A B C D E F G H I J K L M N O P Q R S T U V W X Z

A

AArrayFilter - Class in maltcms.commands.filters.array

AArrayFilter applicable to Array objects, returning Array objects.

AArrayFilter() - Constructor for class maltcms.commands.filters.array.AArrayFilter

AChart<T extends org.jfree.chart.plot.Plot> - Class in maltcms.ui.charts

Abstract base class for Charts of Type T extending Plot of JFreeChart.

AChart() - Constructor for class maltcms.ui.charts.AChart

ACluster - Class in maltcms.datastructures.cluster

Abstract base class for general, n-ary clusters.

ACluster() - Constructor for class maltcms.datastructures.cluster.ACluster

actionPerformed(ActionEvent) - Method in class maltcms.db.ui.FilterButtonActionListener

actionPerformed(ActionEvent) - Method in class maltcms.db.ui.MetaboliteQueryAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.TabbedPanel

actionPerformed(ActionEvent) - Method in class maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.wizard.PipelineWizard.EditConfigurationAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction

actionPerformed(ActionEvent) - Method in class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction

add(IFileFragment, Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

add(T) - Method in class maltcms.datastructures.cluster.Clique

add(T) - Method in interface maltcms.datastructures.cluster.IClique

add(E) - Method in class maltcms.datastructures.peak.FiFoQueue

add(IFileFragment, Peak2D) - Method in class maltcms.datastructures.peak.Peak2DClique

addActivePoint(Point) - Method in class maltcms.datastructures.peak.PeakArea2D

Adds a point to list of active points.

addAlChars(boolean) - Method in class smueller.alignment.OptimalAlignmentVector

addAlChars(char, char) - Method in class smueller.alignment.OptimalAlignmentVector

addAlChars(char, char, int, int) - Method in class smueller.alignment.OptimalAlignmentVector

addALChars(AlignedPairVector) - Method in class smueller.alignment.OptimalAlignmentVector

addAll(Collection<? extends E>) - Method in class maltcms.datastructures.peak.FiFoQueue

addAnchors(List<List<Peak>>, TupleND<IFileFragment>, List<Clique<T>>, HashMap<Peak, Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorExporter

FIXME this method seems to create correct scan indices only for the first two files.

addAnnotation(ChartPanel, JFreeChart, XYItemEntity, int, int) - Method in class maltcms.ui.charts.JFreeChartViewer.XYAnnotationAdder

addAreaIntensity(Integer, Double) - Method in class maltcms.datastructures.peak.PeakArea2D

Setter.

addAttribute(Attribute) - Method in class maltcms.datastructures.ms.Experiment1D

addbaseclean(Array, double) - Static method in class smueller.datastructure.ReBuild

addBoundaryPoint(Point) - Method in class maltcms.datastructures.peak.PeakArea2D

Add a point to this list of boundaries.

addChart(JFreeChart, String) - Method in class maltcms.ui.charts.JFreeChartViewer

addChild(Tuple2D<Point2D, T>) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

addChildren(IVariableFragment...) - Method in class maltcms.datastructures.ms.Experiment1D

addChromatogram(T) - Method in interface maltcms.datastructures.ms.ITreatmentGroup

addChromatogram(IChromatogram1D) - Method in class maltcms.datastructures.ms.TreatmentGroup1D

addChromatogram(IChromatogram2D) - Method in class maltcms.datastructures.ms.TreatmentGroup2D

addComponents(JFrame) - Method in class maltcms.db.ui.MetaboliteView

addDefaultConfiguration(CompositeConfiguration) - Method in class net.sf.maltcms.apps.Maltcms

addDimensions(Dimension...) - Method in class maltcms.datastructures.ms.Experiment1D

addEntity(Category, Entity) - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

addEntity(Category, Entity) - Method in class net.sf.maltcms.evaluation.api.EntityGroup

addFeature(String, Array) - Method in class maltcms.commands.ArrayStatsMap

addFeature(String, Array) - Method in interface maltcms.datastructures.array.IMutableFeatureVector

addFeature(String, Array) - Method in class maltcms.datastructures.feature.DefaultFeatureVector

addFeatures(IFileFragment, int) - Method in class maltcms.datastructures.feature.MaltcmsFeatureVector

addFeaturesToFeatureVectorList(List<DefaultFeatureVector>, List<Array>, String) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

addFeatureToFeatureVector(DefaultFeatureVector, Array, String) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

addIfNew(AnnotationType, AnnotationsType) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

addIfNew(AttributeType, AnnotationType) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

AdditionFilter - Class in maltcms.commands.filters.array

Add a given double to elements of an array.

AdditionFilter() - Constructor for class maltcms.commands.filters.array.AdditionFilter

AdditionFilter(double) - Constructor for class maltcms.commands.filters.array.AdditionFilter

addLine(Vector<Vector<String>>, String) - Method in class maltcms.io.csv.CSVReader

addListener(IListener<IEvent<IWorkflowResult>>) - Method in class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated.

addListener(IListener<IEvent<Configuration>>) - Method in class maltcms.ui.wizard.PipelineWizard

addMissingChromatogram(Integer) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

addMS(Array) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

addNeighOf(Point) - Method in class maltcms.datastructures.peak.PeakArea2D

Adds all neighbours of p to the active point list.

addNodeK(int, int, int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

addPeak(Peak) - Method in class maltcms.datastructures.peak.Clique

Returns false, if a peak did not meet the criteria to be added to the clique.

addPeak(T) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

Returns false, if a peak did not meet the criteria to be added to the clique.

addPeak2(Peak) - Method in class maltcms.datastructures.peak.Clique

addPeakAnnotation(MaltcmsAnnotation, String, Peak) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

addPeakAnnotation(MaltcmsAnnotation, String, Peak1D) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

addPeakAnnotation(MaltcmsAnnotation, String, Peak2D) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

addPeakAreaToImage(BufferedImage, List<PeakArea2D>, int[], int[], int[], int) - Static method in class maltcms.tools.ImageTools

Adds all peaks to an image.

addPeakLists(List<Peak2D>) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

Adds a peak list to a internal peak list.

addPeakLists(List<Peak2D>) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

Adds a peak list to a internal peak list.

addPeakMarker(JFreeChart, Tuple2D<Array, Array>, IFileFragment, IFileFragment, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, int) - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Adds the peak marker.

addPeakMarker(JFreeChart, Tuple2D<Array, Array>, IFileFragment, IFileFragment, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, int) - Method in interface maltcms.commands.fragments2d.warp.visualization.IVisualization

Adds the peak marker.

addPeakToImage(BufferedImage, List<Peak2D>, int[], int[], int[], int) - Static method in class maltcms.tools.ImageTools

Adds all peaks to an image.

addPoint(int, int, double[]) - Method in class maltcms.datastructures.ridge.Ridge

AddRandomNoise - Class in maltcms.commands.filters.array

Add additive gaussian noise to array values with given mean and std deviation.

AddRandomNoise() - Constructor for class maltcms.commands.filters.array.AddRandomNoise

AddRandomNoise(double, double) - Constructor for class maltcms.commands.filters.array.AddRandomNoise

addRank(String, double) - Method in class maltcms.datastructures.rank.Rank

addRatio(String, String, Double) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

addRatio(String, String, Double) - Method in class maltcms.datastructures.peak.Peak2DClique

addRegionPoint(Point, Array, double) - Method in class maltcms.datastructures.peak.PeakArea2D

Will add the point p to the list.

addRel(double) - Method in class maltcms.commands.fragments2d.peakfinding.Reliability

addScanIndexMap(Alignment, URI, List<Integer>, boolean) - Method in class maltcms.datastructures.alignment.AlignmentFactory

addSeries(String, Array, Color) - Method in class maltcms.ui.charts.MassSpectrumPlot

Add a new mass spectra to the plot.

addSimilarity(Peak, Double) - Method in class maltcms.datastructures.peak.Peak

Add a similarity to Peak p.

addSourceFile(Collection<IFileFragment>) - Method in class maltcms.datastructures.ms.Experiment1D

addSourceFile(IFileFragment...) - Method in class maltcms.datastructures.ms.Experiment1D

addStepN(Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

addStepNW(Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

addStepW(Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

addXYZDataset(List<double[]>, double[], int) - Static method in class maltcms.tools.JFreeChartTools

AdminType - Class in maltcms.io.xml.mzData

'Header' information - sample description, contact details, comments Java class for adminType complex type.

AdminType() - Constructor for class maltcms.io.xml.mzData.AdminType

ADynamicTimeWarp - Class in maltcms.commands.distances.dtw

Base class for dynamic time warping implementations.

ADynamicTimeWarp() - Constructor for class maltcms.commands.distances.dtw.ADynamicTimeWarp

AElementFilter - Class in maltcms.commands.filters

Transformation base class to perform operations on Double values.

AElementFilter() - Constructor for class maltcms.commands.filters.AElementFilter

AffineAlignment - Class in smueller.alignment

AffineAlignment(IFileFragment, IFileFragment) - Constructor for class smueller.alignment.AffineAlignment

AFragmentCommandTest - Class in maltcms.test

AFragmentCommandTest() - Constructor for class maltcms.test.AFragmentCommandTest

align(Tuple2D<List<Array>, List<Array>>, AnchorPairSet, double, ArrayDouble.D1, ArrayDouble.D1) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

align(Tuple2D<List<Array>, List<Array>>, AnchorPairSet, double, ArrayDouble.D1, ArrayDouble.D1) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

AlignedPairVector - Class in smueller.alignment

AlignedPairVector() - Constructor for class smueller.alignment.AlignedPairVector

AlignedPairVector(boolean) - Constructor for class smueller.alignment.AlignedPairVector

AlignedPairVector(char, char, int, int) - Constructor for class smueller.alignment.AlignedPairVector

AlignedPairVector(int, int) - Constructor for class smueller.alignment.AlignedPairVector

Alignment - Class in maltcms.io.xml.bindings.alignment

Java class for anonymous complex type.

Alignment() - Constructor for class maltcms.io.xml.bindings.alignment.Alignment

Alignment - Class in smueller.alignment

Alignment(IFileFragment, IFileFragment) - Constructor for class smueller.alignment.Alignment

Alignment2D - Class in maltcms.commands.fragments2d.testing

Alignment2D() - Constructor for class maltcms.commands.fragments2d.testing.Alignment2D

AlignmentColumn - Class in net.sf.maltcms.evaluation.api.alignment

AlignmentColumn(double...) - Constructor for class net.sf.maltcms.evaluation.api.alignment.AlignmentColumn

AlignmentColumnComparator - Class in net.sf.maltcms.evaluation.api.alignment

AlignmentColumnComparator(double) - Constructor for class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

AlignmentFactory - Class in maltcms.commands.distances.dtwng

AlignmentFactory() - Constructor for class maltcms.commands.distances.dtwng.AlignmentFactory

AlignmentFactory - Class in maltcms.datastructures.alignment

AlignmentFactory() - Constructor for class maltcms.datastructures.alignment.AlignmentFactory

AlignmentMapChart - Class in maltcms.ui.charts

Creates a Plot displaying the mapping between two aligned time series.

AlignmentMapChart(List<Tuple2DI>, Array, Array, String, int, int) - Constructor for class maltcms.ui.charts.AlignmentMapChart

AlignmentOutput - Class in smueller.datastructure

AlignmentOutput() - Constructor for class smueller.datastructure.AlignmentOutput

AlignmentPane - Class in maltcms.ui.wizard

AlignmentPane() - Constructor for class maltcms.ui.wizard.AlignmentPane

Creates new form AlignmentPane

AlignmentPath2D - Class in maltcms.commands.fragments2d.testing

.

allInfinite(double, double, double) - Static method in class maltcms.tools.PathTools

AnchorDefinitionPane - Class in maltcms.ui.wizard

AnchorDefinitionPane() - Constructor for class maltcms.ui.wizard.AnchorDefinitionPane

Creates new form AnchorDefinition

AnchorExporter<T extends Peak> - Class in maltcms.experimental.bipace.peakCliqueAlignment.io

AnchorExporter() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorExporter

AnchorImporter - Class in maltcms.experimental.bipace.peakCliqueAlignment.io

AnchorImporter() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorImporter

AnchorPairSet - Class in maltcms.datastructures.alignment

Represents a set of matched pairs of anchors.

AnchorPairSet(List<IAnchor>, List<IAnchor>, int, int, int) - Constructor for class maltcms.datastructures.alignment.AnchorPairSet

AnchorPairSet(List<IAnchor>, List<IAnchor>, int, int) - Constructor for class maltcms.datastructures.alignment.AnchorPairSet

ANDIChromImporter - Class in maltcms.commands.fragments.io

Currently only generates scan_acquisition_time for plotting and alignment purposes.

ANDIChromImporter() - Constructor for class maltcms.commands.fragments.io.ANDIChromImporter

ANDIMSExporter - Class in maltcms.commands.fragments.io

ANDIMSExporter() - Constructor for class maltcms.commands.fragments.io.ANDIMSExporter

AnnotationsType - Class in maltcms.io.xml.bindings.annotation

Java class for annotationsType complex type.

AnnotationsType() - Constructor for class maltcms.io.xml.bindings.annotation.AnnotationsType

AnnotationType - Class in maltcms.io.xml.bindings.annotation

Java class for annotationType complex type.

AnnotationType() - Constructor for class maltcms.io.xml.bindings.annotation.AnnotationType

APipeline<T extends Serializable> - Class in net.sf.maltcms.evaluation.spi.tasks.execution

APipeline() - Constructor for class net.sf.maltcms.evaluation.spi.tasks.execution.APipeline

append(IFileFragment, List<IPeakNormalizer>, List<Peak1D>, Array, String, String) - Static method in class maltcms.datastructures.peak.Peak1D

appendXML(Element) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

appendXML(Element) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

appendXML(Element) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

appendXML(Element) - Method in class maltcms.datastructures.fragments.PairwiseDistances

appendXML(Element) - Method in class maltcms.datastructures.ms.Experiment1D

appendXML(Element) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

appendXML(Element) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

appendXML(Element) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorExporter

appendXML(Element) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter

appendXML(Element) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.XmlAlignmentWriter

appendXML(Element) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.PeakSimilarityVisualizer

appendXML(Element) - Method in class maltcms.io.csv.CSVWriter

appendXML(Element) - Method in class maltcms.io.misc.StatsWriter

appendXML(Element) - Method in class maltcms.statistics.LogDeltaEvaluation

appendXML(Element) - Method in class maltcms.statistics.OneWayPeakAnova

ApplicationContextWorkerFactory - Class in maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

Use this if you are instantiating a workflow containing PairwiseDistanceCalculator using any of the spring xml bean configuration files.

