maltcms.io.xml.mzML, maltcms.io.xml.mzXML, maltcms.math.functions, maltcms.math.functions.similarities, maltcms.mpaxs, maltcms.runtime, maltcms.statistics, maltcms.test, maltcms.tools, maltcms.ui, maltcms.ui.charts, maltcms.ui.renderer, maltcms.ui.wizard, net.sf.maltcms.apps, net.sf.maltcms.evaluation.api, net.sf.maltcms.evaluation.api.alignment, net.sf.maltcms.evaluation.api.classification, net.sf.maltcms.evaluation.api.tasks, net.sf.maltcms.evaluation.spi, net.sf.maltcms.evaluation.spi.alignment, net.sf.maltcms.evaluation.spi.caap, net.sf.maltcms.evaluation.spi.classification, net.sf.maltcms.evaluation.spi.hohenheim, net.sf.maltcms.evaluation.spi.tasks, net.sf.maltcms.evaluation.spi.tasks.execution, net.sf.maltcms.evaluation.spi.tasks.maltcms, net.sf.maltcms.evaluation.spi.xcalibur, net.sf.maltcms.tutorials, smueller, smueller.alignment, smueller.datastructure, smueller.tools

Class Hierarchy

• java.lang.Object
  • maltcms.commands.filters.array.AArrayFilter (implements cross.commands.ICommand<IN,OUT>)
    • maltcms.commands.filters.array.AdditionFilter
    • maltcms.commands.filters.array.AddRandomNoise
    • maltcms.commands.filters.array.ArrayMerge
    • maltcms.commands.filters.array.BottomHatFilter
    • maltcms.commands.filters.array.ExpFilter
    • maltcms.commands.filters.array.FirstDerivativeFilter
    • maltcms.commands.filters.array.LogFilter
    • maltcms.commands.filters.array.MeanStdDevNormalizationFilter
    • maltcms.commands.filters.array.MedianBaselineFilter
    • maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter
    • maltcms.commands.filters.array.MinimumFilter
    • maltcms.commands.filters.array.MinMaxNormalizationFilter
    • maltcms.commands.filters.array.MovingAverageFilter
    • maltcms.commands.filters.array.MovingMedianFilter
    • maltcms.commands.filters.array.MultiplicationFilter
    • maltcms.commands.filters.array.NormalizationFilter
    • maltcms.commands.filters.array.SavitzkyGolayFilter
    • maltcms.commands.filters.array.SqrtFilter
    • maltcms.commands.filters.array.TopHatFilter
  • javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
    • maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction
    • maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction
    • maltcms.ui.charts.JFreeChartViewer.FileOpenAction
    • maltcms.db.ui.MetaboliteQueryAction
    • maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction
    • maltcms.ui.wizard.PipelineWizard.EditConfigurationAction
    • maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction
    • maltcms.ui.wizard.PipelineWizard.RunConfigurationAction
  • org.jfree.chart.renderer.AbstractRenderer (implements java.lang.Cloneable, java.io.Serializable)
    • org.jfree.chart.renderer.xy.AbstractXYItemRenderer (implements java.lang.Cloneable, java.io.Serializable, org.jfree.chart.renderer.xy.XYItemRenderer)
      • org.jfree.chart.renderer.xy.VectorRenderer (implements java.lang.Cloneable, org.jfree.util.PublicCloneable, java.io.Serializable, org.jfree.chart.renderer.xy.XYItemRenderer)
        • maltcms.ui.renderer.LineVectorRenderer
  • javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    • maltcms.db.ui.MetaboliteViewModel
  • maltcms.ui.charts.AChart<T> (implements cross.IConfigurable)
    • maltcms.ui.charts.AlignmentMapChart
    • maltcms.ui.charts.BHeatMapChart
    • maltcms.ui.charts.CombinedDomainXYChart
    • maltcms.ui.charts.HeatMapChart
    • maltcms.ui.charts.MassSpectrumPlot
    • maltcms.ui.charts.SpiderWebChart
    • maltcms.ui.charts.XYChart
    • maltcms.ui.charts.XYZChart
  • maltcms.datastructures.cluster.ACluster (implements maltcms.datastructures.cluster.ICluster)
    • maltcms.datastructures.cluster.BinaryCluster
  • maltcms.io.xml.mzData.AdminType
  • maltcms.commands.distances.dtw.ADynamicTimeWarp (implements maltcms.commands.distances.dtw.IDynamicTimeWarp)
    • maltcms.commands.distances.dtw.MZIDynamicTimeWarp
    • maltcms.commands.fragments2d.warp.ScanlineFilterTicWarp
    • maltcms.commands.fragments2d.warp.ScanlineHorizontalTicWarp
    • maltcms.commands.fragments2d.warp.ScanlineMaxMSWarp
    • maltcms.commands.fragments2d.warp.ScanlineMeanMSWarp
    • maltcms.commands.fragments2d.warp.ScanlineTicWarp
    • maltcms.commands.distances.dtw.TICDynamicTimeWarp
  • maltcms.commands.filters.AElementFilter (implements cross.commands.ICommand<IN,OUT>)
  • cross.commands.fragments.AFragmentCommand (implements cross.commands.fragments.IFragmentCommand)
    • maltcms.commands.fragments2d.testing.Alignment2D
    • maltcms.commands.fragments.io.ANDIChromImporter
    • maltcms.commands.fragments.io.ANDIMSExporter
    • maltcms.commands.fragments.visualization.Array1DVisualizer
    • maltcms.commands.fragments.alignment.CenterStarAlignment
    • maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer
    • maltcms.commands.fragments.visualization.ChromatogramVisualizer
    • maltcms.commands.fragments.warp.ChromatogramWarp
    • maltcms.commands.fragments.warp.ChromatogramWarp2
    • maltcms.commands.fragments.cluster.ClusteringAlgorithm (implements maltcms.commands.fragments.cluster.IClusteringAlgorithm)
      • maltcms.commands.fragments.cluster.CompleteLinkageAlgorithm
      • maltcms.commands.fragments.cluster.NeighborJoinAlgorithm
      • maltcms.commands.fragments.cluster.SingleLinkageAlgorithm
      • maltcms.commands.fragments.cluster.UPGMAAlgorithm
    • maltcms.commands.fragments2d.warp.CreateHorizontalTicVector
    • maltcms.commands.fragments.io.CSVAnchorReader
    • maltcms.commands.fragments.peakfinding.CwtEicPeakFinder
    • maltcms.commands.fragments2d.peakfinding.CwtPeakFinder
    • maltcms.commands.fragments.peakfinding.CwtTicPeakFinder
    • maltcms.commands.fragments2d.preprocessing.Data2DNormalizer
    • maltcms.commands.fragments2d.preprocessing.Default2DVarLoader
    • maltcms.commands.fragments.preprocessing.DefaultVarLoader
    • maltcms.commands.fragments2d.visualization.DeltaMasses
    • maltcms.commands.fragments.preprocessing.DenseArrayProducer
    • maltcms.commands.fragments2d.warp.DTW2DTicVisualizer
      • maltcms.commands.fragments2d.warp.DTW2DPeakAreaVisualizer
    • maltcms.commands.fragments.peakfinding.EICPeakFinder
    • maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment
    • maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter
    • maltcms.commands.fragments2d.visualization.GradientVisualizer
    • maltcms.commands.fragments.preprocessing.MassFilter
    • maltcms.commands.fragments2d.visualization.MassSpectrumVisualization
