Class Hierarchy
- java.lang.Object
- maltcms.commands.filters.array.AArrayFilter (implements cross.commands.ICommand<IN,OUT>)
- javax.swing.AbstractAction (implements javax.swing.Action, java.lang.Cloneable, java.io.Serializable)
- java.util.AbstractCollection<E> (implements java.util.Collection<E>)
- java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
- org.jfree.chart.renderer.AbstractRenderer (implements java.lang.Cloneable, java.io.Serializable)
- org.jfree.chart.renderer.xy.AbstractXYItemRenderer (implements org.jfree.chart.event.AnnotationChangeListener, 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)
- javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
- maltcms.ui.charts.AChart<T> (implements cross.IConfigurable)
- maltcms.datastructures.cluster.ACluster (implements maltcms.datastructures.cluster.ICluster)
- maltcms.io.xml.mzData.AdminType
- maltcms.commands.distances.dtw.ADynamicTimeWarp (implements maltcms.commands.distances.dtw.IDynamicTimeWarp)
- maltcms.commands.filters.AElementFilter (implements cross.commands.ICommand<IN,OUT>)
- cross.commands.fragments.AFragmentCommand (implements cross.commands.fragments.IFragmentCommand)
- maltcms.test.AFragmentCommandTest
- maltcms.io.xlsx.impl.AgilentPeakReportDataSource (implements maltcms.io.xlsx.IXLSDataSource)
- maltcms.io.xlsx.impl.AgilentPeakReportDataSource.Mapping
- smueller.alignment.AlignedPairVector (implements java.lang.Cloneable)
- maltcms.io.xml.bindings.alignment.Alignment
- smueller.alignment.Alignment
- 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
- net.sf.maltcms.db.search.spi.similarities.AMDISMSSimilarity
- 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>)
- ucar.ma2.Array
- 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.datastructures.cluster.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.io.xml.bindings.annotation.AttributeType
- maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.AWorkerFactory (implements java.io.Serializable)
- 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>, java.io.Serializable)
- net.sf.maltcms.evaluation.spi.classification.CategoryPairClassificationResult (implements java.lang.Comparable<T>)
- maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder<T> (implements cross.datastructures.workflow.IWorkflowElement)
- maltcms.io.csv.chromatof.ChromaTOFParser
- net.sf.maltcms.evaluation.spi.classification.ChromaTOFPeakListEntityTable<T>
- net.sf.maltcms.evaluation.spi.xcalibur.Chromatogram
- maltcms.datastructures.ms.Chromatogram1D (implements maltcms.datastructures.ms.IChromatogram1D)
- maltcms.datastructures.ms.Chromatogram2D (implements maltcms.datastructures.ms.IChromatogram2D)
- maltcms.datastructures.ms.ChromatogramFactory (implements cross.IConfigurable)
- net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest<T>
- net.sf.maltcms.evaluation.api.ClassificationPerformanceTest<T>
- maltcms.datastructures.peak.Clique<T>
- maltcms.datastructures.cluster.Clique<T> (implements maltcms.datastructures.cluster.IClique<T>)
- 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.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)
- maltcms.datastructures.constraint.ConstraintFactory
- maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform
- maltcms.test.CopyFilesOnFailure
- 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.cwt.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.datastructures.feature.DefaultBinnedMSFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
- maltcms.datastructures.feature.DefaultFeatureVector (implements maltcms.datastructures.array.IFeatureVector)
- maltcms.datastructures.peak.PeakNG (implements maltcms.datastructures.peak.IBipacePeak)
- maltcms.experimental.bipace.datastructures.spi.Peak2D
- maltcms.commands.fragments.alignment.peakCliqueAlignment.Peak2D
- maltcms.datastructures.alignment.DefaultPairSet<T> (implements java.lang.Iterable<T>)
- net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult (implements net.sf.maltcms.evaluation.api.tasks.ITaskResult)
- 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
- 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<T> (implements java.io.Serializable)
- net.sf.maltcms.evaluation.api.EntityGroup (implements java.lang.Comparable<T>)