ApplicationContextWorkerFactory() - Constructor for class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.ApplicationContextWorkerFactory

apply(IFileFragment, IFileFragment) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

apply(Tuple2D<Array[], Array[]>) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

apply(List<IFeatureVector>, List<IFeatureVector>) - Method in class maltcms.commands.distances.dtwng.DTW

apply(IFeatureVector, IFeatureVector) - Method in class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity

apply(int...) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

apply(List<IFeatureVector>, List<IFeatureVector>) - Method in interface maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation

apply(int...) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

apply(IFeatureVector, IFeatureVector) - Method in class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation

apply(int, int, double, double, Array, Array) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

if i1 && i2 > 0 => apply distance to indices only else apply to all elements of array

apply(IFileFragment, IFileFragment) - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

apply(Array) - Method in class maltcms.commands.filters.array.AArrayFilter

apply(Array[]) - Method in class maltcms.commands.filters.array.AArrayFilter

apply(Array) - Method in class maltcms.commands.filters.array.AdditionFilter

apply(Array) - Method in class maltcms.commands.filters.array.AddRandomNoise

apply(Array[]) - Method in class maltcms.commands.filters.array.ArrayMerge

apply(Array) - Method in class maltcms.commands.filters.array.BottomHatFilter

apply(Array) - Method in class maltcms.commands.filters.array.ExpFilter

apply(Array) - Method in class maltcms.commands.filters.array.FirstDerivativeFilter

apply(Array) - Method in class maltcms.commands.filters.array.LogFilter

apply(Array) - Method in class maltcms.commands.filters.array.MeanStdDevNormalizationFilter

apply(Array) - Method in class maltcms.commands.filters.array.MedianBaselineFilter

apply(Array[]) - Method in class maltcms.commands.filters.array.MedianBaselineFilter

apply(Array) - Method in class maltcms.commands.filters.array.MinimumFilter

apply(Array) - Method in class maltcms.commands.filters.array.MinMaxNormalizationFilter

apply(Array) - Method in class maltcms.commands.filters.array.MovingAverageFilter

apply(Array) - Method in class maltcms.commands.filters.array.MovingMedianFilter

apply(Array) - Method in class maltcms.commands.filters.array.MultiplicationFilter

apply(Array[]) - Method in class maltcms.commands.filters.array.NormalizationFilter

apply(Array) - Method in class maltcms.commands.filters.array.SavitzkyGolayFilter

apply(Array) - Method in class maltcms.commands.filters.array.SqrtFilter

apply(Array) - Method in class maltcms.commands.filters.array.TopHatFilter

apply(double[], double, double...) - Method in class maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform

apply(Array) - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.alignment.CenterStarAlignment

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

apply(TupleND<IFileFragment>) - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.ANDIChromImporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.ANDIMSExporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

Simply return the same FileFragments as were received. apply will add the necessary fragments automatically to those fragments in the tuple which have an associated RI file.

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.MSPExporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.ObiWarplmataExporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.PeakAreaTableExporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.TICPeakListImporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.io.VariableDataExporter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.peakfinding.CwtTicPeakFinder

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.peakfinding.EICPeakFinder

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.preprocessing.DefaultVarLoader

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.preprocessing.DenseArrayProducer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.preprocessing.MassFilter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.spectratyping.VBetaFamilyComparison

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.EICHeatmapCoplot

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.MZIDistributionVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.visualization.TICHeatmapCoplot

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

apply(MZIWarpInput, IFileFragment) - Method in class maltcms.commands.fragments.warp.PathWarp

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.warp.PathWarp

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarProducer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarVis

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.ModulationExtractor

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator

Deprecated.

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.testing.Alignment2D

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.visualization.DeltaMasses

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.visualization.GradientVisualizer

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.CreateHorizontalTicVector

apply(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer

apply(Array[]) - Method in class maltcms.commands.scanners.ArrayStatsScanner

apply(IFeatureVector, IFeatureVector) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

apply(Array, Array, Array, Array) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

apply(int, int, double, double, Array, Array) - Method in class maltcms.math.functions.DtwPairwiseSimilarity

apply(int, int, double, double, Array, Array) - Method in class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity

apply(Array, Array) - Method in interface maltcms.math.functions.IArraySimilarity

apply(double[], double[], Array, Array) - Method in interface maltcms.math.functions.IScalarArraySimilarity

apply(double, double) - Method in interface maltcms.math.functions.IScalarSimilarity

apply(double[], double[], Array, Array) - Method in class maltcms.math.functions.ProductSimilarity

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayBhattacharryya

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCorr

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCos

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCosLp

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayCov

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayDot

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayDotLp

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayDotMap

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayHamming

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayLp

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayRankCorr

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayTanimoto

apply(Array, Array) - Method in class maltcms.math.functions.similarities.ArrayWeightedCosine

apply(double, double) - Method in class maltcms.math.functions.similarities.GaussianDifferenceSimilarity

Calculates the scalar

apply(TupleND<IFileFragment>) - Method in class smueller.SymbolicRepresentationAlignment

applyFilters(Array, List<AArrayFilter>) - Static method in class maltcms.commands.filters.array.BatchFilter

applyInverse(List<double[]>, List<Double>, double...) - Method in class maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform

applyInverseTransform(List<double[]>, List<Double>) - Method in class maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform

applyLut(BufferedImage, LookupTable) - Static method in class maltcms.tools.ImageTools

applyMotherWavelet(double, double...) - Method in interface maltcms.commands.filters.array.wavelet.IWavelet

applyMotherWavelet(double, double...) - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWavelet

First param in params is expected to be the variance sigma.

applyWarp() - Method in class maltcms.datastructures.warp.WarpMap2D

Calculates a warp function, based on the supplied anchors.

AREA_DEFAULT - Static variable in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

Array1DVisualizer - Class in maltcms.commands.fragments.visualization

Plot 1-dimensional arrays, possibly with an additional array providing domain values.

Array1DVisualizer() - Constructor for class maltcms.commands.fragments.visualization.Array1DVisualizer

ArrayBhattacharryya - Class in maltcms.math.functions.similarities

ArrayBhattacharryya() - Constructor for class maltcms.math.functions.similarities.ArrayBhattacharryya

ArrayCorr - Class in maltcms.math.functions.similarities

Calculates Pearson's product moment correlation as similarity between arrays.

ArrayCorr() - Constructor for class maltcms.math.functions.similarities.ArrayCorr

ArrayCos - Class in maltcms.math.functions.similarities

Cosine similarity between arrays.

ArrayCos() - Constructor for class maltcms.math.functions.similarities.ArrayCos

ArrayCosLp - Class in maltcms.math.functions.similarities

Combinded distance of ArrayCos and ArrayLp.

ArrayCosLp() - Constructor for class maltcms.math.functions.similarities.ArrayCosLp

ArrayCov - Class in maltcms.math.functions.similarities

Calculates Pearson's product moment correlation as similarity between arrays.

ArrayCov() - Constructor for class maltcms.math.functions.similarities.ArrayCov

ArrayDot - Class in maltcms.math.functions.similarities

Dot product as similarity measure between arrays.

ArrayDot() - Constructor for class maltcms.math.functions.similarities.ArrayDot

ArrayDotLp - Class in maltcms.math.functions.similarities

ArrayDotLp() - Constructor for class maltcms.math.functions.similarities.ArrayDotLp

ArrayDotMap - Class in maltcms.math.functions.similarities

Calculates the dotmap, but instead of the weighting by mz bin this class uses the standard deviation.

ArrayDotMap() - Constructor for class maltcms.math.functions.similarities.ArrayDotMap

ArrayFactory - Class in maltcms.datastructures.array

A factory abstraction for creation of IArrayD2Double implementations.

ArrayFactory() - Constructor for class maltcms.datastructures.array.ArrayFactory

ArrayHamming - Class in maltcms.math.functions.similarities

Hamming distance between binary vectors.

ArrayHamming() - Constructor for class maltcms.math.functions.similarities.ArrayHamming

ArrayLp - Class in maltcms.math.functions.similarities

Lp-norm based distance between arrays.

ArrayLp() - Constructor for class maltcms.math.functions.similarities.ArrayLp

ArrayMerge - Class in maltcms.commands.filters.array

Returns a list of all arrays, processed to be consistent with this objects merging strategy.

ArrayMerge() - Constructor for class maltcms.commands.filters.array.ArrayMerge

ArrayRankCorr - Class in maltcms.math.functions.similarities

Calculates Spearman's rank correlation as similarity between arrays.

ArrayRankCorr() - Constructor for class maltcms.math.functions.similarities.ArrayRankCorr

ArrayStatsMap - Class in maltcms.commands

ArrayStatsMap() - Constructor for class maltcms.commands.ArrayStatsMap

ArrayStatsScanner - Class in maltcms.commands.scanners

Scans a number of arrays for statistics, such as mean and variance, storing results for each array in a HashMap indexed by Elements of

ArrayStatsScanner() - Constructor for class maltcms.commands.scanners.ArrayStatsScanner

ArrayTanimoto - Class in maltcms.math.functions.similarities

Implementation of Tanimoto score.

ArrayTanimoto() - Constructor for class maltcms.math.functions.similarities.ArrayTanimoto

ArrayTools - Class in maltcms.commands.fragments2d.tools

ArrayTools() - Constructor for class maltcms.commands.fragments2d.tools.ArrayTools

ArrayTools - Class in maltcms.tools

Utility class providing methods for Sparse and Dense Arrays.

ArrayTools() - Constructor for class maltcms.tools.ArrayTools

ArrayTools - Class in smueller.tools

ArrayTools() - Constructor for class smueller.tools.ArrayTools

ArrayTools2 - Class in maltcms.tools

Array tools.

ArrayTools2() - Constructor for class maltcms.tools.ArrayTools2

ArrayWeightedCosine - Class in maltcms.math.functions.similarities

ArrayWeightedCosine() - Constructor for class maltcms.math.functions.similarities.ArrayWeightedCosine

AScanLineCache - Class in maltcms.datastructures.caches

This class is a dataholder for mass spectra.

asMatchList(Collection<DBMatch>) - Static method in class maltcms.db.predicates.metabolite.DBMatch

asSimilarity(double) - Static method in class maltcms.math.functions.similarities.SimilarityTools

AttributeType - Class in maltcms.io.xml.bindings.annotation

Java class for attributeType complex type.

AttributeType() - Constructor for class maltcms.io.xml.bindings.annotation.AttributeType

ausgabe() - Method in class smueller.alignment.Alignment

AWorkerFactory - Class in maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

Extend this Factory in order to create custom worker instances.

AWorkerFactory() - Constructor for class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.AWorkerFactory

B

BatchFilter - Class in maltcms.commands.filters.array

BatchFilter() - Constructor for class maltcms.commands.filters.array.BatchFilter

BBHFinder - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

BBHFinder() - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.BBHFinder

BBHFinder - Class in maltcms.experimental.bipace.peakCliqueAlignment

BBHFinder() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder

BBHTools - Class in maltcms.commands.fragments2d.peakfinding.bbh

BBHTools() - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.BBHTools

BeansXmlGenerator - Class in net.sf.maltcms.evaluation.spi

BeansXmlGenerator(LinkedHashMap<String, List<?>>, File, File, HashMap<String, String>) - Constructor for class net.sf.maltcms.evaluation.spi.BeansXmlGenerator

BHeatMapChart - Class in maltcms.ui.charts

Creates a chart with labeled domain axis, displaying a heatmap as backgroundimage.

BHeatMapChart(String, String, String, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, String) - Constructor for class maltcms.ui.charts.BHeatMapChart

Default constructor.

BidirectionalBestHit - Class in maltcms.commands.fragments2d.peakfinding.bbh

Will compute a list of bidirectional best hits.

BidirectionalBestHit() - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

Default constructor.

BinaryCluster - Class in maltcms.datastructures.cluster

Concrete implementation of a binary cluster.

BinaryCluster(BinaryCluster, BinaryCluster, double, double, double[], int) - Constructor for class maltcms.datastructures.cluster.BinaryCluster

BinaryCluster(String, int, double[]) - Constructor for class maltcms.datastructures.cluster.BinaryCluster

binMZ(double, double, double, double) - Static method in class maltcms.tools.MaltcmsTools

Calculates the normalized index of mz, by subtracting minmz and dividing by maxmz-minmz.

binMZDefault(double) - Static method in class maltcms.tools.MaltcmsTools

Use standard rounding.

binMZFloor(double) - Static method in class maltcms.tools.MaltcmsTools

binMZHeiko(double) - Static method in class maltcms.tools.MaltcmsTools

Use rounding according to Heiko's distribution analysis.

BiPace<T extends Peak> - Class in maltcms.experimental.bipace

BiPace() - Constructor for class maltcms.experimental.bipace.BiPace

BiPaceBidirectionalBestHit - Class in maltcms.commands.fragments2d.peakfinding.bbh

BiPaceBidirectionalBestHit() - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit

BiPaceResult<T extends Peak> - Class in maltcms.experimental.bipace

BiPaceResult() - Constructor for class maltcms.experimental.bipace.BiPaceResult

BottomHatFilter - Class in maltcms.commands.filters.array

BottomHatFilter() - Constructor for class maltcms.commands.filters.array.BottomHatFilter

BreakPoints - Class in smueller.datastructure

BreakPoints(Array, Array) - Constructor for class smueller.datastructure.BreakPoints

buildBinaryMassVectors(IFileFragment, String, String, String, String, List<Integer>) - Static method in class maltcms.tools.MaltcmsTools

buildCSVPeakAssociationGroups(File) - Method in class net.sf.maltcms.evaluation.spi.EntityGroupBuilder

Peak association in csv files is via row, header has names of files, used as categories Format: FILE1\tFILE2\tFILE3...

buildCSVTablePeakAssociationGroups(File) - Method in class net.sf.maltcms.evaluation.spi.EntityGroupBuilder

Peak association in csv files via column, first element in row has name of file Format: FILE1\tFEAT1_1\tFEAT2_1...

buildXcaliburPeakAssociationGroups(Eval, ObjectContainer) - Method in class net.sf.maltcms.evaluation.spi.EntityGroupBuilder

Peak association in xcalibur reports is via peak/compound name.

C

CachedScanLineList - Class in maltcms.datastructures.caches

Implementation of IScanLine with CachedList.

calc(List<Peak2D>, List<Peak2D>, List<List<Point>>) - Method in class maltcms.commands.fragments2d.peakfinding.QualityControl

calcbreakpoints(Array, double[], int) - Method in class smueller.datastructure.BreakPoints

calcEstimatedAutoCorrelation(Array, double, double, int) - Method in class maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask

calcFisherRatios(Collection<Clique>, Collection<IFileFragment>, String) - Method in class maltcms.statistics.OneWayPeakAnova

calcmax(Array) - Static method in class smueller.tools.ArrayTools

calcmin(Array) - Static method in class smueller.tools.ArrayTools

calcPercentDone(long, long) - Static method in class maltcms.tools.ArrayTools

calcR(int) - Method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

calcRatios(List<Peak2DClique>, Collection<IFileFragment>) - Method in class maltcms.statistics.LogDeltaEvaluation

calculateEditDistanceMatrix(String, String) - Method in class maltcms.experimental.operations.EditDistance

Calculates the edit distance matrix of strings a and b.

calculateLayout(int, int, int, AnchorPairSet, double, int, int) - Method in class maltcms.datastructures.constraint.ConstraintFactory

calculateMeanVarSparse(List<Array>) - Static method in class maltcms.tools.MaltcmsTools

calculatePairwiseDistances(IArrayD2Double, ArrayDouble.D1, ArrayDouble.D1, List<Array>, List<Array>) - Method in class maltcms.commands.distances.PairwiseFeatureSimilarity

This method can be called for precalculation of all distances/similarites.

calculateSimilarity(T, T) - Method in class maltcms.experimental.bipace.api.PeakSimilarityCalculator

calculateSimilarity(Peak, Peak) - Method in class maltcms.experimental.bipace.spi.Peak1DSimilarityCalculator

calculateSimilarity(Peak2D, Peak2D) - Method in class maltcms.experimental.bipace.spi.Peak2DSimilarityCalculator

call() - Method in class maltcms.commands.distances.PartitionCalculator

call() - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker

call() - Method in class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceWorker

call() - Method in class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtEicPeakFinderCallable

call() - Method in class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtTicPeakFinderCallable

call() - Method in class maltcms.commands.fragments.preprocessing.defaultVarLoader.DefaultVarLoaderWorker

call() - Method in class maltcms.commands.fragments.preprocessing.denseArrayProducer.DenseArrayProducerWorker

call() - Method in class maltcms.commands.fragments.preprocessing.denseArrayProducer.MinMaxMassFinderWorker

call() - Method in class maltcms.commands.fragments2d.peakfinding.CwtRunnable

call() - Method in class maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask

call() - Method in class maltcms.db.QueryCallable

call() - Method in class maltcms.experimental.bipace.api.PeakSimilarityCalculator

call() - Method in class maltcms.experimental.bipace.BiPace

call() - Method in class maltcms.mpaxs.TestCallable

call() - Method in class maltcms.ui.charts.EPlotRunner

call() - Method in class maltcms.ui.charts.PlotRunner

call() - Method in class net.sf.maltcms.evaluation.spi.tasks.execution.FilePipeline

call() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

cancel(Map) - Method in class maltcms.ui.wizard.Main

cancel(Map) - Method in class maltcms.ui.wizard.PipelineWizard

canRead(IFileFragment) - Method in class maltcms.io.andims.NetcdfDataSource

canRead(IFileFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

canRead(IFileFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

canRead(IFileFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

canRead(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

canRead(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

Checks, if passed in file is valid mzXML, by trying to invoke the parser on it.

canRead(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

Checks, if passed in file is valid mzXML, by trying to invoke the parser on it.