    • maltcms.commands.fragments2d.preprocessing.MeanVarProducer
    • maltcms.commands.fragments2d.preprocessing.MeanVarVis
    • maltcms.commands.fragments2d.preprocessing.ModulationExtractor
    • maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator
    • maltcms.commands.fragments.io.MSPExporter
    • maltcms.commands.fragments.visualization.MZIDistributionVisualizer
    • maltcms.commands.fragments.io.ObiWarplmataExporter
    • maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer
    • maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer
    • maltcms.commands.fragments.cluster.PairwiseDistanceCalculator
    • maltcms.commands.fragments.warp.PathWarp
    • maltcms.commands.fragments.io.PeakAreaTableExporter
    • maltcms.commands.fragments.alignment.PeakCliqueAlignment
    • maltcms.commands.fragments.alignment.ProgressiveTreeAlignment
    • maltcms.commands.fragments.warp.RTGroupCorrectionWarp
    • maltcms.commands.fragments.visualization.ScoreDistributionVisualizer
    • maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing
    • smueller.SymbolicRepresentationAlignment
    • maltcms.commands.fragments.visualization.TICHeatmapCoplot
      • maltcms.commands.fragments.visualization.EICHeatmapCoplot
    • maltcms.commands.fragments.peakfinding.TICPeakFinder
    • maltcms.commands.fragments.io.TICPeakListImporter
    • maltcms.commands.fragments.io.VariableDataExporter
    • maltcms.commands.fragments.spectratyping.VBetaFamilyComparison
  • maltcms.test.AFragmentCommandTest
  • smueller.alignment.AlignedPairVector (implements java.lang.Cloneable)
  • maltcms.io.xml.bindings.alignment.Alignment
  • smueller.alignment.Alignment
    • smueller.alignment.AffineAlignment
    • smueller.alignment.OneAffineAlignment
  • net.sf.maltcms.evaluation.api.alignment.AlignmentColumn (implements maltcms.datastructures.array.IFeatureVector)
  • net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator
  • maltcms.datastructures.alignment.AlignmentFactory
  • maltcms.commands.distances.dtwng.AlignmentFactory
  • smueller.datastructure.AlignmentOutput
  • maltcms.commands.fragments2d.testing.AlignmentPath2D
  • maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorExporter<T> (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorImporter
  • maltcms.io.xml.bindings.annotation.AnnotationsType
  • maltcms.io.xml.bindings.annotation.AnnotationType
  • net.sf.maltcms.evaluation.spi.tasks.execution.APipeline<T> (implements net.sf.maltcms.evaluation.spi.tasks.execution.IPipeline<T>)
    • net.sf.maltcms.evaluation.spi.tasks.execution.FilePipeline
  • ucar.ma2.Array
    • ucar.ma2.ArrayDouble
      • ucar.ma2.ArrayDouble.D1
        • maltcms.datastructures.array.Sparse
  • maltcms.math.functions.similarities.ArrayBhattacharryya (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayCorr (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayCos (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayCosLp (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayCov (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayDot (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayDotLp (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayDotMap (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.datastructures.array.ArrayFactory
  • maltcms.math.functions.similarities.ArrayHamming (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayLp (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.math.functions.similarities.ArrayRankCorr (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.commands.ArrayStatsMap (implements maltcms.datastructures.array.IMutableFeatureVector)
  • maltcms.commands.scanners.ArrayStatsScanner (implements cross.commands.ICommand<IN,OUT>)
  • maltcms.math.functions.similarities.ArrayTanimoto (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.tools.ArrayTools
  • maltcms.commands.fragments2d.tools.ArrayTools
  • smueller.tools.ArrayTools
  • maltcms.tools.ArrayTools2
  • maltcms.math.functions.similarities.ArrayWeightedCosine (implements maltcms.math.functions.IArraySimilarity)
  • maltcms.datastructures.caches.AScanLineCache (implements maltcms.datastructures.caches.IScanLine)
    • maltcms.datastructures.caches.CachedScanLineList
  • maltcms.io.xml.bindings.annotation.AttributeType
  • maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.AWorkerFactory (implements java.io.Serializable)
    • maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.ApplicationContextWorkerFactory (implements org.springframework.context.ApplicationContextAware)
    • maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.MziDtwWorkerFactory
    • maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.TicDtwWorkerFactory
  • maltcms.commands.filters.array.BatchFilter
  • maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.BBHFinder
  • maltcms.commands.fragments2d.peakfinding.bbh.BBHTools
  • net.sf.maltcms.evaluation.spi.BeansXmlGenerator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  • maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit (implements maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit)
  • maltcms.experimental.bipace.BiPace<T> (implements java.util.concurrent.Callable<V>)
  • maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit (implements maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit)
  • maltcms.experimental.bipace.BiPaceResult<T>
  • smueller.datastructure.BreakPoints
  • net.sf.maltcms.evaluation.api.Category (implements java.lang.Comparable<T>)
  • net.sf.maltcms.evaluation.api.classification.Category (implements java.lang.Comparable<T>)
  • maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder<T> (implements cross.datastructures.workflow.IWorkflowElement)
  • net.sf.maltcms.evaluation.spi.xcalibur.Chromatogram
  • maltcms.datastructures.ms.Chromatogram1D (implements maltcms.datastructures.ms.IChromatogram1D)
    • maltcms.datastructures.ms.ProfileChromatogram1D
  • maltcms.datastructures.ms.Chromatogram2D (implements maltcms.datastructures.ms.IChromatogram2D)
  • maltcms.datastructures.ms.ChromatogramFactory (implements cross.IConfigurable)
  • net.sf.maltcms.evaluation.spi.classification.ClassificationPerformancePostProcessor (implements net.sf.maltcms.evaluation.api.tasks.IPostProcessor)
  • net.sf.maltcms.evaluation.api.ClassificationPerformanceTest<T>
  • net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest<T>
  • maltcms.datastructures.cluster.Clique<T> (implements maltcms.datastructures.cluster.IClique<T>)