- net.sf.maltcms.evaluation.api.classification.EntityGroup<T> (implements java.lang.Comparable<T>, java.io.Serializable)
- net.sf.maltcms.evaluation.spi.EntityGroupBuilder
- net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult (implements java.lang.Comparable<T>)
- net.sf.maltcms.evaluation.api.EntityGroupClassificationResult (implements java.lang.Comparable<T>)
- net.sf.maltcms.evaluation.api.classification.EntityGroupList<T> (implements java.util.List<E>)
- 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.ExperimentFactory
- org.junit.rules.ExternalResource (implements org.junit.rules.TestRule)
- maltcms.test.ExtractHelper
- 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.fsa.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.math.functions.similarities.InverseGaussianDifferenceSimilarity (implements maltcms.math.functions.IScalarSimilarity)
- maltcms.tools.JFreeChartTools
- maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener (implements org.jfree.chart.ChartMouseListener)
- maltcms.ui.charts.JFreeChartViewer.XYAnnotationAdder
- net.sf.maltcms.apps.JoinScans
- maltcms.io.xlsx.bridge.impl.jexcelapi.JXLCell (implements maltcms.io.xlsx.bridge.ICell)
- maltcms.io.xlsx.bridge.impl.jexcelapi.JXLRow (implements maltcms.io.xlsx.bridge.IRow)
- maltcms.io.xlsx.bridge.impl.jexcelapi.JXLSheet (implements maltcms.io.xlsx.bridge.ISheet)
- maltcms.io.xlsx.bridge.impl.jexcelapi.JXLWorkbook (implements maltcms.io.xlsx.bridge.IWorkbook)
- 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>)
- 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.mpaxs.api.concurrent.ConfigurableRunnable<V>)
- net.sf.maltcms.cv.MaltcmsCvProvider (implements cross.vocabulary.IControlledVocabularyProvider)
- 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.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)
- net.sf.maltcms.apps.MoveOutput
- net.sf.maltcms.evaluation.api.MspaPerformanceMetrics
- maltcms.db.MSPFormatMetaboliteParser
- net.sf.maltcms.db.search.spi.parser.MSPFormatMetaboliteParser2
- net.sf.maltcms.apps.MSScanVisualizer
- net.sf.maltcms.evaluation.spi.classification.MultiMap<K,V>
- net.sf.maltcms.evaluation.api.alignment.MultipleAlignment (implements java.util.Map<K,V>)
- maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter (implements cross.datastructures.workflow.IWorkflowElement)
- net.sf.maltcms.tutorials.MyWorkflow
- maltcms.io.hdf5.mz5.MZ5DataSource (implements cross.io.IDataSource)
- 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.commands.fragments.io.MZMLExporterWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
- maltcms.commands.fragments.io.MZMLExporterWorker.RunBuilder
- uk.ac.ebi.jmzml.model.mzml.MzMLObject
- uk.ac.ebi.jmzml.model.mzml.SpectrumList (implements java.io.Serializable)
- maltcms.io.xml.mzXML.MZXMLDataSource (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.io.xml.bindings.alignment.ObjectFactory
- maltcms.io.xml.bindings.annotation.ObjectFactory
- maltcms.io.xml.mzData.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)
- net.sf.maltcms.evaluation.spi.classification.PairwiseClassificationPerformanceTest<T>
- 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)
- net.sf.maltcms.evaluation.spi.classification.PairwisePerformanceMetrics (implements net.sf.maltcms.evaluation.api.classification.IPerformanceMetrics)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker (implements java.util.concurrent.Callable<V>, java.io.Serializable)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker2D (implements java.util.concurrent.Callable<V>, java.io.Serializable)
- maltcms.datastructures.feature.PairwiseValueMap (implements java.io.Serializable)
- maltcms.datastructures.feature.PairwiseValueMap.ColumnComparator (implements cern.colt.function.IntComparator)
- maltcms.datastructures.feature.PairwiseValueMap.PermutationSwapper (implements cern.colt.Swapper)
- maltcms.io.xml.mzData.ParamType
- 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)
- 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.cluster.Peak1DBidiBestHitsCriterion (implements maltcms.datastructures.cluster.ICliqueMemberCriterion<T>)
- maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities
- maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.Peak1DFactory (implements maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.IPeakFactory)
- net.sf.maltcms.evaluation.spi.classification.Peak1DFeatureVector (implements net.sf.maltcms.evaluation.api.classification.IRowIndexNamedPeakFeatureVector)
- maltcms.datastructures.peak.Peak1DGroup (implements java.lang.Iterable<T>)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.Peak1DMSFactory (implements maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.IPeakFactory)
- maltcms.datastructures.peak.Peak2DClique
- maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique
- net.sf.maltcms.evaluation.spi.classification.Peak2DFeatureVector (implements net.sf.maltcms.evaluation.api.classification.IRowIndexNamedPeakFeatureVector)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.Peak2DMSFactory (implements maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.IPeakFactory)
- maltcms.datastructures.peak.annotations.PeakAnnotation
- 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.datastructures.peak.PeakEdge (implements java.io.Serializable)
- 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
- net.sf.maltcms.evaluation.api.classification.PeakNameFeatureVectorComparator (implements net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator<T>)
- maltcms.commands.fragments2d.peakfinding.output.PeakNormalization
- maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet
- net.sf.maltcms.evaluation.api.classification.PeakRowIndexFeatureVectorComparator (implements net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator<T>)
- net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector (implements net.sf.maltcms.evaluation.api.classification.INamedPeakFeatureVector)
- net.sf.maltcms.evaluation.api.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<T>)
- maltcms.commands.fragments2d.peakfinding.PeakSeparator
- maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakSimilarities
- maltcms.experimental.bipace.api.PeakSimilarityCalculator<T> (implements java.util.concurrent.Callable<V>, java.io.Serializable)
- maltcms.experimental.bipace.peakCliqueAlignment.PeakSimilarityVisualizer (implements cross.datastructures.workflow.IWorkflowElement)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakSimilarityVisualizer (implements cross.datastructures.workflow.IWorkflowElement)
- net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics<T> (implements net.sf.maltcms.evaluation.api.classification.IPerformanceMetrics)
- net.sf.maltcms.evaluation.api.PerformanceMetrics
- maltcms.datastructures.quadTree.distances.PerpendicularDistance
- maltcms.io.xml.mzData.PersonType
- org.jfree.chart.plot.Plot (implements org.jfree.chart.event.AnnotationChangeListener, 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.PlotRunner (implements java.util.concurrent.Callable<V>, cross.IConfigurable)
- maltcms.io.xlsx.bridge.impl.poi.POICell (implements maltcms.io.xlsx.bridge.ICell)
- maltcms.io.xml.bindings.alignment.PointMapType
- maltcms.io.xml.bindings.alignment.PointType
- maltcms.io.xml.bindings.alignment.PointType.Dimension
- maltcms.io.xlsx.bridge.impl.poi.POIRow (implements maltcms.io.xlsx.bridge.IRow)
- maltcms.io.xlsx.bridge.impl.poi.POISheet (implements maltcms.io.xlsx.bridge.ISheet)
- maltcms.io.xlsx.bridge.impl.poi.POIWorkbook (implements maltcms.io.xlsx.bridge.IWorkbook)
- maltcms.io.xml.mzData.PrecursorType
- com.db4o.query.Predicate<ExtentType> (implements java.io.Serializable)
- 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.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.datastructures.peak.RetentionIndexCalculator
- net.sf.maltcms.db.search.api.ri.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 java.io.Externalizable, 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
- 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
- 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>)
- 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.mpaxs.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)
- 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.io.xml.bindings.openms.featurexml.UserParam
- maltcms.io.xml.mzData.UserParamType
- maltcms.commands.fragments2d.testing.Visualization2D
- maltcms.datastructures.warp.WarpMap2D