Category - Class in net.sf.maltcms.evaluation.api

A class which allows the definition of a category for an entity.

Category(String) - Constructor for class net.sf.maltcms.evaluation.api.Category

Category - Class in net.sf.maltcms.evaluation.api.classification

A class which allows the definition of a category for an entity.

Category(String) - Constructor for class net.sf.maltcms.evaluation.api.classification.Category

CenterFinder<T extends Peak> - Class in maltcms.experimental.bipace.peakCliqueAlignment

CenterFinder() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

CenterStarAlignment - Class in maltcms.commands.fragments.alignment

Implementation of the center star approximation for multiple alignment.

CenterStarAlignment() - Constructor for class maltcms.commands.fragments.alignment.CenterStarAlignment

changeAlChars(int, int) - Method in class smueller.alignment.OptimalAlignmentVector

chartMouseClicked(ChartMouseEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener

chartMouseMoved(ChartMouseEvent) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener

chartoNumber(char) - Method in class smueller.alignment.Alignment

checkAnchors(int, int, List<Tuple2D<IAnchor, IAnchor>>, int) - Method in class maltcms.datastructures.alignment.AnchorPairSet

checkCategories(List<EntityGroup>, List<EntityGroup>) - Method in class net.sf.maltcms.evaluation.api.ClassificationPerformanceTest

checkCategories(EntityGroup, EntityGroup) - Method in class net.sf.maltcms.evaluation.api.ClassificationPerformanceTest

checkCategories(List<EntityGroup>, List<EntityGroup>) - Method in class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest

checkCategories(EntityGroup, EntityGroup) - Method in class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest

checkConsistency(List<Tuple2D<T, T>>) - Method in class maltcms.datastructures.alignment.DefaultPairSet

checkEqualLength(List<ArrayDouble.D1>...) - Method in class maltcms.io.csv.CSVWriter

checkEqualLength(List<ArrayDouble.D1>) - Method in class maltcms.io.csv.CSVWriter

checkExtremum(double[], double[], ArrayList<Integer>, double, int, int) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

checkMinimum(double[], ArrayList<Integer>, int, int) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

checkOverwrite() - Method in class maltcms.ui.wizard.PipelineWizard

chrom2crs(Chromatogram1D) - Static method in class maltcms.tools.MaltcmsTools

Chromatogram - Class in net.sf.maltcms.evaluation.spi.xcalibur

Chromatogram(String) - Constructor for class net.sf.maltcms.evaluation.spi.xcalibur.Chromatogram

Chromatogram1D - Class in maltcms.datastructures.ms

Concrete Implementation of a 1-dimensional chromatogram.

Chromatogram1D(IFileFragment) - Constructor for class maltcms.datastructures.ms.Chromatogram1D

Chromatogram2D - Class in maltcms.datastructures.ms

Concrete Implementation of a 1-dimensional chromatogram.

Chromatogram2D(IFileFragment) - Constructor for class maltcms.datastructures.ms.Chromatogram2D

Chromatogram2DVisualizer - Class in maltcms.commands.fragments2d.visualization

Creates an image.

Chromatogram2DVisualizer() - Constructor for class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer

ChromatogramFactory - Class in maltcms.datastructures.ms

ChromatogramFactory() - Constructor for class maltcms.datastructures.ms.ChromatogramFactory

ChromatogramVisualizer - Class in maltcms.commands.fragments.visualization

Visualizes a chromatogram as a heat map, based on the empirical distribution of intensity values, using a user defined sample model and color model.

ChromatogramVisualizer() - Constructor for class maltcms.commands.fragments.visualization.ChromatogramVisualizer

ChromatogramWarp - Class in maltcms.commands.fragments.warp

Deprecated.

ChromatogramWarp() - Constructor for class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

ChromatogramWarp2 - Class in maltcms.commands.fragments.warp

Use Objects of this class to apply an alignment, warping a source chromatogram to the time/scans of reference chromatogram.

ChromatogramWarp2() - Constructor for class maltcms.commands.fragments.warp.ChromatogramWarp2

ClassificationPerformancePostProcessor - Class in net.sf.maltcms.evaluation.spi.classification

ClassificationPerformancePostProcessor() - Constructor for class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformancePostProcessor

ClassificationPerformanceTest<T extends IFeatureVector> - Class in net.sf.maltcms.evaluation.api

Performs a classification performance test of a collection of EntityGroup instances as ground truth versus a collection of EntityGroup instances, which are to be evaluated.

ClassificationPerformanceTest(List<EntityGroup>, IFeatureVectorComparator) - Constructor for class net.sf.maltcms.evaluation.api.ClassificationPerformanceTest

ClassificationPerformanceTest<T extends IFeatureVector> - Class in net.sf.maltcms.evaluation.spi.classification

Performs a classification performance test of a collection of EntityGroup instances as ground truth versus a collection of EntityGroup instances, which are to be evaluated.

ClassificationPerformanceTest(List<EntityGroup>, IFeatureVectorComparator) - Constructor for class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest

cleanbase(Array, double, double) - Method in class smueller.tools.Standardizer

cleanbaseline(Array) - Method in class smueller.tools.Standardizer

clear() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

clear() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit

clear() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

clear() - Method in interface maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit

clear() - Method in class maltcms.datastructures.caches.AScanLineCache

clear() - Method in interface maltcms.datastructures.caches.IScanLine

clear() - Method in class maltcms.datastructures.caches.ScanLineCache

clear() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

clear() - Method in class maltcms.datastructures.caches.SparseScanLineCache

clear() - Method in class maltcms.datastructures.cluster.Clique

clear() - Method in interface maltcms.datastructures.cluster.IClique

clear() - Method in class maltcms.datastructures.peak.Clique

clear() - Method in class maltcms.datastructures.peak.FiFoQueue

clear() - Method in class maltcms.datastructures.peak.PeakArea2D

clear() - Method in class maltcms.datastructures.quadTree.QuadTree

clear() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

clear() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

clearArrays() - Method in class maltcms.datastructures.ms.Experiment1D

clearSimilarities() - Method in class maltcms.datastructures.peak.Peak

Clique<T extends IFeatureVector> - Class in maltcms.datastructures.cluster

Clique(Comparator<T>, ICliqueMemberCriterion<T>, ICliqueUpdater<T>) - Constructor for class maltcms.datastructures.cluster.Clique

Clique - Class in maltcms.datastructures.peak

Clique() - Constructor for class maltcms.datastructures.peak.Clique

Clique<T extends Peak> - Class in maltcms.experimental.bipace.datastructures.api

Clique() - Constructor for class maltcms.experimental.bipace.datastructures.api.Clique

CliqueFactory - Class in maltcms.datastructures.cluster

CliqueFactory() - Constructor for class maltcms.datastructures.cluster.CliqueFactory

CliqueFinder<T extends Peak> - Class in maltcms.experimental.bipace.peakCliqueAlignment

CliqueFinder() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

CliqueStatistics<T extends Peak> - Class in maltcms.experimental.bipace.datastructures.api

CliqueStatistics() - Constructor for class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

CliqueTable - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

CliqueTable allows for easy retrieval of common clique information.

CliqueTable(TupleND<IFileFragment>, List<Clique>) - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.CliqueTable

CliqueTable<T extends Peak> - Class in maltcms.experimental.bipace.peakCliqueAlignment

CliqueTable allows for easy retrieval of common clique information.

CliqueTable(TupleND<IFileFragment>, List<Clique<T>>) - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.CliqueTable

clone() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

clone() - Method in class smueller.alignment.AlignedPairVector

clone() - Method in class smueller.alignment.OptimalAlignmentVector

cloneAl() - Method in class smueller.alignment.Alignment

ClusteringAlgorithm - Class in maltcms.commands.fragments.cluster

Abstract base class for clustering algorithms based on similarity or distance matrices.

ClusteringAlgorithm() - Constructor for class maltcms.commands.fragments.cluster.ClusteringAlgorithm

coefficients - Static variable in class maltcms.commands.filters.array.SavitzkyGolayFilter

ColorRampReader - Class in maltcms.io.csv

Reads in custom color ramps.

ColorRampReader() - Constructor for class maltcms.io.csv.ColorRampReader

columns() - Method in class maltcms.datastructures.array.DenseArray

columns() - Method in interface maltcms.datastructures.array.IArrayD2Byte

columns() - Method in interface maltcms.datastructures.array.IArrayD2Double

columns() - Method in class maltcms.datastructures.array.PartitionedArray

columns() - Method in class maltcms.datastructures.array.SparseArray

columns() - Method in class maltcms.datastructures.array.TiledArray

ColumnWiseComparison - Class in net.sf.maltcms.evaluation.spi.alignment

ColumnWiseComparison() - Constructor for class net.sf.maltcms.evaluation.spi.alignment.ColumnWiseComparison

combine(ArrayDouble.D1, ArrayDouble.D1, boolean) - Static method in class maltcms.tools.ArrayTools

combineBiDiBestHits(TupleND<IFileFragment>, HashMap<String, List<T>>, List<List<T>>, int, HashMap<T, Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

CombinedDomainXYChart - Class in maltcms.ui.charts

Combines Different plots (favorably XYPlots) to share a common domain, such that they are vertically stacked (default).

CombinedDomainXYChart(String, String, boolean, List<XYPlot>) - Constructor for class maltcms.ui.charts.CombinedDomainXYChart

COMMENTS - Variable in class maltcms.db.ui.MetaboliteViewModel

compare(Peak, Peak) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakComparator

compare(Peak, Peak) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakFileFragmentComparator

compare(Point, Point) - Method in class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking.PointComparator

compare(PeakArea2D, PeakArea2D) - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing.PeakAreaComparator

compare(Peak2D, Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing.PeakComparator

compare(IFragment, IFragment) - Method in class maltcms.datastructures.ms.Experiment1D

compare(Rank<? extends T>, Rank<? extends T>) - Method in class maltcms.datastructures.rank.Rank.ResponseComparator

compare(Rank<Ridge>, Rank<Ridge>) - Method in class maltcms.datastructures.rank.RankComparator

compare(Peak, Peak) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.PeakComparator

compare(Peak, Peak) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.PeakFileFragmentComparator

compare(AlignmentColumn, AlignmentColumn) - Method in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

compare(String, String) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.StringListByDoubleComparator

compareCliques(Clique<T>, Clique<T>) - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

compareDraw(T, T) - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

compareRanks(String, Rank<? extends T>) - Method in class maltcms.datastructures.rank.Rank

compareTo(Object) - Method in class maltcms.datastructures.ms.Experiment1D

compareTo(IAnchor) - Method in class maltcms.datastructures.ms.Metabolite

compareTo(IAnchor) - Method in class maltcms.datastructures.ms.RetentionInfo

compareTo(Rank<? extends T>) - Method in class maltcms.datastructures.rank.Rank

compareTo(Ridge) - Method in class maltcms.datastructures.ridge.Ridge

compareTo(Object) - Method in class maltcms.db.predicates.metabolite.DBMatch

compareTo(Category) - Method in class net.sf.maltcms.evaluation.api.Category

compareTo(Category) - Method in class net.sf.maltcms.evaluation.api.classification.Category

compareTo(EntityGroup) - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

compareTo(EntityGroup) - Method in class net.sf.maltcms.evaluation.api.EntityGroup

compareTo(EntityGroupClassificationResult) - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

compareTo(EntityGroupClassificationResult) - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

CompleteLinkageAlgorithm - Class in maltcms.commands.fragments.cluster

Work in progress.

CompleteLinkageAlgorithm() - Constructor for class maltcms.commands.fragments.cluster.CompleteLinkageAlgorithm

componentHidden(ComponentEvent) - Method in class maltcms.db.ui.MetaboliteView

componentMoved(ComponentEvent) - Method in class maltcms.db.ui.MetaboliteView

componentResized(ComponentEvent) - Method in class maltcms.db.ui.MetaboliteView

componentShown(ComponentEvent) - Method in class maltcms.db.ui.MetaboliteView

compress(List<Array>, int, int) - Static method in class maltcms.tools.ArrayTools

computeMatrix(String, String) - Method in class smueller.alignment.AffineAlignment

computeMatrix(String, String) - Method in class smueller.alignment.Alignment

computeMatrix(String, String) - Method in class smueller.alignment.OneAffineAlignment

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.andims.NetcdfDataSource

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.csv.FsaTxtDataSource

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.xml.mzData.MZDataDataSource

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.xml.mzML.MZMLDataSource

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

configurationChanged(ConfigurationEvent) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

configure(Configuration) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

configure(Configuration) - Method in class maltcms.commands.distances.dtw.MZIDynamicTimeWarp

configure(Configuration) - Method in class maltcms.commands.distances.dtw.TICDynamicTimeWarp

configure(Configuration) - Method in class maltcms.commands.distances.dtwng.DTW

configure(Configuration) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

configure(Configuration) - Method in class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation

configure(Configuration) - Method in class maltcms.commands.distances.DtwRecurrence

configure(Configuration) - Method in class maltcms.commands.distances.PairwiseFeatureSimilarity

configure(Configuration) - Method in class maltcms.commands.distances.PartitionCalculator

configure(Configuration) - Method in class maltcms.commands.filters.AElementFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.AArrayFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.AdditionFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.AddRandomNoise

configure(Configuration) - Method in class maltcms.commands.filters.array.BottomHatFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.MeanStdDevNormalizationFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.MedianBaselineFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.MinMaxNormalizationFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.MovingAverageFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.MovingMedianFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.MultiplicationFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.NormalizationFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.SavitzkyGolayFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.TopHatFilter

configure(Configuration) - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

configure(Configuration) - Method in class maltcms.commands.fragments.alignment.CenterStarAlignment

configure(Configuration) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

configure(Configuration) - Method in class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment

configure(Configuration) - Method in class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment

configure(Configuration) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

configure(Configuration) - Method in class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator

configure(Configuration) - Method in class maltcms.commands.fragments.io.ANDIChromImporter

configure(Configuration) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

configure(Configuration) - Method in class maltcms.commands.fragments.io.TICPeakListImporter

configure(Configuration) - Method in class maltcms.commands.fragments.io.VariableDataExporter

configure(Configuration) - Method in class maltcms.commands.fragments.peakfinding.EICPeakFinder

configure(Configuration) - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

configure(Configuration) - Method in class maltcms.commands.fragments.preprocessing.DenseArrayProducer

configure(Configuration) - Method in class maltcms.commands.fragments.preprocessing.MassFilter

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.EICHeatmapCoplot

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.MZIDistributionVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments.visualization.TICHeatmapCoplot

configure(Configuration) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

configure(Configuration) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

configure(Configuration) - Method in class maltcms.commands.fragments.warp.PathWarp

configure(Configuration) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.CwtRunnable

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakIdentification

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakIntegration

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing

configure(Configuration) - Method in class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarProducer

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarVis

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.ModulationExtractor

configure(Configuration) - Method in class maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator

Deprecated.

configure(Configuration) - Method in class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments2d.visualization.GradientVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.DTW2DPeakAreaVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.ScanlineFilterTicWarp