  • maltcms.datastructures.peak.Clique
  • maltcms.experimental.bipace.datastructures.api.Clique<T>
  • maltcms.datastructures.cluster.CliqueFactory
  • maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder<T> (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.experimental.bipace.datastructures.api.CliqueStatistics<T>
    • maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics
    • maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics
  • maltcms.experimental.bipace.peakCliqueAlignment.CliqueTable<T>
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.CliqueTable
  • maltcms.io.csv.ColorRampReader
  • net.sf.maltcms.evaluation.spi.alignment.ColumnWiseComparison
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • maltcms.db.ui.MetaboliteListCellRenderer (implements javax.swing.ListCellRenderer)
          • maltcms.db.ui.QueryResultListCellRenderer (implements javax.swing.ListCellRenderer)
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • maltcms.experimental.ui.ImagePanel
          • maltcms.db.ui.MetaboliteQueryPanel (implements java.awt.event.KeyListener)
          • maltcms.ui.TabbedPanel (implements java.awt.event.ActionListener)
          • maltcms.ui.charts.VariableSelectionPanel
          • org.netbeans.spi.wizard.WizardPage (implements org.netbeans.spi.wizard.WizardPanel)
            • maltcms.ui.wizard.AlignmentPane
            • maltcms.ui.wizard.AnchorDefinitionPane (implements javax.swing.event.ListDataListener, javax.swing.event.TableModelListener)
            • maltcms.ui.wizard.FileInputOutputPane
            • maltcms.ui.wizard.PreprocessingPane
            • maltcms.ui.wizard.VisualizationPane
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • maltcms.ui.charts.JFreeChartViewer
            • net.sf.maltcms.apps.MetaboliteBrowser
            • maltcms.db.ui.MetaboliteSearchPreferences
  • maltcms.datastructures.constraint.ConstraintFactory
  • maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform
  • net.sf.maltcms.evaluation.spi.xcalibur.Creator
  • maltcms.io.csv.CSVReader
  • maltcms.io.csv.CSVWriter (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.io.xml.mzData.CvLookupType
  • maltcms.io.xml.mzData.CvParamType
  • maltcms.commands.fragments2d.peakfinding.CwtChartFactory
  • maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtEicPeakFinderCallable (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.commands.fragments2d.peakfinding.CwtRunnable (implements java.util.concurrent.Callable<V>, maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking, java.io.Serializable)
  • maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtTicPeakFinderCallable (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.io.xml.mzData.DataProcessingType
  • maltcms.db.connection.DB4oServer (implements java.lang.Runnable)
  • maltcms.db.predicates.metabolite.DBMatch (implements java.lang.Comparable<T>)
  • maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer (implements maltcms.commands.fragments2d.warp.visualization.IVisualization)
    • maltcms.commands.fragments2d.warp.visualization.Ident2DTWVisualizer
  • maltcms.datastructures.feature.DefaultBinnedMSFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
  • maltcms.datastructures.feature.DefaultFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
  • maltcms.datastructures.alignment.DefaultPairSet<T> (implements java.lang.Iterable<T>)
    • maltcms.datastructures.alignment.AnchorPairSet
  • net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult (implements net.sf.maltcms.evaluation.api.tasks.ITaskResult)
    • net.sf.maltcms.evaluation.spi.tasks.maltcms.MaltcmsTaskResult
  • maltcms.commands.fragments.preprocessing.defaultVarLoader.DefaultVarLoaderWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.datastructures.array.DenseArray (implements maltcms.datastructures.array.IArrayD2Double)
  • maltcms.commands.fragments.preprocessing.denseArrayProducer.DenseArrayProducerWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • smueller.tools.DimensionReduce
  • smueller.datastructure.DistanceMatrix
    • smueller.datastructure.NewDistanceMatrix
  • maltcms.commands.distances.dtwng.DTW (implements maltcms.commands.distances.dtwng.IAlignment, java.io.Serializable)
  • net.sf.maltcms.apps.DTWNew
  • maltcms.math.functions.DtwPairwiseSimilarity (implements maltcms.commands.distances.IDtwSimilarityFunction)
  • maltcms.commands.distances.DtwRecurrence (implements maltcms.commands.distances.IRecurrence)
  • maltcms.commands.fragments2d.testing.DTWTest
  • maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity (implements maltcms.commands.distances.IDtwSimilarityFunction)
  • maltcms.experimental.operations.EditDistance
  • net.sf.maltcms.evaluation.api.Entity
  • net.sf.maltcms.evaluation.api.classification.Entity
  • net.sf.maltcms.evaluation.api.EntityGroup (implements java.lang.Comparable<T>)
  • net.sf.maltcms.evaluation.api.classification.EntityGroup (implements java.lang.Comparable<T>)
  • net.sf.maltcms.evaluation.spi.EntityGroupBuilder
  • net.sf.maltcms.evaluation.api.EntityGroupClassificationResult (implements java.lang.Comparable<T>)
  • net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult (implements java.lang.Comparable<T>)
  • net.sf.maltcms.evaluation.spi.hohenheim.Eval
  • net.sf.maltcms.evaluation.spi.hohenheim.Eval.StringListByDoubleComparator (implements java.util.Comparator<T>)
  • maltcms.datastructures.ms.Experiment1D (implements maltcms.datastructures.ms.IExperiment1D)
    • maltcms.datastructures.ms.Experiment2D (implements maltcms.datastructures.ms.IExperiment2D)
  • maltcms.datastructures.ms.ExperimentFactory
  • maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit (implements maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit)
  • maltcms.datastructures.feature.FastBinnedMSFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.ProcessingAction
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.Software
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.FeatureList
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.FixedModification
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.VariableModification
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification
  • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint.Hposition
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model.Param
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Position