- maltcms.io.xlsx.bridge.WorkbookBridge
- maltcms.commands.fragments.alignment.peakCliqueAlignment.Worker2DFactory (implements maltcms.commands.fragments.alignment.peakCliqueAlignment.IWorkerFactory)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.WorkerFactory (implements maltcms.commands.fragments.alignment.peakCliqueAlignment.IWorkerFactory)
- net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider
- maltcms.io.xlsx.XLSXDataSource (implements cross.io.IDataSource)
- maltcms.experimental.bipace.peakCliqueAlignment.io.XmlAlignmentWriter (implements cross.datastructures.workflow.IWorkflowElement)
- maltcms.test.ZipResourceExtractor
Interface Hierarchy
- java.util.concurrent.Callable<V>
- java.lang.Comparable<T>
- java.util.Comparator<T>
- org.apache.commons.configuration.event.ConfigurationListener
- maltcms.db.predicates.metabolite.IAggregatePredicateFactory<T>
- maltcms.commands.fragments.peakfinding.ticPeakFinder.IBaselineEstimator
- maltcms.io.xlsx.bridge.ICell
- 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<T>
- maltcms.io.xlsx.bridge.IInputStreamProvider
- maltcms.db.predicates.IMatchPredicate<T>
- net.sf.maltcms.db.search.api.IMatchPredicate<T>
- maltcms.datastructures.peak.IPeak
- maltcms.commands.fragments.peakfinding.ticPeakFinder.IPeakFinder
- maltcms.commands.fragments.peakfinding.ticPeakFinder.IPeakIntegrator
- maltcms.experimental.bipace.api.IPeakListProvider<T>
- maltcms.datastructures.peak.normalization.IPeakNormalizer
- net.sf.maltcms.evaluation.api.classification.IPerformanceMetrics
- maltcms.datastructures.ms.IRetentionInfo2D
- maltcms.datastructures.ridge.IRidgeCost
- java.lang.Iterable<T>
- maltcms.datastructures.ms.ITreatmentGroup<T>
- maltcms.datastructures.warp.IWarpInput
- maltcms.commands.filters.array.wavelet.IWavelet
- maltcms.io.xlsx.bridge.IWorkbook
- cross.io.xml.IXMLSerializable
- maltcms.datastructures.quadTree.QuadTreeNodeVisitor<T>
- java.io.Serializable
- java.io.Externalizable
- maltcms.commands.distances.dtwng.IAlignment
- maltcms.datastructures.array.IArrayD2Byte
- maltcms.datastructures.array.IArrayD2Double
- maltcms.math.functions.IArraySimilarity
- maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit
- maltcms.datastructures.ms.IChromatogram
- 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>
- cross.IConfigurable
- cross.io.IDataSource (also extends org.apache.commons.configuration.event.ConfigurationListener, cross.IConfigurable)
- 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.array.IFeatureVector
- cross.datastructures.fragments.IFileFragment (also extends java.io.Externalizable, cross.datastructures.fragments.IFragment, cross.datastructures.fragments.IGroupFragment)
- maltcms.datastructures.IFileFragmentModifier
- maltcms.datastructures.array.IMutableFeatureVector
- net.sf.maltcms.evaluation.api.classification.INamedPeakFeatureVector
- maltcms.commands.distances.dtwng.IOptimizationFunction
- maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation<RESULT>
- maltcms.commands.fragments2d.peakfinding.output.IPeakExporter (also extends cross.IConfigurable, cross.datastructures.workflow.IWorkflowElement)
- maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.IPeakFactory
- maltcms.commands.fragments.alignment.peakCliqueAlignment.peakFactory.IPeakFactoryImpl
- 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
- net.sf.maltcms.evaluation.api.classification.IRowIndexNamedPeakFeatureVector
- maltcms.math.functions.IScalarArraySimilarity
- maltcms.math.functions.IScalarSimilarity
- maltcms.datastructures.ms.IScan
- maltcms.datastructures.ms.IScan1D
- maltcms.datastructures.ms.IScan1DProvider
- maltcms.datastructures.ms.IScan2D
- maltcms.datastructures.ms.IScan2DProvider
- maltcms.datastructures.caches.IScanLine
- maltcms.datastructures.ms.IScanProvider<T> (also extends cross.IConfigurable, java.lang.Iterable<T>)
- 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.fragments.alignment.peakCliqueAlignment.IWorkerFactory
- maltcms.io.xlsx.IXLSDataSource
- maltcms.commands.distances.PairwiseFeatureSequenceSimilarity (also extends cross.commands.ICommand<IN,OUT>, cross.datastructures.workflow.IWorkflowElement)
Enum Hierarchy
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