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.ScanlineMaxMSWarp

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.ScanlineMeanMSWarp

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.ScanlineTicWarp

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

configure(Configuration) - Method in class maltcms.commands.fragments2d.warp.visualization.Ident2DTWVisualizer

configure(Configuration) - Method in class maltcms.commands.scanners.ArrayStatsScanner

configure(Configuration) - Method in class maltcms.datastructures.caches.AScanLineCache

configure(Configuration) - Method in class maltcms.datastructures.caches.CachedScanLineList

configure(Configuration) - Method in class maltcms.datastructures.caches.ScanLineCache

configure(Configuration) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

configure(Configuration) - Method in class maltcms.datastructures.caches.SparseScanLineCache

configure(Configuration) - Method in class maltcms.datastructures.feature.FeatureVectorList

configure(Configuration) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

configure(Configuration) - Method in class maltcms.datastructures.fragments.PairwiseDistances

configure(Configuration) - Method in class maltcms.datastructures.ms.Chromatogram1D

configure(Configuration) - Method in class maltcms.datastructures.ms.Chromatogram2D

configure(Configuration) - Method in class maltcms.datastructures.ms.ChromatogramFactory

configure(Configuration) - Method in class maltcms.datastructures.ms.Experiment1D

configure(Configuration) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

configure(Configuration) - Method in class maltcms.io.andims.NetcdfDataSource

configure(Configuration) - Method in class maltcms.io.csv.FsaTxtDataSource

configure(Configuration) - Method in class maltcms.io.xml.mzData.MZDataDataSource

configure(Configuration) - Method in class maltcms.io.xml.mzML.MZMLDataSource

configure(Configuration) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

configure(Configuration) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

configure(Configuration) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

configure(Configuration) - Method in class maltcms.math.functions.DtwPairwiseSimilarity

configure(Configuration) - Method in class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity

configure(File) - Method in class maltcms.mpaxs.MaltcmsConfigurableRunnable

configure(File) - Method in class maltcms.mpaxs.TestConfigurableCallable

configure(Configuration) - Method in class maltcms.tools.PathTools

configure(Configuration) - Method in class maltcms.ui.charts.AChart

configure(Configuration) - Method in class maltcms.ui.charts.EPlotRunner

configure(Configuration) - Method in class maltcms.ui.charts.GradientPaintScale

configure(Configuration) - Method in class maltcms.ui.charts.PlotRunner

configure(Configuration) - Method in class maltcms.ui.charts.XYChart

configure(Configuration) - Method in class smueller.SymbolicRepresentationAlignment

ConstraintFactory - Class in maltcms.datastructures.constraint

Factory for pairwise DTW alignment layout constraints.

ConstraintFactory() - Constructor for class maltcms.datastructures.constraint.ConstraintFactory

contains(Object) - Method in class maltcms.datastructures.peak.FiFoQueue

contains(Object) - Method in class maltcms.datastructures.quadTree.QuadTree

contains(Point2D) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

containsAll(Collection<?>) - Method in class maltcms.datastructures.peak.FiFoQueue

containsKey(Object) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

containsValue(Object) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

contentsChanged(ListDataEvent) - Method in class maltcms.ui.wizard.AnchorDefinitionPane

ContinuityArgmaxNodeBuilder - Class in maltcms.commands.distances.dtwng

ContinuityArgmaxNodeBuilder(int) - Constructor for class maltcms.commands.distances.dtwng.ContinuityArgmaxNodeBuilder

ContinuousWaveletTransform - Class in maltcms.commands.filters.array.wavelet

Implementation of ContinuousWaveletTransform.

ContinuousWaveletTransform(IWavelet) - Constructor for class maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform

convert(IFileFragment, Variable, IVariableFragment) - Method in class maltcms.io.andims.NetcdfDataSource

convertArrays(List<Array>) - Static method in class maltcms.tools.ArrayTools

convertArraysIntD1(List<Array>) - Static method in class maltcms.tools.ArrayTools

convertScan(Array, Array) - Static method in class maltcms.tools.ArrayTools

convertToScanIndexMap(MappedPointsType) - Method in class maltcms.datastructures.alignment.AlignmentFactory

convertToScans(double) - Method in class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder

convolve(double[], double[]) - Static method in class maltcms.commands.filters.array.SavitzkyGolayFilter

Boundaries are padded internally according to n with values d[0] and d[d.length-1].

copy() - Method in class maltcms.experimental.bipace.api.PeakSimilarityCalculator

copy() - Method in class maltcms.experimental.bipace.spi.Peak1DSimilarityCalculator

copy() - Method in class maltcms.experimental.bipace.spi.Peak2DSimilarityCalculator

copyEics(List<Array>, Integer[]) - Static method in class maltcms.tools.MaltcmsTools

copyLayout(PartitionedArray) - Static method in class maltcms.datastructures.array.PartitionedArray

copyReference(IFileFragment, IWorkflow) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

copyReference(IFileFragment, IFileFragment, IWorkflow) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

copyReference(IFileFragment, IWorkflow) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

countAlChars() - Method in class smueller.alignment.OptimalAlignmentVector

countChar(String, char) - Static method in class smueller.tools.ArrayTools

create(TupleND<IFileFragment>, Map<String, List<Peak>>) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.WorkerFactory

create() - Method in class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.ApplicationContextWorkerFactory

create() - Method in class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.AWorkerFactory

create() - Method in class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.MziDtwWorkerFactory

create() - Method in class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.TicDtwWorkerFactory

create(Array) - Method in class maltcms.datastructures.array.ArrayFactory

Wraps an Array within a DenseArray.

create(int, int, AnchorPairSet, int, double, double, boolean) - Method in class maltcms.datastructures.array.ArrayFactory

Creates a PartitionedArray if number of passed in anchors is greater than 2.

create(int, int, double) - Method in class maltcms.datastructures.array.ArrayFactory

Creates a DenseArray with given number of rows, columns and default_value as initial value of elements.

create(int, int, double, Area) - Method in class maltcms.datastructures.array.ArrayFactory

Create an optimized array storing only those elements contained within the area bounds.

create(int, int, AnchorPairSet, int, double, double, boolean) - Static method in class maltcms.datastructures.array.PartitionedArray

create(int, int, double, Area) - Static method in class maltcms.datastructures.array.PartitionedArray

create(Array, Array, double) - Static method in class maltcms.datastructures.array.Sparse

create(Array, Array, int, int, int, double) - Static method in class maltcms.datastructures.array.Sparse

create(List<Array>, List<Array>, int, int, int, double) - Static method in class maltcms.tools.SparseTools

Deprecated.

create() - Method in class maltcms.ui.charts.AChart

create() - Method in class maltcms.ui.charts.AlignmentMapChart

create() - Method in class maltcms.ui.charts.BHeatMapChart

create() - Method in class maltcms.ui.charts.CombinedDomainXYChart

create() - Method in class maltcms.ui.charts.HeatMapChart

create() - Method in class maltcms.ui.charts.MassSpectrumPlot

create() - Method in class maltcms.ui.charts.SpiderWebChart

create() - Method in class maltcms.ui.charts.XYChart

create() - Method in class maltcms.ui.charts.XYZChart

create(ObjectContainer, MetaboliteBrowser) - Static method in class net.sf.maltcms.apps.MetaboliteBrowser

create2DImage(String, List<Array>, int, double, double, int[][], Class<T>) - Static method in class maltcms.tools.ImageTools

Creates an image of an 2D chromatogramm.

create2DRidgeCostDS(int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

create2DRidgeNeighborhoodDS(int, QuadTree<Ridge>, int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createAdaptiveColorHeatmap(ArrayDouble.D2) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createAdminType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of AdminType

createAlignment() - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of Alignment

createAlignments(String, String) - Method in class smueller.alignment.Alignment

createAnnotation(AnnotationType) - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of JAXBElement<AnnotationType>}

createAnnotations(AnnotationsType) - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of JAXBElement<AnnotationsType>}

createAnnotationsType() - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of AnnotationsType

createAnnotationType() - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of AnnotationType

createApexTicBoxAndWhisker() - Method in class maltcms.datastructures.peak.Clique

createAsList(List<Array>, List<Array>, int, int, int, double) - Static method in class maltcms.tools.SparseTools

Deprecated.

createAttribute(AttributeType) - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of JAXBElement<AttributeType>}

createAttributeType() - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of AttributeType

createBandConstraint(int, int, int, int, double) - Method in class maltcms.datastructures.constraint.ConstraintFactory

createBinnedMSFeatureVectorList(IFileFragment, int, int, boolean) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

createBinnedMSFeatureVectorList(IFileFragment, boolean) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

createCategoryDataset(String[], String[], double[][]) - Static method in class maltcms.ui.charts.SpiderWebChart

createChart(String, String, String, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>) - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Creates a AChart.

createChart(String, String, String, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>) - Method in interface maltcms.commands.fragments2d.warp.visualization.IVisualization

Creates a AChart.

createChromatogram1D(IFileFragment) - Method in class maltcms.datastructures.ms.ChromatogramFactory

createChromatogram2D(IFileFragment) - Method in class maltcms.datastructures.ms.ChromatogramFactory

createColorHeatmap(ArrayDouble.D2) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createColorRampImage(double[], int, Color...) - Static method in class maltcms.tools.ImageTools

createCombinedArray(List<Sparse>) - Static method in class maltcms.tools.ArrayTools

Returns a Tuple2D holding an ArrayInt.D1 as scan indices to the arrays held in the Tuple2D, mass values and intensity values.

createCompatibleImage(int, int, int) - Static method in class maltcms.tools.ImageTools

createConcatenatedFile(String, String[], String[], HashSet<Integer>, HashMap<String, HashMap<Integer, Integer>>) - Static method in class net.sf.maltcms.apps.JoinScans

createCopiedLayout(IArrayD2Double) - Method in class maltcms.datastructures.array.ArrayFactory

Creates a copied layout.

createCostHistogramDS(int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createCvLookupType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of CvLookupType

createCvParamType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of CvParamType

createDatabase(String, boolean) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

createDataProcessingType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of DataProcessingType

createDataProcessingTypeSoftware() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of DataProcessingType.Software

createDB(boolean, String[]) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

createDenseArray(Array, Array, Tuple2D<Array, Array>, double, double, int, double, double) - Static method in class maltcms.tools.ArrayTools

Create binned arrays from source mass_values and intensity_values arrays.

createDescriptionType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of DescriptionType

createExperiment(IFileFragment) - Static method in class maltcms.datastructures.ms.ExperimentFactory

Create an instance of Experiment1D.

createExperiment1D(IFileFragment) - Static method in class maltcms.datastructures.ms.ExperimentFactory

Create an instance of IExperiment1D and initialize with IFileFragment.

createExperiment2D(IFileFragment) - Static method in class maltcms.datastructures.ms.ExperimentFactory

Create an instance of IExperiment2D and initialize with IFileFragment.

createFeatureMap() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap

createFeatureMapDataProcessing() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.DataProcessing

createFeatureMapDataProcessingProcessingAction() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.DataProcessing.ProcessingAction

createFeatureMapDataProcessingSoftware() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.DataProcessing.Software

createFeatureMapDataProcessingUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.DataProcessing.UserParam

createFeatureMapFeatureList() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.FeatureList

createFeatureMapIdentificationRun() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.IdentificationRun

createFeatureMapIdentificationRunProteinIdentification() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.IdentificationRun.ProteinIdentification

createFeatureMapIdentificationRunProteinIdentificationProteinHit() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

createFeatureMapIdentificationRunSearchParameters() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.IdentificationRun.SearchParameters

createFeatureMapIdentificationRunSearchParametersFixedModification() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.IdentificationRun.SearchParameters.FixedModification

createFeatureMapIdentificationRunSearchParametersVariableModification() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.IdentificationRun.SearchParameters.VariableModification

createFeatureMapUnassignedPeptideIdentification() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.UnassignedPeptideIdentification

createFeatureMapUnassignedPeptideIdentificationPeptideHit() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureMap.UnassignedPeptideIdentification.PeptideHit

createFeatureType() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType

createFeatureTypeConvexhull() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Convexhull

createFeatureTypeConvexhullHullpoint() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Convexhull.Hullpoint

createFeatureTypeConvexhullHullpointHposition() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Convexhull.Hullpoint.Hposition

createFeatureTypeModel() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Model

createFeatureTypeModelParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Model.Param

createFeatureTypePeptideIdentification() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.PeptideIdentification

createFeatureTypePeptideIdentificationPeptideHit() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.PeptideIdentification.PeptideHit

createFeatureTypePosition() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Position

createFeatureTypeQuality() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Quality

createFeatureTypeSubordinate() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of FeatureType.Subordinate

createFeatureVector(Array, String) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

createFeatureVectorList(List<Array>) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

createFeatureVectorList(List<Array>, String) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

createFlattenedArrays(IFileFragment, List<Array>, List<Array>) - Static method in class maltcms.tools.MaltcmsTools

CreateHorizontalTicVector - Class in maltcms.commands.fragments2d.warp

Creates all reference-query horizontal tic scanlines vectors.

CreateHorizontalTicVector() - Constructor for class maltcms.commands.fragments2d.warp.CreateHorizontalTicVector

createImage(List<Array>, List<Array>, List<Point>, List<Point>) - Method in class maltcms.commands.fragments2d.testing.Visualization2D

createImage(List<Array>, List<Array>, Array, Array) - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Will create a BufferedImage from the given scanlines and a warp path.

createImage(List<Array>, List<Array>, Array, Array) - Method in class maltcms.commands.fragments2d.warp.visualization.Ident2DTWVisualizer

Will create a BufferedImage from the given scanlines and a warp path.

createImage(List<Array>, List<Array>, Array, Array) - Method in interface maltcms.commands.fragments2d.warp.visualization.IVisualization

Will create a BufferedImage from the given scanlines and a warp path.

createInstrumentDescriptionType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of InstrumentDescriptionType

createInstrumentDescriptionTypeAnalyzerList() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of InstrumentDescriptionType.AnalyzerList

createIntegerArray(Array) - Static method in class maltcms.tools.ArrayTools2

Creates an ArrayInt out of an other array.

createIntegerArray(Array, List<Integer>) - Static method in class maltcms.tools.ArrayTools2

Creates an ArrayInt out of an other array.

createIntegerArray(Vector<Integer>) - Static method in class maltcms.tools.ArrayTools2

Creates an ArrayInt from a given Vector.

createIntegratedValueArray(IFileFragment, String, List<Array>) - Static method in class maltcms.tools.MaltcmsTools

createIntensitiesArray(IFileFragment, Array) - Static method in class maltcms.tools.MaltcmsTools

createLayoutImage(IArrayD2Double) - Method in class maltcms.datastructures.array.ArrayFactory

createLayoutImage(DenseArray, Color, Color) - Static method in class maltcms.datastructures.array.DenseArray

createLayoutImage(PartitionedArray, Color, Color) - Static method in class maltcms.datastructures.array.PartitionedArray

createLookupTable(BufferedImage, float, int) - Static method in class maltcms.tools.ImageTools

createMaltcmsAnnotation() - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of MaltcmsAnnotation

createMapImage(List<Tuple2DI>, int, int, int) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

createMappedPoints(MappedPointsType) - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of JAXBElement<MappedPointsType>}

createMappedPointsType() - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of MappedPointsType

createMetabolite() - Method in class maltcms.db.MSPFormatMetaboliteParser

createMinMaxMassValueArrays(IFileFragment, List<Array>) - Static method in class maltcms.tools.MaltcmsTools

createModifiedLookupImage(Color[], double[], double, double, int, float) - Static method in class maltcms.tools.ImageTools

createMSFeatureVectorList(IFileFragment) - Method in class maltcms.datastructures.feature.FeatureVectorFactory

createMzData() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of MzData

createMzDataDescription() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of MzData.Description

createMzDataSpectrumList() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of MzData.SpectrumList

createMzDataSpectrumListSpectrum() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of MzData.SpectrumList.Spectrum

createNeighborhoodHistogramDS(int, int, QuadTree<Ridge>, int, Ridge...) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

createNewAlignment(String, boolean) - Method in class maltcms.datastructures.alignment.AlignmentFactory

createNewClique(T, T, HashMap<T, Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

createNewMaltcmsAnnotationType(URI) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

createNewScanlines(List<Array>, List<Array>, List<Point>, boolean, boolean) - Method in class maltcms.commands.fragments2d.testing.Visualization2D

createPAIm(BufferedImage) - Method in class maltcms.ui.TabbedPanel

createParamType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of ParamType

createPath(Array, Array) - Static method in class maltcms.tools.ArrayTools2

Creates a warp map.