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Quality
  • maltcms.io.xml.bindings.openms.featurexml.FeatureType.Subordinate
  • maltcms.datastructures.feature.FeatureVectorFactory
  • maltcms.datastructures.feature.FeatureVectorList<T> (implements maltcms.datastructures.IFileFragmentModifier)
  • maltcms.datastructures.peak.FiFoQueue<E> (implements java.util.Queue<E>)
  • net.sf.maltcms.apps.FileCopy
  • maltcms.db.ui.FilterButtonActionListener (implements java.awt.event.ActionListener)
  • maltcms.io.csv.FsaTxtDataSource (implements cross.io.IDataSource)
  • maltcms.math.functions.similarities.GaussianDifferenceSimilarity (implements maltcms.math.functions.IScalarSimilarity)
  • smueller.tools.GenerateTicChart
  • maltcms.ui.charts.GradientPaintScale (implements cross.IConfigurable, org.jfree.chart.renderer.PaintScale, java.io.Serializable)
  • net.sf.maltcms.evaluation.spi.xcalibur.Group
  • maltcms.tools.ImageTools
  • maltcms.mpaxs.ImpaxsExecution
  • maltcms.io.xml.mzData.InstrumentDescriptionType
  • maltcms.io.xml.mzData.InstrumentDescriptionType.AnalyzerList
  • maltcms.tools.JFreeChartTools
  • maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener (implements org.jfree.chart.ChartMouseListener)
  • maltcms.ui.charts.JFreeChartViewer.XYAnnotationAdder
  • net.sf.maltcms.apps.JoinScans
  • maltcms.runtime.LocalHostLauncher (implements javax.swing.event.HyperlinkListener, cross.event.IListener<V>, java.beans.PropertyChangeListener, java.lang.Runnable, java.lang.Thread.UncaughtExceptionHandler)
  • maltcms.commands.fragments.peakfinding.ticPeakFinder.LoessMinimaBaselineEstimator (implements maltcms.commands.fragments.peakfinding.ticPeakFinder.IBaselineEstimator)
  • maltcms.statistics.LogDeltaEvaluation (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.db.predicates.metabolite.MAggregatePredicateFactory (implements maltcms.db.predicates.metabolite.IAggregatePredicateFactory<T>)
  • maltcms.ui.wizard.Main (implements org.netbeans.spi.wizard.WizardPage.WizardResultProducer)
  • net.sf.maltcms.apps.Maltcms (implements java.lang.Thread.UncaughtExceptionHandler)
  • maltcms.io.xml.bindings.annotation.MaltcmsAnnotation
  • maltcms.datastructures.peak.MaltcmsAnnotationFactory
  • maltcms.mpaxs.MaltcmsConfigurableRunnable (implements net.sf.maltcms.execution.api.concurrent.ConfigurableRunnable<V>)
  • maltcms.datastructures.feature.MaltcmsFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
  • maltcms.tools.MaltcmsTools
  • net.sf.maltcms.evaluation.spi.tasks.maltcms.MaltcmsWorkflow
  • maltcms.io.xml.bindings.alignment.MappedPointsType
  • maltcms.db.predicates.MatchPredicate<T> (implements maltcms.db.predicates.IMatchPredicate<T>)
  • maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking (implements maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking)
  • maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking.PointComparator (implements java.util.Comparator<T>)
  • maltcms.datastructures.ms.Metabolite (implements maltcms.datastructures.ms.IMetabolite)
    • maltcms.datastructures.ms.Metabolite2D (implements maltcms.datastructures.ms.IRetentionInfo2D)
  • maltcms.db.ui.MetaboliteListSelectionListener (implements javax.swing.event.ListSelectionListener, java.awt.event.MouseListener, java.awt.event.WindowListener)
  • maltcms.db.ui.MetaboliteView (implements java.awt.event.ComponentListener, javax.swing.event.TableModelListener)
  • maltcms.commands.filters.array.wavelet.MexicanHatWavelet (implements maltcms.commands.filters.array.wavelet.IWavelet)
  • maltcms.commands.fragments.preprocessing.denseArrayProducer.MinMaxMassFinderWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D
  • maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.db.MSPFormatMetaboliteParser
  • net.sf.maltcms.apps.MSScanVisualizer
  • net.sf.maltcms.evaluation.api.alignment.MultipleAlignment (implements java.util.Map<K,V>)
  • net.sf.maltcms.apps.MultipleAlignmentColumnEvaluation
  • net.sf.maltcms.apps.MultipleAlignmentRowEvaluation
  • maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter (implements cross.datastructures.workflow.IWorkflowElement)
  • net.sf.maltcms.tutorials.MyWorkflow
  • maltcms.io.xml.mzData.MzData
  • maltcms.io.xml.mzData.MzData.Description
  • maltcms.io.xml.mzData.MzData.SpectrumList
  • maltcms.io.xml.mzData.MZDataDataSource (implements cross.io.IDataSource)
  • maltcms.datastructures.warp.MZIWarpInput (implements maltcms.datastructures.warp.IWarpInput)
  • maltcms.io.xml.mzML.MZMLDataSource (implements cross.io.IDataSource)
  • maltcms.io.xml.mzXML.MZXMLDataSource (implements cross.io.IDataSource)
  • maltcms.io.xml.mzXML.MZXMLSaxDataSource (implements cross.io.IDataSource)
  • maltcms.io.xml.mzXML.MZXMLStaxDataSource (implements cross.io.IDataSource)
  • maltcms.io.andims.NetcdfDataSource (implements cross.io.IDataSource)
  • maltcms.commands.distances.dtwng.NodeBuilder
    • maltcms.commands.distances.dtwng.ContinuityArgmaxNodeBuilder
    • maltcms.commands.distances.dtwng.IdentityNodeBuilder
  • maltcms.io.xml.mzData.ObjectFactory
  • maltcms.io.xml.bindings.alignment.ObjectFactory
  • maltcms.io.xml.bindings.annotation.ObjectFactory
  • maltcms.io.xml.bindings.openms.featurexml.ObjectFactory
  • maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing (implements maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing)
  • maltcms.statistics.OneWayPeakAnova (implements cross.datastructures.workflow.IWorkflowElement)
  • smueller.alignment.OptimalAlignmentVector (implements java.lang.Cloneable)
  • maltcms.datastructures.fragments.PairwiseAlignment (implements cross.IConfigurable, cross.io.IFileFragmentProvider, cross.datastructures.workflow.IWorkflowElement)
  • maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceResult (implements java.io.Serializable)
  • maltcms.datastructures.fragments.PairwiseDistances (implements cross.IConfigurable, maltcms.datastructures.IFileFragmentModifier, cross.datastructures.workflow.IWorkflowElement)
  • maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.commands.distances.PairwiseFeatureSimilarity (implements cross.IConfigurable)
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.io.xml.mzData.ParamType
    • maltcms.io.xml.mzData.DescriptionType
    • maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification.Acquisition
    • maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument
  • maltcms.commands.distances.PartitionCalculator (implements java.util.concurrent.Callable<V>, cross.IConfigurable)