createPeak1DEicRaw(File, int, int, int, double, double) - Static method in class maltcms.datastructures.peak.PeakFactory

createPeak1DEicRaw(IFileFragment, int, int, int, double, double) - Static method in class maltcms.datastructures.peak.PeakFactory

createPeak1DTic(File, int, int, int) - Static method in class maltcms.datastructures.peak.PeakFactory

createPeak1DTic(IFileFragment, int, int, int) - Static method in class maltcms.datastructures.peak.PeakFactory

createPeakCandidatesArray(Array, ArrayList<Integer>) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

createPeakClique() - Static method in class maltcms.datastructures.cluster.CliqueFactory

createPeakListBinaryType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of PeakListBinaryType

createPeakListBinaryTypeData() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of PeakListBinaryType.Data

createPersonType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of PersonType

createPoint(PointType) - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of JAXBElement<PointType>}

createPointMap(PointMapType) - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of JAXBElement<PointMapType>}

createPointMapType() - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of PointMapType

createPointType() - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of PointType

createPointTypeDimension() - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of PointType.Dimension

createPrecursorType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of PrecursorType

createPrintWriter(String, String, List<String>, WorkflowSlot) - Method in class maltcms.io.csv.CSVWriter

createProfileChromatogram1D(IFileFragment) - Method in class maltcms.datastructures.ms.ChromatogramFactory

createReducedFile(String, String, Set<Integer>, HashMap<Integer, Integer>) - Static method in class net.sf.maltcms.apps.JoinScans

createResource(ResourceType) - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of JAXBElement<ResourceType>}

createResource(ResourceType) - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of JAXBElement<ResourceType>}

createResourceType() - Method in class maltcms.io.xml.bindings.alignment.ObjectFactory

Create an instance of ResourceType

createResourceType() - Method in class maltcms.io.xml.bindings.annotation.ObjectFactory

Create an instance of ResourceType

createResultsArray() - Static method in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

createRTBoxAndWhisker() - Method in class maltcms.datastructures.peak.Clique

createSampleTable(int) - Static method in class maltcms.tools.ImageTools

createSharedLayout(IArrayD2Double) - Method in class maltcms.datastructures.array.ArrayFactory

Creating a shared layout is recommended, if you want to use a layout for multiple arrays.

createSmoothPath(List<Tuple2DI>) - Method in class maltcms.tools.PathTools

Deprecated.

createSoftwareType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SoftwareType

createSourceFileType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SourceFileType

createSparse(IVariableFragment, IVariableFragment, int, int, int, double) - Static method in class maltcms.tools.MaltcmsTools

createSparseArray(int, int) - Method in class maltcms.datastructures.array.ArrayFactory

Create a two-dimensional array, which is backed by some sparse implementation (rcs or hashing).

createSparseIndexArray(ArrayDouble.D1, ArrayDouble.D1, int, int, int, double) - Static method in class maltcms.tools.ArrayTools

createSpectrumDescType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumDescType

createSpectrumDescTypePrecursorList() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumDescType.PrecursorList

createSpectrumSettingsType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumSettingsType

createSpectrumSettingsTypeAcqSpecification() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumSettingsType.AcqSpecification

createSpectrumSettingsTypeAcqSpecificationAcquisition() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumSettingsType.AcqSpecification.Acquisition

createSpectrumSettingsTypeSpectrumInstrument() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumSettingsType.SpectrumInstrument

createSpectrumType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SpectrumType

createSupDataBinaryType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SupDataBinaryType

createSupDataType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SupDataType

createSupDescType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of SupDescType

createSuperimposedImage(List<Tuple2DI>, Array, Array, int) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.distances.dtw.MZIDynamicTimeWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.distances.dtw.TICDynamicTimeWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.ScanlineFilterTicWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.ScanlineHorizontalTicWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.ScanlineMaxMSWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.ScanlineMeanMSWarp

createTuple(Tuple2D<IFileFragment, IFileFragment>) - Method in class maltcms.commands.fragments2d.warp.ScanlineTicWarp

createUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create an instance of UserParam

createUserParamType() - Method in class maltcms.io.xml.mzData.ObjectFactory

Create an instance of UserParamType

createWorkflow(File, List<IFragmentCommand>, List<File>) - Method in class maltcms.test.AFragmentCommandTest

createWorkflow(File, List<IFragmentCommand>, List<File>) - Static method in class net.sf.maltcms.tutorials.MyWorkflow

Creator - Class in net.sf.maltcms.evaluation.spi.xcalibur

Creator(String, String) - Constructor for class net.sf.maltcms.evaluation.spi.xcalibur.Creator

CSVAnchorReader - Class in maltcms.commands.fragments.io

Class reading retention indices/anchors/identified compounds from files with specialized tab-separated structure.

CSVAnchorReader() - Constructor for class maltcms.commands.fragments.io.CSVAnchorReader

CSVReader - Class in maltcms.io.csv

Configurable Reader for CSV-like files.

CSVReader() - Constructor for class maltcms.io.csv.CSVReader

CSVWriter - Class in maltcms.io.csv

Provides various methods to write arrays and other data to csv files.

CSVWriter() - Constructor for class maltcms.io.csv.CSVWriter

current() - Method in class maltcms.datastructures.caches.RingBuffer

CvLookupType - Class in maltcms.io.xml.mzData

Information about an ontology/CV source and a short 'lookup' tag to refer to.

CvLookupType() - Constructor for class maltcms.io.xml.mzData.CvLookupType

CvParamType - Class in maltcms.io.xml.mzData

Parameters from a controlled vocbulary.

CvParamType() - Constructor for class maltcms.io.xml.mzData.CvParamType

CwtChartFactory - Class in maltcms.commands.fragments2d.peakfinding

CwtChartFactory() - Constructor for class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

CwtEicPeakFinder - Class in maltcms.commands.fragments.peakfinding

CwtEicPeakFinder() - Constructor for class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder

CwtEicPeakFinderCallable - Class in maltcms.commands.fragments.peakfinding.cwtEicPeakFinder

CwtEicPeakFinderCallable() - Constructor for class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtEicPeakFinderCallable

CwtPeakFinder - Class in maltcms.commands.fragments2d.peakfinding

CwtPeakFinder() - Constructor for class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

CwtRunnable - Class in maltcms.commands.fragments2d.peakfinding

CwtRunnable() - Constructor for class maltcms.commands.fragments2d.peakfinding.CwtRunnable

CwtTicPeakFinder - Class in maltcms.commands.fragments.peakfinding

CwtTicPeakFinder() - Constructor for class maltcms.commands.fragments.peakfinding.CwtTicPeakFinder

CwtTicPeakFinderCallable - Class in maltcms.commands.fragments.peakfinding.cwtEicPeakFinder

CwtTicPeakFinderCallable() - Constructor for class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtTicPeakFinderCallable

D

d(int, int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

Data2DNormalizer - Class in maltcms.commands.fragments2d.preprocessing

Data2DNormalizer() - Constructor for class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer

DataProcessingType - Class in maltcms.io.xml.mzData

Description of the software, and the way in which it was used to generate the peak list.

DataProcessingType() - Constructor for class maltcms.io.xml.mzData.DataProcessingType

DataProcessingType.Software - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

DataProcessingType.Software() - Constructor for class maltcms.io.xml.mzData.DataProcessingType.Software

DATE - Variable in class maltcms.db.ui.MetaboliteViewModel

DB4oServer - Class in maltcms.db.connection

DB4oServer(String, String) - Constructor for class maltcms.db.connection.DB4oServer

DBMatch - Class in maltcms.db.predicates.metabolite

DBMatch() - Constructor for class maltcms.db.predicates.metabolite.DBMatch

decorate(IFileFragment, IArrayD2Double) - Method in class maltcms.tools.PathTools

Default2DTWVisualizer - Class in maltcms.commands.fragments2d.warp.visualization

Default visualizer for a 2d time warp.

Default2DTWVisualizer() - Constructor for class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Default2DVarLoader - Class in maltcms.commands.fragments2d.preprocessing

This command should be the first in all 2d pipelines.

Default2DVarLoader() - Constructor for class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader

DefaultBinnedMSFeatureVector - Class in maltcms.datastructures.feature

This feature vector retrieves mass and intensity values for this ms from directly referenced (possibly cached) lists.

DefaultBinnedMSFeatureVector(IFileFragment, int, Tuple2D<List<Array>, List<Array>>) - Constructor for class maltcms.datastructures.feature.DefaultBinnedMSFeatureVector

DefaultFeatureVector - Class in maltcms.datastructures.feature

DefaultFeatureVector() - Constructor for class maltcms.datastructures.feature.DefaultFeatureVector

DefaultPairSet<T extends IAnchor> - Class in maltcms.datastructures.alignment

Implementation of a pairset for anything implementing DefaultPairSet.

DefaultPairSet(List<T>, List<T>) - Constructor for class maltcms.datastructures.alignment.DefaultPairSet

DefaultTaskResult - Class in net.sf.maltcms.evaluation.spi.tasks.maltcms

Created by IntelliJ IDEA.

DefaultTaskResult() - Constructor for class net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult

DefaultVarLoader - Class in maltcms.commands.fragments.preprocessing

Load variables defined by the option default.variables.

DefaultVarLoader() - Constructor for class maltcms.commands.fragments.preprocessing.DefaultVarLoader

DefaultVarLoaderWorker - Class in maltcms.commands.fragments.preprocessing.defaultVarLoader

DefaultVarLoaderWorker() - Constructor for class maltcms.commands.fragments.preprocessing.defaultVarLoader.DefaultVarLoaderWorker

DeltaMasses - Class in maltcms.commands.fragments2d.visualization

Computes relative deltamasses.

DeltaMasses() - Constructor for class maltcms.commands.fragments2d.visualization.DeltaMasses

DenseArray - Class in maltcms.datastructures.array

A simple dense array encapsulation class.

DenseArray(Array) - Constructor for class maltcms.datastructures.array.DenseArray

Copy a and save it in internal array

DenseArray(int, int, double) - Constructor for class maltcms.datastructures.array.DenseArray

Create new Array with specified number of rows and columns.

DenseArrayProducer - Class in maltcms.commands.fragments.preprocessing

Creates bins of fixed size (currently 1) from a given set of spectra with masses and intensities.

DenseArrayProducer() - Constructor for class maltcms.commands.fragments.preprocessing.DenseArrayProducer

DenseArrayProducerWorker - Class in maltcms.commands.fragments.preprocessing.denseArrayProducer

DenseArrayProducerWorker() - Constructor for class maltcms.commands.fragments.preprocessing.denseArrayProducer.DenseArrayProducerWorker

DescriptionType - Class in maltcms.io.xml.mzData

Extension of 'paramType' with an added free-text comment attribute.

DescriptionType() - Constructor for class maltcms.io.xml.mzData.DescriptionType

diff(Array, Array) - Static method in class maltcms.tools.ArrayTools

Calculates A-B elementwise.

digestCommandLine(String[]) - Method in interface maltcms.db.predicates.metabolite.IAggregatePredicateFactory

RetentionIndex=[1500,2000] => NumRangePredicate on method getRetentionIndex Name=BLABLA => StringMatchPredicate on method getName Name=BLABLA< => StringContainsPredicate on method getName, BLABLA should be a substring

digestCommandLine(String[]) - Method in class maltcms.db.predicates.metabolite.MAggregatePredicateFactory

DigestionEnzyme - Enum in maltcms.io.xml.bindings.openms.featurexml

Java class for DigestionEnzyme.

DimensionReduce - Class in smueller.tools

DimensionReduce() - Constructor for class smueller.tools.DimensionReduce

DistanceMatrix - Class in smueller.datastructure

DistanceMatrix(double[]) - Constructor for class smueller.datastructure.DistanceMatrix

div(Array, Array) - Static method in class maltcms.tools.ArrayTools

Calculates A/B elementwise.

divBy60(Array) - Static method in class maltcms.tools.ArrayTools

Divides values in array by 60, convenience method for second to minute conversion.

dmat(int, int, int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

dmat(int, int, int) - Method in class maltcms.commands.fragments.cluster.CompleteLinkageAlgorithm

dmat(int, int, int) - Method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

dmat(int, int, int) - Method in class maltcms.commands.fragments.cluster.SingleLinkageAlgorithm

dmat(int, int, int) - Method in class maltcms.commands.fragments.cluster.UPGMAAlgorithm

doInBackground() - Method in class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated.

draw(Graphics2D) - Method in class maltcms.datastructures.ridge.Ridge

drawItem(Graphics2D, XYItemRendererState, Rectangle2D, PlotRenderingInfo, XYPlot, ValueAxis, ValueAxis, XYDataset, int, int, CrosshairState, int) - Method in class maltcms.ui.renderer.LineVectorRenderer

drawMatrix() - Method in class smueller.alignment.Alignment

drawPathway() - Method in class smueller.alignment.Alignment

drawSquareMatrixWithLabels(List<Integer>, List<String>, Array, double) - Static method in class maltcms.tools.ImageTools

DTW - Class in maltcms.commands.distances.dtwng

DTW() - Constructor for class maltcms.commands.distances.dtwng.DTW

DTW2DPeakAreaVisualizer - Class in maltcms.commands.fragments2d.warp

Default visualization pipeline command.

DTW2DPeakAreaVisualizer() - Constructor for class maltcms.commands.fragments2d.warp.DTW2DPeakAreaVisualizer

DTW2DTicVisualizer - Class in maltcms.commands.fragments2d.warp

Default visualization pipeline command.

DTW2DTicVisualizer() - Constructor for class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer

DTWNew - Class in net.sf.maltcms.apps

DTWNew() - Constructor for class net.sf.maltcms.apps.DTWNew

DtwPairwiseSimilarity - Class in maltcms.math.functions

DtwPairwiseSimilarity() - Constructor for class maltcms.math.functions.DtwPairwiseSimilarity

DtwRecurrence - Class in maltcms.commands.distances

Objects of this type are used to calculate the cumulative distance within the ADynamicTimeWarp Implementations.

DtwRecurrence() - Constructor for class maltcms.commands.distances.DtwRecurrence

DTWTest - Class in maltcms.commands.fragments2d.testing

DTWTest() - Constructor for class maltcms.commands.fragments2d.testing.DTWTest

DtwTimePenalizedPairwiseSimilarity - Class in maltcms.math.functions

DtwTimePenalizedPairwiseSimilarity() - Constructor for class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity

E

EditDistance - Class in maltcms.experimental.operations

Implementation of the Edit-Distance on Strings.

EditDistance() - Constructor for class maltcms.experimental.operations.EditDistance

EICHeatmapCoplot - Class in maltcms.commands.fragments.visualization

EICHeatmapCoplot() - Constructor for class maltcms.commands.fragments.visualization.EICHeatmapCoplot

EICPeakFinder - Class in maltcms.commands.fragments.peakfinding

Work in progress.

EICPeakFinder() - Constructor for class maltcms.commands.fragments.peakfinding.EICPeakFinder

EIMSDBMetaboliteAssignment - Class in maltcms.commands.fragments.assignment

EIMSDBMetaboliteAssignment() - Constructor for class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment

element() - Method in class maltcms.datastructures.peak.FiFoQueue

ElementNotFoundException - Exception in maltcms.datastructures.quadTree

ElementNotFoundException() - Constructor for exception maltcms.datastructures.quadTree.ElementNotFoundException

EMPTY - Static variable in class net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult

Entity - Class in net.sf.maltcms.evaluation.api.classification

An entity represents a classified object.

Entity(IFeatureVector, Category, String) - Constructor for class net.sf.maltcms.evaluation.api.classification.Entity

Entity - Class in net.sf.maltcms.evaluation.api

An entity represents a classified object.

Entity(IFeatureVector, Category, String) - Constructor for class net.sf.maltcms.evaluation.api.Entity

EntityGroup - Class in net.sf.maltcms.evaluation.api.classification

A group of Entity objects which all share the same class label, meaning they are grouped by some algorithm as related entities.

EntityGroup(Entity...) - Constructor for class net.sf.maltcms.evaluation.api.classification.EntityGroup

EntityGroup - Class in net.sf.maltcms.evaluation.api

A group of Entity objects which all share the same class label, meaning they are grouped by some algorithm as related entities.

EntityGroup(Entity...) - Constructor for class net.sf.maltcms.evaluation.api.EntityGroup

EntityGroupBuilder - Class in net.sf.maltcms.evaluation.spi

EntityGroupBuilder() - Constructor for class net.sf.maltcms.evaluation.spi.EntityGroupBuilder

EntityGroupClassificationResult - Class in net.sf.maltcms.evaluation.api

EntityGroupClassificationResult(EntityGroup, EntityGroup, int, int, int, int, double) - Constructor for class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

EntityGroupClassificationResult - Class in net.sf.maltcms.evaluation.spi.classification

EntityGroupClassificationResult(EntityGroup, EntityGroup, int, int, int, int, double) - Constructor for class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

entrySet() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

EPlotRunner - Class in maltcms.ui.charts

This class is an extension of the normal PlotRunner and will generate a serialized file.

EPlotRunner(Plot, String, String, File) - Constructor for class maltcms.ui.charts.EPlotRunner

Old constructor.

EPlotRunner(JFreeChart, String, File) - Constructor for class maltcms.ui.charts.EPlotRunner

Default constructor.

equals(Object) - Method in class maltcms.datastructures.ms.Experiment1D

equals(Object) - Method in class maltcms.datastructures.peak.Clique

equals(Object) - Method in class maltcms.datastructures.peak.Peak

equals(Object) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

equals(Object) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

equals(Object) - Method in class net.sf.maltcms.evaluation.api.Category

equals(Object) - Method in class net.sf.maltcms.evaluation.api.classification.Category

equals(Object) - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

equals(Object) - Method in class net.sf.maltcms.evaluation.api.EntityGroup

equals(Object) - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

equals(Object) - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

eval(List<double[]>, int) - Method in class maltcms.commands.distances.dtwng.ContinuityArgmaxNodeBuilder

eval(List<double[]>, int) - Method in class maltcms.commands.distances.dtwng.IdentityNodeBuilder

eval(List<double[]>, int) - Method in class maltcms.commands.distances.dtwng.NodeBuilder

eval(int, int, IArrayD2Double, double, byte[][]) - Method in class maltcms.commands.distances.DtwRecurrence

eval(int, int, IArrayD2Double, IArrayD2Double, double) - Method in class maltcms.commands.distances.DtwRecurrence

eval(int, int, IArrayD2Double, double, byte[][]) - Method in interface maltcms.commands.distances.IRecurrence

eval(int, int, IArrayD2Double, IArrayD2Double, double) - Method in interface maltcms.commands.distances.IRecurrence

eval(double) - Method in class net.sf.maltcms.apps.MultipleAlignmentColumnEvaluation

Run evaluation on all given instances of tool results against the configured ground truth, with a maximum deviation of delta.

eval(double) - Method in class net.sf.maltcms.apps.MultipleAlignmentRowEvaluation

Run evaluation on all given instances of tool results against the configured ground truth, with a maximum deviation of delta.

Eval - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval(String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval

Eval.AggregatePeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.AggregatePeakPredicate(Eval.PeakPredicate...) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.AggregatePeakPredicate

Eval.ByCreatorNameFilenameRTPeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ByCreatorNameFilenameRTPeakPredicate(String, Chromatogram, double, double) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNameFilenameRTPeakPredicate

Eval.ByCreatorNamePeakNamePredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ByCreatorNamePeakNamePredicate(String, String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakNamePredicate

Eval.ByCreatorNamePeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ByCreatorNamePeakPredicate(String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakPredicate

Eval.ChromatogramCreatorPeakNamePeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ChromatogramCreatorPeakNamePeakPredicate(Chromatogram, String, String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakNamePeakPredicate

Eval.ChromatogramCreatorPeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ChromatogramCreatorPeakPredicate(Chromatogram, String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakPredicate

Eval.ChromatogramNamePredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ChromatogramNamePredicate(String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramNamePredicate

Eval.ChromatogramPeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ChromatogramPeakPredicate(Chromatogram) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPeakPredicate

Eval.ChromatogramPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.ChromatogramPredicate() - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPredicate

Eval.CreatorPeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.CreatorPeakPredicate(String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPeakPredicate

Eval.CreatorPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.CreatorPredicate() - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPredicate

Eval.CreatorPredicate(String) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPredicate

Eval.PeakPredicate - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.PeakPredicate() - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.PeakPredicate

Eval.StringListByDoubleComparator - Class in net.sf.maltcms.evaluation.spi.hohenheim

Eval.StringListByDoubleComparator(HashMap<String, Double>) - Constructor for class net.sf.maltcms.evaluation.spi.hohenheim.Eval.StringListByDoubleComparator

excludeSparse(Tuple2D<Array, Array>, List<Integer>) - Static method in class maltcms.tools.ArrayTools2

execChroma(PropertiesConfiguration, Container) - Method in class maltcms.ui.wizard.PipelineWizard

expand(Array, int) - Static method in class maltcms.tools.ArrayTools

Expansion, as used in Dynamic Time Warping, defined as copying the expanded element length times.

Experiment1D - Class in maltcms.datastructures.ms

Concrete implementation of an Experiment containing a 1-dimensional chromatogram.

Experiment1D() - Constructor for class maltcms.datastructures.ms.Experiment1D

Experiment1D(IFileFragment) - Constructor for class maltcms.datastructures.ms.Experiment1D

Experiment2D - Class in maltcms.datastructures.ms

Concrete Implementation containing a 2-dimensional chromatogram, e.g. from GCxGC-MS.

Experiment2D() - Constructor for class maltcms.datastructures.ms.Experiment2D

Experiment2D(IFileFragment) - Constructor for class maltcms.datastructures.ms.Experiment2D

ExperimentFactory - Class in maltcms.datastructures.ms

Factory to create Experiments.

ExperimentFactory() - Constructor for class maltcms.datastructures.ms.ExperimentFactory

ExpFilter - Class in maltcms.commands.filters.array

Applies exp(x) to all elements of an array.

ExpFilter() - Constructor for class maltcms.commands.filters.array.ExpFilter

exportBBHInformation(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, IPeakExporter, List<String>) - Static method in class maltcms.commands.fragments2d.peakfinding.bbh.BBHTools

This Method will call all methods of IPeakExporter.

exportBBHInformation(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, List<Reliability>) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Will export the information about the bidirectional best hits.

exportBBHInformation(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, List<Reliability>) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Will export the information about the bidirectional best hits.

exportBBHMultipleAlignmentRT(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, List<Reliability>) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Will export the alignment of retention times about the bidirectional best hits.

exportBBHMultipleAlignmentRT(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, List<Reliability>) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Will export the alignment of retention times about the bidirectional best hits.

exportDetailedBBHInformation(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, List<Reliability>, String) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Will export a detailed list about the bidirectional best hits.

exportDetailedBBHInformation(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, List<Reliability>, String) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Will export a detailed list about the bidirectional best hits.

exportDetailedPeakInformation(String, List<Peak2D>) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Will export some detailed peak information like unique mass integration, ...

exportDetailedPeakInformation(String, List<Peak2D>) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Will export some detailed peak information like unique mass integration, ...

exportPeakInformation(String, List<Peak2D>) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Will export some peakinformation like retentiontime, name, ...

exportPeakInformation(String, List<Peak2D>) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Will export some peakinformation like retentiontime, name, ...

exportPeakNames(List<Peak2D>, String) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Exports all identifications available for a peak.

exportPeakNames(List<Peak2D>, String) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Exports all identifications available for a peak.

exportPeakOccurrenceMap(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, String) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Will export an peak occurrence map which will allow an easy plotting by R.

exportPeakOccurrenceMap(List<List<Point>>, List<List<Peak2D>>, IBidirectionalBestHit, List<String>, String) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Will export an peak occurrence map which will allow an easy plotting by R.

exportPeaksToMSP(String, List<Peak2D>, IScanLine) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Exports all given peaks as msp compatible format

exportPeaksToMSP(String, List<Peak2D>, IScanLine) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Exports all given peaks as msp compatible format

exportXLS(Vector<String[]>, File) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

exportXLS(JTable, File) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

exportXLS(JTable) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

extract(String, File) - Static method in class maltcms.io.ZipResourceExtractor

F

factory(double...) - Static method in class maltcms.tools.ArrayTools

factory(int...) - Static method in class maltcms.tools.ArrayTools

factory(float...) - Static method in class maltcms.tools.ArrayTools

factoryScalar(Object) - Static method in class maltcms.tools.ArrayTools

This factory is usable for scalar values and primitive array instances.

FastBidirectionalBestHit - Class in maltcms.commands.fragments2d.peakfinding.bbh

Will compute a list of bidirectional best hits.

FastBidirectionalBestHit() - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

Default constructor.

FastBinnedMSFeatureVector - Class in maltcms.datastructures.feature

This feature vector keeps direct copies of mass and intensity values, as opposed to DefaultBinnedMSFeatureVector, which requests them possibly from a CachedList backed implementation.

FastBinnedMSFeatureVector(IFileFragment, int) - Constructor for class maltcms.datastructures.feature.FastBinnedMSFeatureVector

FeatureMap - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

FeatureMap.DataProcessing - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.DataProcessing() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

FeatureMap.DataProcessing.ProcessingAction - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.DataProcessing.ProcessingAction() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.ProcessingAction

FeatureMap.DataProcessing.Software - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.DataProcessing.Software() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.Software

FeatureMap.DataProcessing.UserParam - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.DataProcessing.UserParam() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.UserParam

FeatureMap.FeatureList - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.FeatureList() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.FeatureList

FeatureMap.IdentificationRun - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.IdentificationRun() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

FeatureMap.IdentificationRun.ProteinIdentification - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.IdentificationRun.ProteinIdentification() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

FeatureMap.IdentificationRun.SearchParameters - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.IdentificationRun.SearchParameters() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

FeatureMap.IdentificationRun.SearchParameters.FixedModification - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.IdentificationRun.SearchParameters.FixedModification() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.FixedModification

FeatureMap.IdentificationRun.SearchParameters.VariableModification - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.IdentificationRun.SearchParameters.VariableModification() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.VariableModification

FeatureMap.UnassignedPeptideIdentification - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.UnassignedPeptideIdentification() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

FeatureMap.UnassignedPeptideIdentification.PeptideHit - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureMap.UnassignedPeptideIdentification.PeptideHit() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

FeatureType - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for featureType complex type.

FeatureType() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType

FeatureType.Convexhull - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Convexhull() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull

FeatureType.Convexhull.Hullpoint - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Convexhull.Hullpoint() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint

FeatureType.Convexhull.Hullpoint.Hposition - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Convexhull.Hullpoint.Hposition() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint.Hposition

FeatureType.Model - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Model() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model

FeatureType.Model.Param - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Model.Param() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model.Param

FeatureType.PeptideIdentification - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.PeptideIdentification() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

FeatureType.PeptideIdentification.PeptideHit - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.PeptideIdentification.PeptideHit() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

FeatureType.Position - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Position() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Position

FeatureType.Quality - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Quality() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Quality

FeatureType.Subordinate - Class in maltcms.io.xml.bindings.openms.featurexml

Java class for anonymous complex type.

FeatureType.Subordinate() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Subordinate

FeatureVectorDtwSimilarity - Class in maltcms.commands.distances.dtwng

FeatureVectorDtwSimilarity() - Constructor for class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity

FeatureVectorFactory - Class in maltcms.datastructures.feature

Implementation of a Factory for some common FeatureVector types.

FeatureVectorList<T extends IFeatureVector> - Class in maltcms.datastructures.feature

FeatureVectorList(List<T>, List<String>) - Constructor for class maltcms.datastructures.feature.FeatureVectorList

FiFoQueue<E> - Class in maltcms.datastructures.peak

This class represents a first in first out queue.

FiFoQueue() - Constructor for class maltcms.datastructures.peak.FiFoQueue

Default constructor.

FileCopy - Class in net.sf.maltcms.apps

Copy the named Variables given on the command line from a source file to an output file in a different directory.

FileCopy() - Constructor for class net.sf.maltcms.apps.FileCopy

FileInputOutputPane - Class in maltcms.ui.wizard

FileInputOutputPane() - Constructor for class maltcms.ui.wizard.FileInputOutputPane

Creates new form FileInputOutputPane

FilePipeline - Class in net.sf.maltcms.evaluation.spi.tasks.execution

FilePipeline() - Constructor for class net.sf.maltcms.evaluation.spi.tasks.execution.FilePipeline

fill(Array, double) - Static method in class maltcms.tools.ArrayTools

Fill array a with double value d.

fillArray(Array, Double) - Static method in class maltcms.tools.ArrayTools

Fill array a with Double value d.

fillArray(Array, int) - Static method in class maltcms.tools.ArrayTools

Fill array a with int value i.

fillArray(Array, Integer) - Static method in class maltcms.tools.ArrayTools

Fill array a with Integer value i.

filter(Array, AArrayFilter) - Static method in class maltcms.tools.ArrayTools2

Filters one array with a given filter.

filter(Array, Array, boolean) - Static method in class maltcms.tools.ArrayTools2

Deprecated.

filter(Array, List<Integer>, boolean) - Static method in class maltcms.tools.ArrayTools2

.

filter(List<Array>, AArrayFilter) - Static method in class maltcms.tools.ArrayTools2

Filters a list of all array with a given filter.

filter(ArrayList<Array>, int) - Static method in class maltcms.tools.ImageTools

FilterButtonActionListener - Class in maltcms.db.ui

FilterButtonActionListener(MetaboliteViewModel, boolean, HashMap<Integer, JTextField>, MetaboliteSearchPreferences) - Constructor for class maltcms.db.ui.FilterButtonActionListener

filterExclude(Array, List<Integer>) - Static method in class maltcms.tools.ArrayTools2

Returns an new array where all listed indices are excluded.

filterExclude(List<Array>, List<Integer>) - Static method in class maltcms.tools.ArrayTools2

Excludes all indices from all arrays of a given list.

filterInclude(Array, List<Integer>) - Static method in class maltcms.tools.ArrayTools2

Returns an new array where all not listed indices are excluded.

filterInclude(List<Array>, List<Integer>) - Static method in class maltcms.tools.ArrayTools2

Returns a list of array, where each array has only th indices which are given by the second list.

filterIndices(Array, List<Integer>, double) - Static method in class maltcms.tools.ArrayTools

filterIndices(Array, List<Integer>, boolean, double) - Static method in class maltcms.tools.ArrayTools

Given an array and a list of indices within that array, removes all values at those indices and returns a new array where the respective values have been set to a definable minimum value.