  • maltcms.datastructures.array.PartitionedArray (implements maltcms.datastructures.array.IArrayD2Double)
  • maltcms.tools.PathTools (implements cross.IConfigurable)
  • maltcms.datastructures.peak.Peak (implements maltcms.datastructures.array.IFeatureVector)
    • maltcms.experimental.bipace.datastructures.spi.Peak2D
  • net.sf.maltcms.evaluation.spi.xcalibur.Peak (implements maltcms.datastructures.array.IFeatureVector)
  • maltcms.datastructures.peak.Peak1D (implements maltcms.datastructures.array.IFeatureVector, java.lang.Iterable<T>, java.io.Serializable)
    • maltcms.datastructures.peak.Peak2D (implements java.io.Serializable)
  • maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion (implements maltcms.datastructures.cluster.ICliqueMemberCriterion<T>)
  • maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities
  • maltcms.datastructures.peak.Peak1DGroup (implements java.lang.Iterable<T>)
  • maltcms.datastructures.peak.Peak2DClique
  • maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique
  • maltcms.datastructures.peak.annotations.PeakAnnotation
    • maltcms.datastructures.peak.annotations.RetentionIndexPeakAnnotation
  • maltcms.datastructures.peak.PeakArea2D
  • maltcms.experimental.bipace.peakCliqueAlignment.PeakComparator (implements java.util.Comparator<T>)
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakComparator (implements java.util.Comparator<T>)
  • maltcms.commands.fragments2d.peakfinding.output.PeakExporter (implements maltcms.commands.fragments2d.peakfinding.output.IPeakExporter)
  • maltcms.datastructures.peak.PeakFactory
  • net.sf.maltcms.evaluation.spi.caap.PeakFactory
  • maltcms.experimental.bipace.peakCliqueAlignment.PeakFileFragmentComparator (implements java.util.Comparator<T>)
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakFileFragmentComparator (implements java.util.Comparator<T>)
  • maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils
  • maltcms.commands.fragments2d.peakfinding.output.PeakIdentification (implements maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification)
  • maltcms.commands.fragments2d.peakfinding.output.PeakIntegration (implements maltcms.commands.fragments2d.peakfinding.output.IPeakIntegration)
  • maltcms.experimental.bipace.PeakList<T> (implements java.io.Serializable)
  • maltcms.experimental.bipace.spi.PeakList1DProvider (implements maltcms.experimental.bipace.api.IPeakListProvider<T>)
  • maltcms.experimental.bipace.spi.PeakList2DProvider (implements maltcms.experimental.bipace.api.IPeakListProvider<T>)
  • maltcms.io.xml.mzData.PeakListBinaryType
  • maltcms.io.xml.mzData.PeakListBinaryType.Data
  • maltcms.commands.fragments2d.peakfinding.output.PeakNormalization
  • maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet
  • net.sf.maltcms.evaluation.api.PeakRTFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
  • net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
  • net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator (implements net.sf.maltcms.evaluation.api.IFeatureVectorComparator)
  • net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator (implements net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator)
  • maltcms.commands.fragments2d.peakfinding.PeakSeparator
  • maltcms.experimental.bipace.api.PeakSimilarityCalculator<T> (implements java.util.concurrent.Callable<V>, java.io.Serializable)
    • maltcms.experimental.bipace.spi.Peak1DSimilarityCalculator
    • maltcms.experimental.bipace.spi.Peak2DSimilarityCalculator
  • maltcms.experimental.bipace.peakCliqueAlignment.PeakSimilarityVisualizer (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakSimilarityVisualizer
  • net.sf.maltcms.evaluation.api.PerformanceMetrics
  • net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics
  • maltcms.io.xml.mzData.PersonType
  • maltcms.ui.wizard.PipelineWizard (implements javax.swing.event.HyperlinkListener, cross.event.IEventSource<V>, org.netbeans.spi.wizard.WizardPage.WizardResultProducer)
  • org.jfree.chart.plot.Plot (implements org.jfree.chart.event.AxisChangeListener, java.lang.Cloneable, org.jfree.data.general.DatasetChangeListener, org.jfree.chart.LegendItemSource, org.jfree.chart.event.MarkerChangeListener, org.jfree.util.PublicCloneable, java.io.Serializable)
    • org.jfree.chart.plot.XYPlot (implements java.lang.Cloneable, org.jfree.chart.plot.Pannable, org.jfree.util.PublicCloneable, org.jfree.chart.event.RendererChangeListener, java.io.Serializable, org.jfree.chart.plot.ValueAxisPlot, org.jfree.chart.plot.Zoomable)
      • maltcms.ui.charts.XYBPlot (implements java.io.Serializable)
  • maltcms.ui.charts.PlotRunner (implements java.util.concurrent.Callable<V>, cross.IConfigurable)
    • maltcms.ui.charts.EPlotRunner
  • maltcms.io.xml.bindings.alignment.PointMapType
  • maltcms.io.xml.bindings.alignment.PointType
  • maltcms.io.xml.bindings.alignment.PointType.Dimension
  • maltcms.io.xml.mzData.PrecursorType
  • com.db4o.query.Predicate<ExtentType> (implements java.io.Serializable)
    • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakNamePeakPredicate
    • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakPredicate
    • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramNamePredicate
    • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPredicate
    • net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPredicate
    • net.sf.maltcms.evaluation.spi.hohenheim.Eval.PeakPredicate
      • net.sf.maltcms.evaluation.spi.hohenheim.Eval.AggregatePeakPredicate
      • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNameFilenameRTPeakPredicate
      • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakNamePredicate
      • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakPredicate
      • net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPeakPredicate
      • net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPeakPredicate
    • maltcms.db.predicates.metabolite.MetabolitePredicate (implements maltcms.db.predicates.IMatchPredicate<T>)
      • maltcms.db.predicates.metabolite.MAggregatePredicate
      • maltcms.db.predicates.metabolite.MNumRangePredicate
      • maltcms.db.predicates.metabolite.MSimilarityPredicate
      • maltcms.db.predicates.metabolite.MStringMatchPredicate
        • maltcms.db.predicates.metabolite.MStringContainsPredicate
    • maltcms.db.predicates.metabolite.MetaboliteSimilarity
  • maltcms.math.functions.ProductSimilarity (implements maltcms.math.functions.IScalarArraySimilarity)