findAndSetBoundary() - Method in class maltcms.datastructures.peak.PeakArea2D

findBaseline(double[]) - Method in interface maltcms.commands.fragments.peakfinding.ticPeakFinder.IBaselineEstimator

findBaseline(double[]) - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.LoessMinimaBaselineEstimator

findBaseline(double[], int, double, double, int) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

findBaseline(double[], int) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

findBest(EntityGroup, List<EntityGroup>) - Method in class net.sf.maltcms.evaluation.api.ClassificationPerformanceTest

We expect to find at least one positive assignment in a group.

findBest(EntityGroup, List<EntityGroup>) - Method in class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest

We expect to find at least one positive assignment in a group.

findBestD(int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

findBestD(int) - Method in class maltcms.commands.fragments.cluster.CompleteLinkageAlgorithm

findBestD(int) - Method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

findBestD(int) - Method in class maltcms.commands.fragments.cluster.SingleLinkageAlgorithm

findBestD(int) - Method in class maltcms.commands.fragments.cluster.UPGMAAlgorithm

findBiDiBestHits(TupleND<IFileFragment>, HashMap<String, List<Peak>>) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.BBHFinder

findBiDiBestHits(TupleND<IFileFragment>, HashMap<String, List<Peak>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder

findCenter(TupleND<IFileFragment>, List<Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

findCliques(TupleND<IFileFragment>, HashMap<String, List<T>>, List<List<T>>, HashMap<T, Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

findGlobalMinMax(TupleND<IFileFragment>, String, String, String) - Static method in class maltcms.tools.MaltcmsTools

findMaskedMasses(Array, List<Double>, double) - Static method in class maltcms.tools.MaltcmsTools

findMaxima(Array, ArrayList<Integer>) - Method in class maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask

Find maxima in array a, returning an array containing all maxima, with the same shape as a, and an array maximaDiff, which contains all differences between maxima, of size (#of maxima - 1).

findPeakAreas(IFileFragment, List<Integer>, String, Array, Array, double[]) - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

findPeakPositions(Array) - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

findPeakPositions(Array) - Method in interface maltcms.commands.fragments.peakfinding.ticPeakFinder.IPeakFinder

findPeakPositions(Array) - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.QuantileSnrPeakFinder

findPeaks(IFileFragment) - Method in class maltcms.commands.fragments2d.peakfinding.CwtRunnable

findPeaks(IFileFragment) - Method in interface maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking

findPeaks(IFileFragment) - Method in class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking

findPeaks(IFileFragment) - Method in class maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking

findPeaksNear(IFileFragment, Point, int, int) - Method in class maltcms.commands.fragments2d.peakfinding.CwtRunnable

findPeaksNear(IFileFragment, Point, int, int) - Method in interface maltcms.commands.fragments2d.peakfinding.picking.IPeakPicking

findPeaksNear(IFileFragment, Point, int, int) - Method in class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking

findPeaksNear(IFileFragment, Point, int, int) - Method in class maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking

findReference(List<List<Peak2D>>, List<List<Point>>, Collection<IFileFragment>) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakNormalization

finish(Map) - Method in class maltcms.ui.wizard.Main

finish(Map) - Method in class maltcms.ui.wizard.PipelineWizard

fireEvent(IEvent<IWorkflowResult>) - Method in class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated.

fireEvent(IEvent<Configuration>) - Method in class maltcms.ui.wizard.PipelineWizard

FirstDerivativeFilter - Class in maltcms.commands.filters.array

Calculate first derivative on array stored in a new array.

FirstDerivativeFilter() - Constructor for class maltcms.commands.filters.array.FirstDerivativeFilter

flatten() - Method in class maltcms.datastructures.array.DenseArray

flatten() - Method in interface maltcms.datastructures.array.IArrayD2Byte

Return array in row compressed storage format.

flatten() - Method in interface maltcms.datastructures.array.IArrayD2Double

Return array in row compressed storage format.

flatten() - Method in class maltcms.datastructures.array.PartitionedArray

flatten() - Method in class maltcms.datastructures.array.SparseArray

flatten() - Method in class maltcms.datastructures.array.TiledArray

flipHorizontal(RenderedImage) - Static method in class maltcms.tools.ImageTools

flipVertical(RenderedImage) - Static method in class maltcms.tools.ImageTools

FN - Static variable in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

FORMULA - Variable in class maltcms.db.ui.MetaboliteViewModel

FP - Static variable in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

fromArrays(Array, Array) - Static method in class maltcms.tools.PathTools

Constructs List of pairs of indices from array representation.

fromCRS(ArrayInt.D1, Array) - Static method in class maltcms.tools.ArrayTools

Restore List of Array objects from contiguous representation, using an index array containing the offsets for each individual array.

fromFileFragment(IFileFragment) - Static method in class maltcms.datastructures.fragments.PairwiseDistances

Static factory method which reconstructs a PairwiseDistances object from the given FileFragment.

fromFragment(IFileFragment) - Static method in class maltcms.datastructures.peak.Peak1D

fromValue(String) - Static method in enum maltcms.io.xml.bindings.openms.featurexml.DigestionEnzyme

fromValue(String) - Static method in enum maltcms.io.xml.bindings.openms.featurexml.MassType

fromValue(String) - Static method in enum maltcms.io.xml.bindings.openms.featurexml.UserParamType

FsaTxtDataSource - Class in maltcms.io.csv

Implementation of IDataSource for csv files containing variables in columns and values in rows.

FsaTxtDataSource() - Constructor for class maltcms.io.csv.FsaTxtDataSource

fullSpectrum(String, List<Array>, int, int[][], int, boolean, double) - Static method in class maltcms.tools.ImageTools

G

GaussianDifferenceSimilarity - Class in maltcms.math.functions.similarities

GaussianDifferenceSimilarity() - Constructor for class maltcms.math.functions.similarities.GaussianDifferenceSimilarity

GCGCToGCMSConverter - Class in maltcms.commands.fragments2d.preprocessing

GCGCToGCMSConverter() - Constructor for class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter

generalizeList(List<ArrayDouble.D1>) - Static method in class maltcms.tools.ArrayTools

Return a list, which is more generally typed than the input list.

generateMenuBar(MetaboliteViewModel) - Method in class net.sf.maltcms.apps.MetaboliteBrowser

generates the menu bar for selecting the shown table columns

generatePlot(String, String, Array) - Static method in class smueller.tools.GenerateTicChart

GenerateTicChart - Class in smueller.tools

GenerateTicChart() - Constructor for class smueller.tools.GenerateTicChart

get(IFileFragment) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

get(int, int) - Method in class maltcms.datastructures.array.DenseArray

get(int, int) - Method in interface maltcms.datastructures.array.IArrayD2Byte

get(int, int) - Method in interface maltcms.datastructures.array.IArrayD2Double

get(int, int) - Method in class maltcms.datastructures.array.PartitionedArray

get(int) - Method in class maltcms.datastructures.array.Sparse

get(int, int) - Method in class maltcms.datastructures.array.SparseArray

get(int, int) - Method in class maltcms.datastructures.array.TiledArray

get(IFileFragment) - Method in class maltcms.datastructures.peak.Peak2DClique

get(Point2D) - Method in class maltcms.datastructures.quadTree.QuadTree

get() - Method in class maltcms.mpaxs.MaltcmsConfigurableRunnable

get() - Method in class maltcms.mpaxs.TestConfigurableCallable

get(Object) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

getA() - Method in class smueller.alignment.AlignedPairVector

getAaAfter() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the aaAfter property.

getAaAfter() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the aaAfter property.

getAaBefore() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the aaBefore property.

getAaBefore() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the aaBefore property.

getAbsolutePath() - Method in class maltcms.datastructures.ms.Experiment1D

getAccession() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Gets the value of the accession property.

getAccession() - Method in class maltcms.io.xml.mzData.CvParamType

Gets the value of the accession property.

getAccessionNumber() - Method in class maltcms.io.xml.mzData.MzData

Gets the value of the accessionNumber property.

getAccuracy() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getAccuracy() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getAcqNumber() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification.Acquisition

Gets the value of the acqNumber property.

getAcqSpecification() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType

Gets the value of the acqSpecification property.

getAcquisition() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Gets the value of the acquisition property.

getActivation() - Method in class maltcms.io.xml.mzData.PrecursorType

Gets the value of the activation property.

getActiveChartPanel() - Method in class maltcms.ui.charts.JFreeChartViewer

getAdditional() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Gets the value of the additional property.

getAdditionalEnvironment() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITask

getAdditionalEnvironment() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

getAddress() - Method in class maltcms.io.xml.mzData.CvLookupType

Gets the value of the address property.

getAdmin() - Method in class maltcms.io.xml.mzData.MzData.Description

Gets the value of the admin property.

getAdmissabilityConstant() - Method in interface maltcms.commands.filters.array.wavelet.IWavelet

getAdmissabilityConstant() - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWavelet

getAl() - Method in class smueller.datastructure.AlignmentOutput

getAl() - Static method in class smueller.SymbolicRepresentationAlignment

getAlgorithm() - Method in interface maltcms.datastructures.warp.IWarpInput

getAlgorithm() - Method in class maltcms.datastructures.warp.MZIWarpInput

getAlgorithm() - Method in class maltcms.datastructures.warp.TICWarpInput

getAlignment() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getAlignments() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getAlignmentsFromFragment(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getAll() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

getAll() - Method in class maltcms.datastructures.peak.Peak2DClique

getAllalignments() - Method in class smueller.alignment.Alignment

getAlpha() - Method in class maltcms.ui.charts.GradientPaintScale

getAlphabet() - Static method in class smueller.tools.SymbolConvert

getAlphabetgr() - Static method in class smueller.SymbolicRepresentationAlignment

getAnalyzer() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType.AnalyzerList

Gets the value of the analyzer property.

getAnalyzerList() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Gets the value of the analyzerList property.

getAnchorNamesVariableName() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getAnchorRetentionIndexVariableName() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getAnchors() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

Retrieve paired anchors

getAnchors(IFileFragment, IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getAnchorScanIndexVariableName() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getAnchorTimesVariableName() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getAnnotation() - Method in class maltcms.io.xml.bindings.annotation.AnnotationsType

Gets the value of the annotation property.

getAnnotations(IFileFragment, Array, Array) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

getAnnotations() - Method in class maltcms.io.xml.bindings.annotation.MaltcmsAnnotation

Gets the value of the annotations property.

getAnnotationsTypeFor(MaltcmsAnnotation, String, Object) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

getArea() - Method in class maltcms.datastructures.peak.Peak2D

getArea() - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getArea() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getAreaColumn(Sheet) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getAreaIntensities() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getAreaIntensity() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getAreasFor(List<Point>, IFileFragment, IScanLine) - Method in interface maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing

getAreasFor(List<Point>, IFileFragment, IScanLine) - Method in class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing

getArray() - Method in class maltcms.datastructures.array.DenseArray

getArray() - Method in interface maltcms.datastructures.array.IArrayD2Byte

Use with caution, creates the dense array according to its bounds in memory.

getArray() - Method in interface maltcms.datastructures.array.IArrayD2Double

Use with caution, creates the dense array according to its bounds in memory.

getArray() - Method in class maltcms.datastructures.array.PartitionedArray

getArray() - Method in class maltcms.datastructures.array.SparseArray

getArray() - Method in class maltcms.datastructures.array.TiledArray

getArrayDistanceClassName() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getArrayName() - Method in class maltcms.io.xml.mzData.SupDataBinaryType

Gets the value of the arrayName property.

getArrayName() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the arrayName property.

getArrays() - Method in interface maltcms.datastructures.warp.IWarpInput

getArrays() - Method in class maltcms.datastructures.warp.MZIWarpInput

getArrays() - Method in class maltcms.datastructures.warp.TICWarpInput

getArraySimilarities() - Method in interface maltcms.math.functions.IScalarArraySimilarity

getArrayStatsMap() - Method in class maltcms.datastructures.cluster.Clique

getArrayStatsMap() - Method in interface maltcms.datastructures.cluster.IClique

getAsPairList(int[][]) - Method in class smueller.datastructure.AlignmentOutput

getAttribute(Attribute) - Method in class maltcms.datastructures.ms.Experiment1D

getAttribute(String) - Method in class maltcms.datastructures.ms.Experiment1D

getAttribute() - Method in class maltcms.io.xml.bindings.annotation.AnnotationType

Gets the value of the attribute property.

getAttributes() - Method in class maltcms.datastructures.ms.Experiment1D

getAvailableRidgeCostClasses() - Static method in class maltcms.datastructures.ridge.Ridge

getAverageCount() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getB() - Method in class smueller.alignment.AlignedPairVector

getBarDistance() - Method in class maltcms.ui.charts.MassSpectrumPlot

Getter.

getBarWidth() - Method in class maltcms.ui.charts.MassSpectrumPlot

Getter.

getBasedir() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getBaselineEstimator() - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet

getBBHs() - Method in class maltcms.datastructures.peak.Clique

getBBHs() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getBestHitForLhs(int) - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

getBestHitForRhs(int) - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

getBestHits(int, T) - Method in interface maltcms.db.IDBQuery

getBestHits(int, MSimilarityPredicate) - Method in class maltcms.db.RawMSQuery

getBestHitsForLhs() - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

getBestHitsForRhs() - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

getBeta() - Method in class maltcms.ui.charts.GradientPaintScale

getBidiBestHitList(List<List<Peak2D>>) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

Getter.

getBidiBestHitList(List<List<Peak2D>>) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit

getBidiBestHitList(List<List<Peak2D>>) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

Getter.

getBidiBestHitList(List<List<Peak2D>>) - Method in interface maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit

Getter.

getBidiBestList(int, int, List<List<Point>>) - Static method in class maltcms.commands.fragments2d.peakfinding.bbh.BBHTools

Creates a filtered BBH List.

getBidirectionalBestHits() - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

getBinnedIntensities() - Method in class maltcms.datastructures.ms.ProfileChromatogram1D

getBinnedMasses() - Method in class maltcms.datastructures.ms.ProfileChromatogram1D

getBinnedMS(IFileFragment, int) - Static method in class maltcms.tools.MaltcmsTools

getBinnedMZIs(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getBinSize() - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Getter.

getBinSize() - Method in interface maltcms.commands.fragments2d.warp.visualization.IVisualization

Getter.

getBinsSize() - Method in class maltcms.datastructures.caches.AScanLineCache

Getter.

getBinsSize() - Method in interface maltcms.datastructures.caches.IScanLine

Getter.

getBinsSize() - Method in class maltcms.datastructures.caches.ScanLineCache

Getter.

getBinsSize() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter.

getBinsSize() - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter.

getBoolean() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the boolean property.

getBoundaryPoints() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getBoundaryPointsCopy() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getBoundaryPointsSize() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getBoundsForWavelet(double, double, int) - Method in class maltcms.commands.filters.array.wavelet.ContinuousWaveletTransform

getBpois() - Static method in class smueller.SymbolicRepresentationAlignment

getBreakpoints(Array, int, double) - Static method in class maltcms.tools.ImageTools

getBuffer(T[]) - Method in class maltcms.datastructures.caches.RingBuffer

getC() - Method in class smueller.alignment.AlignedPairVector

getCachedListScanLineCache(IFileFragment) - Static method in class maltcms.datastructures.caches.ScanLineCacheFactory

getCacheModulation() - Method in class maltcms.datastructures.caches.AScanLineCache

Getter.

getCacheModulation() - Method in interface maltcms.datastructures.caches.IScanLine

Getter.

getCacheModulation() - Method in class maltcms.datastructures.caches.ScanLineCache

Getter.

getCacheModulation() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter.

getCacheModulation() - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter.

getCallable() - Method in class maltcms.db.QueryDB

Returns a QueryCallable built according to the arguments supplied to the constructor of this object.

getCallable(Predicate<T>) - Method in class maltcms.db.QueryDB

Use if you want to use a different set of Predicates than defined at construction time.