  • maltcms.tools.PublicMemberGetters<T>
  • maltcms.datastructures.quadTree.QuadTree<T>
  • maltcms.datastructures.quadTree.QuadTreeNode<T>
  • maltcms.datastructures.quadTree.QuadTreeNodeDepthFirstVisitor<T> (implements maltcms.datastructures.quadTree.QuadTreeNodeVisitor<T>)
  • maltcms.commands.fragments2d.peakfinding.QualityControl
  • maltcms.commands.fragments.peakfinding.ticPeakFinder.QuantileSnrPeakFinder (implements maltcms.commands.fragments.peakfinding.ticPeakFinder.IPeakFinder)
  • maltcms.db.QueryCallable<T> (implements java.util.concurrent.Callable<V>)
  • maltcms.db.QueryDB<T>
    • maltcms.db.MetaboliteQueryDB
  • maltcms.datastructures.rank.Rank<T> (implements java.lang.Comparable<T>)
  • maltcms.datastructures.rank.Rank.ResponseComparator<T> (implements java.util.Comparator<T>)
  • maltcms.datastructures.rank.RankComparator (implements java.util.Comparator<T>)
  • maltcms.datastructures.rank.RankSorter
  • maltcms.db.RawMSQuery (implements maltcms.db.IDBQuery<T,G>)
  • smueller.datastructure.ReBuild
  • maltcms.commands.fragments2d.peakfinding.Reliability
  • maltcms.io.xml.bindings.alignment.ResourceType
  • maltcms.io.xml.bindings.annotation.ResourceType
  • maltcms.experimental.bipace.datastructures.api.Result<T> (implements java.io.Serializable)
    • maltcms.experimental.bipace.datastructures.spi.PairwisePeakListSimilarities
  • maltcms.datastructures.peak.RetentionIndexCalculator
  • maltcms.datastructures.ms.RetentionInfo (implements maltcms.datastructures.ms.IRetentionInfo)
  • maltcms.datastructures.ridge.Ridge (implements java.lang.Comparable<T>)
  • maltcms.datastructures.ridge.RidgeCost0 (implements maltcms.datastructures.ridge.IRidgeCost)
  • maltcms.datastructures.ridge.RidgeCost1 (implements maltcms.datastructures.ridge.IRidgeCost)
  • maltcms.datastructures.ridge.RidgeCost2 (implements maltcms.datastructures.ridge.IRidgeCost)
  • maltcms.datastructures.caches.RingBuffer<T>
  • maltcms.datastructures.ms.Scan1D (implements maltcms.datastructures.ms.IScan1D)
    • maltcms.datastructures.ms.Scan2D (implements maltcms.datastructures.ms.IScan2D)
  • maltcms.datastructures.caches.ScanLineCache (implements maltcms.datastructures.caches.IScanLine)
  • maltcms.datastructures.caches.ScanLineCacheFactory
  • maltcms.datastructures.caches.ScanLineCacheOld (implements maltcms.datastructures.caches.IScanLine)
  • maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing.PeakAreaComparator (implements java.util.Comparator<T>)
  • maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing.PeakComparator (implements java.util.Comparator<T>)
  • maltcms.math.functions.similarities.SimilarityTools
  • maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking (implements maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking)
  • maltcms.io.xml.mzData.SoftwareType
    • maltcms.io.xml.mzData.DataProcessingType.Software
  • smueller.datastructure.SortedJavArrays
  • maltcms.io.xml.mzData.SourceFileType
  • maltcms.datastructures.array.SparseArray (implements maltcms.datastructures.array.IArrayD2Double)
  • maltcms.datastructures.caches.SparseScanLineCache (implements maltcms.datastructures.caches.IScanLine)
  • maltcms.tools.SparseTools
  • maltcms.io.xml.mzData.SpectrumDescType
  • maltcms.io.xml.mzData.SpectrumDescType.PrecursorList
  • maltcms.io.xml.mzData.SpectrumSettingsType
  • maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification
  • maltcms.io.xml.mzData.SpectrumType
    • maltcms.io.xml.mzData.MzData.SpectrumList.Spectrum
  • smueller.tools.Standardizer
  • maltcms.io.misc.StatsWriter (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.io.xml.mzData.SupDataBinaryType
  • maltcms.io.xml.mzData.SupDataType
  • maltcms.io.xml.mzData.SupDescType
  • javax.swing.SwingWorker<T,V> (implements java.util.concurrent.RunnableFuture<V>)
    • maltcms.runtime.LocalHostMaltcmsProcess (implements cross.event.IEventSource<V>, cross.event.IListener<V>)
  • smueller.tools.SymbolConvert
  • net.sf.maltcms.evaluation.spi.tasks.Task (implements net.sf.maltcms.evaluation.api.tasks.ITask<T>)
  • maltcms.mpaxs.TestCallable (implements java.util.concurrent.Callable<V>, java.io.Serializable)
  • maltcms.mpaxs.TestConfigurableCallable (implements net.sf.maltcms.execution.api.concurrent.ConfigurableRunnable<V>)
  • maltcms.mpaxs.TestRunnable (implements java.lang.Runnable, java.io.Serializable)
  • maltcms.commands.distances.dtwng.ThreePredecessorsOptimization (implements maltcms.commands.distances.dtwng.IOptimizationFunction)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • maltcms.datastructures.quadTree.ElementNotFoundException
  • maltcms.datastructures.peak.normalization.TicAreaNormalizer (implements maltcms.datastructures.peak.normalization.IPeakNormalizer)
  • maltcms.datastructures.warp.TICWarpInput (implements maltcms.datastructures.warp.IWarpInput)
  • maltcms.datastructures.array.TiledArray (implements maltcms.datastructures.array.IArrayD2Double)
  • maltcms.datastructures.ms.TreatmentGroup1D (implements maltcms.datastructures.ms.ITreatmentGroup<T>)
  • maltcms.datastructures.ms.TreatmentGroup2D (implements maltcms.datastructures.ms.ITreatmentGroup<T>)
  • maltcms.commands.distances.dtwng.TwoFeatureVectorOperation (implements cross.IConfigurable)
    • maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity
    • maltcms.experimental.operations.MSPeaklistAlignment
  • maltcms.io.xml.bindings.openms.featurexml.UserParam
    • maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.UserParam
  • maltcms.io.xml.mzData.UserParamType
  • maltcms.commands.fragments2d.testing.Visualization2D
  • maltcms.datastructures.warp.WarpMap2D
  • maltcms.commands.fragments.alignment.peakCliqueAlignment.WorkerFactory
  • net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider
  • maltcms.experimental.bipace.peakCliqueAlignment.io.XmlAlignmentWriter (implements cross.datastructures.workflow.IWorkflowElement)
  • maltcms.io.ZipResourceExtractor

Interface Hierarchy

• java.util.concurrent.Callable<V>
  • net.sf.maltcms.evaluation.spi.tasks.execution.IPipeline<T> (also extends java.io.Serializable)
  • net.sf.maltcms.evaluation.api.tasks.ITask<T> (also extends java.io.Serializable)
• java.lang.Comparable<T>
  • maltcms.datastructures.ms.IAnchor
    • maltcms.datastructures.ms.IMetabolite
    • maltcms.datastructures.ms.IRetentionInfo
      • maltcms.datastructures.ms.IMetabolite
  • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment1D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFragment (also extends java.util.Comparator<T>, cross.io.xml.IXMLSerializable)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IGroupFragment)
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IMetabolite
  • maltcms.datastructures.ms.IRetentionInfo
    • maltcms.datastructures.ms.IMetabolite
• java.util.Comparator<T>
  • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment1D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFragment (also extends java.lang.Comparable<T>, cross.io.xml.IXMLSerializable)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IGroupFragment)
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
• maltcms.db.predicates.metabolite.IAggregatePredicateFactory<T>
• maltcms.math.functions.IArraySimilarity
• maltcms.commands.fragments.peakfinding.ticPeakFinder.IBaselineEstimator
• maltcms.datastructures.cluster.IClique<T>
• maltcms.datastructures.cluster.ICliqueMemberCriterion<T>
• maltcms.datastructures.cluster.ICliqueUpdater<T>
• maltcms.datastructures.cluster.ICluster
• maltcms.db.IDBQuery<T,G>
• net.sf.maltcms.evaluation.api.IFeatureVectorComparator
• net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator
• maltcms.db.predicates.IMatchPredicate<T>
• maltcms.commands.fragments.peakfinding.ticPeakFinder.IPeakFinder
• maltcms.commands.fragments.peakfinding.ticPeakFinder.IPeakIntegrator
• maltcms.experimental.bipace.api.IPeakListProvider<T>
• maltcms.datastructures.peak.normalization.IPeakNormalizer
• maltcms.datastructures.ms.IRetentionInfo2D
• maltcms.datastructures.ridge.IRidgeCost
• maltcms.math.functions.IScalarArraySimilarity
• maltcms.math.functions.IScalarSimilarity
• java.lang.Iterable<T>
  • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan1DProvider)
  • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan2DProvider)
  • maltcms.commands.fragments.cluster.IClusteringAlgorithm
  • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment1D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IGroupFragment
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment)
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IIterableFragment
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IGroupFragment
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
      • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment)
        • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
          • maltcms.datastructures.ms.IExperiment1D
            • maltcms.datastructures.ms.IExperiment2D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.peak.IPeakGroup1DProvider<T>
  • maltcms.datastructures.ms.IScan1DProvider
    • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram)
  • maltcms.datastructures.ms.IScan2DProvider
    • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram)
  • maltcms.datastructures.ms.IScanProvider<T> (also extends cross.IConfigurable)
    • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan1DProvider)
    • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan2DProvider)
    • maltcms.datastructures.ms.IScan1DProvider
      • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram)
    • maltcms.datastructures.ms.IScan2DProvider
      • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram)
• maltcms.datastructures.ms.ITreatmentGroup<T>
• maltcms.datastructures.warp.IWarpInput
• maltcms.commands.filters.array.wavelet.IWavelet
• cross.io.xml.IXMLSerializable
  • maltcms.commands.distances.dtw.IDynamicTimeWarp
  • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment1D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • cross.datastructures.fragments.IFragment (also extends java.lang.Comparable<T>, java.util.Comparator<T>)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IGroupFragment)
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
  • maltcms.commands.fragments2d.peakfinding.output.IPeakExporter (also extends cross.IConfigurable, cross.datastructures.workflow.IWorkflowElement)
  • cross.datastructures.workflow.IWorkflowElement
    • maltcms.commands.distances.dtw.IDynamicTimeWarp
    • maltcms.commands.fragments2d.peakfinding.output.IPeakExporter (also extends cross.IConfigurable)
    • maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.commands.ICommand<IN,OUT>)
      • maltcms.commands.distances.dtw.IDynamicTimeWarp
  • maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.commands.ICommand<IN,OUT>, cross.datastructures.workflow.IWorkflowElement)
    • maltcms.commands.distances.dtw.IDynamicTimeWarp
• maltcms.datastructures.quadTree.QuadTreeNodeVisitor<T>
• java.io.Serializable
  • java.io.Externalizable
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • cross.datastructures.fragments.IFileFragment (also extends cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
      • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
        • maltcms.datastructures.ms.IExperiment1D
          • maltcms.datastructures.ms.IExperiment2D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
  • maltcms.commands.distances.dtwng.IAlignment
  • maltcms.datastructures.array.IArrayD2Byte
  • maltcms.datastructures.array.IArrayD2Double
  • maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit
  • maltcms.datastructures.ms.IChromatogram
    • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IScan1DProvider)
    • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IScan2DProvider)
  • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan1DProvider)
  • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan2DProvider)
  • cross.commands.ICommand<IN,OUT>
    • maltcms.commands.distances.dtw.IDynamicTimeWarp
    • maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.datastructures.workflow.IWorkflowElement)
      • maltcms.commands.distances.dtw.IDynamicTimeWarp
  • cross.IConfigurable
    • maltcms.commands.distances.dtwng.IAlignment
    • maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit
    • maltcms.datastructures.ms.IChromatogram
      • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IScan1DProvider)
      • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IScan2DProvider)
    • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan1DProvider)
    • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan2DProvider)
    • cross.commands.ICommand<IN,OUT>
      • maltcms.commands.distances.dtw.IDynamicTimeWarp
      • maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.datastructures.workflow.IWorkflowElement)
        • maltcms.commands.distances.dtw.IDynamicTimeWarp
    • maltcms.commands.distances.IDtwSimilarityFunction
    • maltcms.commands.distances.dtw.IDynamicTimeWarp
    • maltcms.datastructures.ms.IExperiment (also extends cross.datastructures.fragments.IFileFragment)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.IFileFragmentModifier
      • maltcms.commands.distances.dtwng.IAlignment
      • maltcms.commands.distances.dtwng.IOptimizationFunction
      • maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation<RESULT>
        • maltcms.commands.distances.dtwng.IAlignment
    • maltcms.commands.distances.dtwng.IOptimizationFunction
    • maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation<RESULT>
      • maltcms.commands.distances.dtwng.IAlignment
    • maltcms.commands.fragments2d.peakfinding.output.IPeakExporter (also extends cross.datastructures.workflow.IWorkflowElement)
    • maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification
    • maltcms.commands.fragments2d.peakfinding.output.IPeakIntegration
    • maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking
    • maltcms.commands.distances.IRecurrence
    • maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing
    • maltcms.datastructures.ms.IScan1DProvider
      • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram)
    • maltcms.datastructures.ms.IScan2DProvider
      • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram)
    • maltcms.datastructures.caches.IScanLine
    • maltcms.datastructures.ms.IScanProvider<T> (also extends java.lang.Iterable<T>)
      • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan1DProvider)
      • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan2DProvider)
      • maltcms.datastructures.ms.IScan1DProvider
        • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram)
      • maltcms.datastructures.ms.IScan2DProvider
        • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram)
    • maltcms.commands.fragments2d.warp.visualization.IVisualization
    • maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.commands.ICommand<IN,OUT>, cross.datastructures.workflow.IWorkflowElement)
      • maltcms.commands.distances.dtw.IDynamicTimeWarp
  • maltcms.commands.distances.IDtwSimilarityFunction
  • maltcms.commands.distances.dtw.IDynamicTimeWarp
  • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable, cross.datastructures.fragments.IFileFragment)
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment1D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.array.IFeatureVector
    • maltcms.datastructures.array.IMutableFeatureVector
    • maltcms.datastructures.ms.IScan
      • maltcms.datastructures.ms.IScan1D
        • maltcms.datastructures.ms.IScan2D
      • maltcms.datastructures.ms.IScan2D
    • maltcms.datastructures.ms.IScan1D
      • maltcms.datastructures.ms.IScan2D
    • maltcms.datastructures.ms.IScan2D
  • cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
    • maltcms.datastructures.ms.IExperiment (also extends cross.IConfigurable)
      • maltcms.datastructures.ms.IExperiment1D
        • maltcms.datastructures.ms.IExperiment2D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment1D
      • maltcms.datastructures.ms.IExperiment2D
    • maltcms.datastructures.ms.IExperiment2D
  • maltcms.datastructures.IFileFragmentModifier
    • maltcms.commands.distances.dtwng.IAlignment
    • maltcms.commands.distances.dtwng.IOptimizationFunction
    • maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation<RESULT>
      • maltcms.commands.distances.dtwng.IAlignment
  • maltcms.datastructures.array.IMutableFeatureVector
  • maltcms.commands.distances.dtwng.IOptimizationFunction
  • maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation<RESULT>
    • maltcms.commands.distances.dtwng.IAlignment
  • maltcms.commands.fragments2d.peakfinding.output.IPeakExporter (also extends cross.IConfigurable, cross.datastructures.workflow.IWorkflowElement)
  • maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification
  • maltcms.commands.fragments2d.peakfinding.output.IPeakIntegration
  • maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking
  • net.sf.maltcms.evaluation.spi.tasks.execution.IPipeline<T> (also extends java.util.concurrent.Callable<V>)
  • net.sf.maltcms.evaluation.api.IPostProcessor
  • net.sf.maltcms.evaluation.api.tasks.IPostProcessor
  • maltcms.commands.distances.IRecurrence
  • maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing
  • maltcms.datastructures.ms.IScan
    • maltcms.datastructures.ms.IScan1D
      • maltcms.datastructures.ms.IScan2D
    • maltcms.datastructures.ms.IScan2D
  • maltcms.datastructures.ms.IScan1D
    • maltcms.datastructures.ms.IScan2D
  • maltcms.datastructures.ms.IScan1DProvider
    • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram)
  • maltcms.datastructures.ms.IScan2D
  • maltcms.datastructures.ms.IScan2DProvider
    • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram)
  • maltcms.datastructures.caches.IScanLine
  • maltcms.datastructures.ms.IScanProvider<T> (also extends cross.IConfigurable, java.lang.Iterable<T>)
    • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan1DProvider)
    • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram, maltcms.datastructures.ms.IScan2DProvider)
    • maltcms.datastructures.ms.IScan1DProvider
      • maltcms.datastructures.ms.IChromatogram1D (also extends maltcms.datastructures.ms.IChromatogram)
    • maltcms.datastructures.ms.IScan2DProvider
      • maltcms.datastructures.ms.IChromatogram2D (also extends maltcms.datastructures.ms.IChromatogram)
  • net.sf.maltcms.evaluation.api.tasks.ITask<T> (also extends java.util.concurrent.Callable<V>)
  • net.sf.maltcms.evaluation.api.tasks.ITaskResult
  • maltcms.commands.fragments2d.warp.visualization.IVisualization
  • maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.commands.ICommand<IN,OUT>, cross.datastructures.workflow.IWorkflowElement)
    • maltcms.commands.distances.dtw.IDynamicTimeWarp

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • maltcms.datastructures.peak.PeakType
    • maltcms.datastructures.peak.PeakIntegration
    • maltcms.tools.PathTools.Direction
    • maltcms.datastructures.quadTree.Quad
    • maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State
    • maltcms.io.xml.bindings.openms.featurexml.UserParamType
    • maltcms.io.xml.bindings.openms.featurexml.MassType
    • maltcms.io.xml.bindings.openms.featurexml.DigestionEnzyme
    • net.sf.maltcms.evaluation.spi.xcalibur.RTUnit