getCategories() - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

getCategories() - Method in class net.sf.maltcms.evaluation.api.EntityGroup

getCategory() - Method in class net.sf.maltcms.evaluation.api.classification.Entity

getCategory() - Method in class net.sf.maltcms.evaluation.api.Entity

getCd() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getCellContent(Cell) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getCharacteristicMass(String) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getCharge() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the charge property.

getCharge() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the charge property.

getCharge() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the charge property.

getCharges() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the charges property.

getCharPair(int) - Method in class smueller.alignment.OptimalAlignmentVector

getChild(String) - Method in class maltcms.datastructures.ms.Experiment1D

getChild(String, boolean) - Method in class maltcms.datastructures.ms.Experiment1D

getChild(Point2D) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getChildren() - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getChildrenInRadius(List<Tuple2D<Point2D, T>>, Point2D, double) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getChildrenInRange(Rectangle2D) - Method in class maltcms.datastructures.quadTree.QuadTree

getChildrenInRange(Rectangle2D) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getChromatogram() - Method in class maltcms.datastructures.ms.Experiment1D

getChromatogram() - Method in interface maltcms.datastructures.ms.IExperiment1D

getChromatogram2D() - Method in class maltcms.datastructures.ms.Experiment2D

getChromatogram2D() - Method in interface maltcms.datastructures.ms.IExperiment2D

getChromatogramDistanceFunction() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getChromatograms() - Method in interface maltcms.datastructures.ms.ITreatmentGroup

getChromatograms() - Method in class maltcms.datastructures.ms.TreatmentGroup1D

getChromatograms() - Method in class maltcms.datastructures.ms.TreatmentGroup2D

getChromatograms(ObjectContainer) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getChromatograms() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Group

getChromatogramWarpCommand() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getClassLabel() - Method in class maltcms.datastructures.ridge.Ridge

getClassLabel() - Method in class net.sf.maltcms.evaluation.api.classification.Entity

getClassLabel() - Method in class net.sf.maltcms.evaluation.api.Entity

getCliqueCentroid() - Method in class maltcms.datastructures.cluster.Clique

getCliqueCentroid() - Method in interface maltcms.datastructures.cluster.IClique

getCliqueCentroid() - Method in class maltcms.datastructures.peak.Clique

getCliqueMean() - Method in class maltcms.datastructures.peak.Clique

getCliqueMean() - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

getCliqueMean() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

getCliqueMean() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

getCliqueRTMean() - Method in class maltcms.datastructures.peak.Clique

getCliqueRTVariance() - Method in class maltcms.datastructures.peak.Clique

getCliqueStatistics() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getCliqueVar() - Method in class maltcms.datastructures.peak.Clique

getCliqueVariance() - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

getCliqueVariance() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

getCliqueVariance() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

getClosestChild(Point2D, double) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getClosestInRadius(Point2D, double) - Method in class maltcms.datastructures.quadTree.QuadTree

getCluster() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getCluster(int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getCluster(int) - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

getClusterNames() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getClusters() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getClusters() - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

getColorrampLocation() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getColStart() - Method in class maltcms.datastructures.array.PartitionedArray

getColumnBounds(int) - Method in class maltcms.datastructures.array.DenseArray

getColumnBounds(int) - Method in interface maltcms.datastructures.array.IArrayD2Byte

getColumnBounds(int) - Method in interface maltcms.datastructures.array.IArrayD2Double

getColumnBounds(int) - Method in class maltcms.datastructures.array.PartitionedArray

getColumnBounds(int) - Method in class maltcms.datastructures.array.SparseArray

getColumnBounds(int) - Method in class maltcms.datastructures.array.TiledArray

getColumnCount() - Method in class maltcms.db.ui.MetaboliteViewModel

getColumnName(int) - Method in class maltcms.db.ui.MetaboliteViewModel

getColumns(Tuple2D<Vector<Vector<String>>, Vector<String>>) - Method in class maltcms.io.csv.CSVReader

getCommandLine() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITask

getCommandLine() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

getComment() - Method in class maltcms.io.csv.CSVReader

getComment() - Method in class maltcms.io.xml.mzData.DescriptionType

Gets the value of the comment property.

getComments() - Method in interface maltcms.datastructures.ms.IMetabolite

getComments() - Method in class maltcms.datastructures.ms.Metabolite

getComments() - Method in class maltcms.io.xml.mzData.SoftwareType

Gets the value of the comments property.

getComments() - Method in class maltcms.io.xml.mzData.SpectrumDescType

Gets the value of the comments property.

getCommon() - Method in class smueller.datastructure.BreakPoints

getCommonCliques(IFileFragment, IFileFragment, List<Clique>) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.CliqueTable

getCommonCliques(IFileFragment, IFileFragment, List<Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueTable

getCommonEntities() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getCommonEntities() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getCommonFeatures(Rank<? extends T>) - Method in class maltcms.datastructures.rank.Rank

getCommonScore(IFileFragment, IFileFragment, List<Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

getCompletionTime() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

Gets the value of the completionTime property.

getCompletionTime() - Method in class maltcms.io.xml.mzData.SoftwareType

Gets the value of the completionTime property.

getCompoundNames(Workbook) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getCompressionWeight() - Method in class maltcms.commands.distances.DtwRecurrence

getCompressionWeight() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

getConfigurationEditor() - Method in class maltcms.ui.wizard.PipelineWizard

getConsensus() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getConsensus() - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

getConstraints() - Method in class maltcms.commands.distances.dtwng.DTW

getConstraints() - Method in interface maltcms.commands.distances.dtwng.IAlignment

getContact() - Method in class maltcms.io.xml.mzData.AdminType

Gets the value of the contact property.

getContactInfo() - Method in class maltcms.io.xml.mzData.PersonType

Gets the value of the contactInfo property.

getContent() - Method in class maltcms.ui.TabbedPanel

getContent(Cell) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getContinuousWaveletTransform() - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

getConvexhull() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the convexhull property.

getCorrectedTIC() - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet

getCorrespondingScans() - Method in class maltcms.datastructures.alignment.DefaultPairSet

getCost(Ridge) - Method in interface maltcms.datastructures.ridge.IRidgeCost

getCost(Ridge) - Method in class maltcms.datastructures.ridge.RidgeCost0

getCost(Ridge) - Method in class maltcms.datastructures.ridge.RidgeCost1

getCost(Ridge) - Method in class maltcms.datastructures.ridge.RidgeCost2

Implements a path integral over the scale space ridge, starting from the initial position x0.

getCount() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.FeatureList

Gets the value of the count property.

getCount() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType.AnalyzerList

Gets the value of the count property.

getCount() - Method in class maltcms.io.xml.mzData.MzData.SpectrumList

Gets the value of the count property.

getCount() - Method in class maltcms.io.xml.mzData.SpectrumDescType.PrecursorList

Gets the value of the count property.

getCount() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Gets the value of the count property.

getCreator() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getCreatorname() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getCreators(ObjectContainer) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getCreatorVersion() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Creator

getCumulativeDistance() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

getCvLabel() - Method in class maltcms.io.xml.mzData.CvLookupType

Gets the value of the cvLabel property.

getCvLabel() - Method in class maltcms.io.xml.mzData.CvParamType

Gets the value of the cvLabel property.

getCvLookup() - Method in class maltcms.io.xml.mzData.MzData

Gets the value of the cvLookup property.

getCvParamOrUserParam() - Method in class maltcms.io.xml.mzData.ParamType

Gets the value of the cvParamOrUserParam property.

getD() - Method in class smueller.alignment.AlignedPairVector

getData() - Method in class maltcms.io.xml.mzData.PeakListBinaryType

Gets the value of the data property.

getData() - Method in class maltcms.io.xml.mzData.SupDataBinaryType

Gets the value of the data property.

getDataArray() - Method in class maltcms.datastructures.array.PartitionedArray

getDataProcessing() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the dataProcessing property.

getDataProcessing() - Method in class maltcms.io.xml.mzData.MzData.Description

Gets the value of the dataProcessing property.

getDate() - Method in interface maltcms.datastructures.ms.IMetabolite

getDate() - Method in class maltcms.datastructures.ms.Metabolite

getDate() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Gets the value of the date property.

getDb() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the db property.

getDBDir() - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getDBNO() - Method in class maltcms.datastructures.ms.Metabolite

getDbVersion() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the dbVersion property.

getDefaultConfig() - Method in class maltcms.runtime.LocalHostLauncher

Deprecated. Builds a composite configuration, adding default configuration and then the system configuration.

getDefaultConfig() - Method in class net.sf.maltcms.apps.Maltcms

Builds a composite configuration, adding default configuration and then the system configuration.

getDefaultPredicate() - Method in class maltcms.db.MetaboliteQueryDB

getDefaultPredicate() - Method in class maltcms.db.QueryDB

getDefaultRamp() - Method in class maltcms.io.csv.ColorRampReader

getDefaultScanLineCache(IFileFragment) - Static method in class maltcms.datastructures.caches.ScanLineCacheFactory

getDefaultValue() - Method in class maltcms.commands.distances.dtwng.DTW

getDefaultValue() - Method in interface maltcms.commands.distances.dtwng.IAlignment

getDefaultValue() - Method in class maltcms.datastructures.array.DenseArray

getDefaultValue() - Method in interface maltcms.datastructures.array.IArrayD2Byte

getDefaultValue() - Method in interface maltcms.datastructures.array.IArrayD2Double

getDefaultValue() - Method in class maltcms.datastructures.array.PartitionedArray

getDefaultValue() - Method in class maltcms.datastructures.array.SparseArray

getDefaultValue() - Method in class maltcms.datastructures.array.TiledArray

getDescription() - Method in class maltcms.commands.fragments.alignment.CenterStarAlignment

getDescription() - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

getDescription() - Method in class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment

getDescription() - Method in class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment

getDescription() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getDescription() - Method in class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator

getDescription() - Method in class maltcms.commands.fragments.io.ANDIChromImporter

getDescription() - Method in class maltcms.commands.fragments.io.ANDIMSExporter

getDescription() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getDescription() - Method in class maltcms.commands.fragments.io.MSPExporter

getDescription() - Method in class maltcms.commands.fragments.io.ObiWarplmataExporter

getDescription() - Method in class maltcms.commands.fragments.io.PeakAreaTableExporter

getDescription() - Method in class maltcms.commands.fragments.io.TICPeakListImporter

getDescription() - Method in class maltcms.commands.fragments.io.VariableDataExporter

getDescription() - Method in class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder

getDescription() - Method in class maltcms.commands.fragments.peakfinding.CwtTicPeakFinder

getDescription() - Method in class maltcms.commands.fragments.peakfinding.EICPeakFinder

getDescription() - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

getDescription() - Method in class maltcms.commands.fragments.preprocessing.DefaultVarLoader

getDescription() - Method in class maltcms.commands.fragments.preprocessing.DenseArrayProducer

getDescription() - Method in class maltcms.commands.fragments.preprocessing.MassFilter

getDescription() - Method in class maltcms.commands.fragments.spectratyping.VBetaFamilyComparison

getDescription() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

getDescription() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getDescription() - Method in class maltcms.commands.fragments.visualization.EICHeatmapCoplot

getDescription() - Method in class maltcms.commands.fragments.visualization.MZIDistributionVisualizer

getDescription() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer

getDescription() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

getDescription() - Method in class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer

getDescription() - Method in class maltcms.commands.fragments.visualization.TICHeatmapCoplot

getDescription() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

getDescription() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

getDescription() - Method in class maltcms.commands.fragments.warp.PathWarp

getDescription() - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

getDescription() - Method in class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

getDescription() - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarProducer

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarVis

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.ModulationExtractor

getDescription() - Method in class maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator

Deprecated.

getDescription() - Method in class maltcms.commands.fragments2d.testing.Alignment2D

getDescription() - Method in class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer

getDescription() - Method in class maltcms.commands.fragments2d.visualization.DeltaMasses

getDescription() - Method in class maltcms.commands.fragments2d.visualization.GradientVisualizer

getDescription() - Method in class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization

getDescription() - Method in class maltcms.commands.fragments2d.warp.CreateHorizontalTicVector

getDescription() - Method in class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer

getDescription() - Method in class maltcms.io.xml.mzData.MzData

Gets the value of the description property.

getDescription() - Static method in class maltcms.ui.wizard.AlignmentPane

getDescription() - Static method in class maltcms.ui.wizard.AnchorDefinitionPane

getDescription() - Static method in class maltcms.ui.wizard.FileInputOutputPane

getDescription() - Static method in class maltcms.ui.wizard.PreprocessingPane

getDescription() - Static method in class maltcms.ui.wizard.VisualizationPane

getDescription() - Method in class smueller.SymbolicRepresentationAlignment

getDetector() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Gets the value of the detector property.

getDiagonalWeight() - Method in class maltcms.commands.distances.DtwRecurrence

getDim() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint.Hposition

Gets the value of the dim property.

getDim() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Position

Gets the value of the dim property.

getDim() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Quality

Gets the value of the dim property.

getDimension() - Method in class maltcms.io.xml.bindings.alignment.PointType

Gets the value of the dimension property.

getDimensionByName(String, PointType) - Method in class maltcms.datastructures.alignment.AlignmentFactory

getDimNumber() - Method in class maltcms.io.xml.bindings.alignment.PointMapType

Gets the value of the dimNumber property.

getDist() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getDist() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getDist() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getDist() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getDist() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getDistance(int, int, double, double, Array, Array) - Method in class maltcms.commands.distances.PairwiseFeatureSimilarity

Returns the IDtwSimilarityFunction Object used to calculate pairwise distances/similarities.

getDistance() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getDistance(String, String) - Method in class maltcms.experimental.operations.EditDistance

Calculates the Edit-Distance on Strings a and b.

getDistanceTo(ICluster) - Method in class maltcms.datastructures.cluster.ACluster

getDistanceTo(int) - Method in class maltcms.datastructures.cluster.ACluster

getDistanceToCentroid(Peak) - Method in class maltcms.datastructures.peak.Clique

getDistanceToCentroid(T) - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

getDistanceToCentroid(Peak) - Method in class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

getDistanceToCentroid(Peak2D) - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

getDistanceToParent() - Method in class maltcms.datastructures.cluster.ACluster

getDistanceToParent() - Method in interface maltcms.datastructures.cluster.ICluster

getDistmat() - Method in class smueller.datastructure.DistanceMatrix

getDistmatrix() - Static method in class smueller.SymbolicRepresentationAlignment

getDocumentId() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the documentId property.

getDouble(Index) - Method in class maltcms.datastructures.array.Sparse

getDouble() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the double property.

getDTWInstance() - Method in class maltcms.commands.distances.dtwng.AlignmentFactory

Returns a new DTW instance, configured by ObjectFactory.

getDTWInstance(IOptimizationFunction, TwoFeatureVectorOperation, Area) - Method in class maltcms.commands.distances.dtwng.AlignmentFactory

getE() - Method in class smueller.alignment.AlignedPairVector

getEIC(IFileFragment, double, double, boolean, boolean, int, int) - Static method in class maltcms.tools.MaltcmsTools

getEIC(IFileFragment, double, double, boolean, boolean) - Static method in class maltcms.tools.MaltcmsTools

getElementsToCalculate() - Method in class maltcms.datastructures.array.PartitionedArray

getElementType() - Method in class maltcms.datastructures.array.Sparse

getEnclosingRectangle() - Method in class maltcms.datastructures.array.PartitionedArray

getEndian() - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Gets the value of the endian property.

getEndTimeColumn(Sheet) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getEntities() - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

getEntities() - Method in class net.sf.maltcms.evaluation.api.EntityGroup

getEntityForCategory(Category) - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

getEntityForCategory(Category) - Method in class net.sf.maltcms.evaluation.api.EntityGroup

getEnzyme() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the enzyme property.

getExpansionWeight() - Method in class maltcms.commands.distances.DtwRecurrence

getExpansionWeight() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

getExpectedBBHs() - Method in class maltcms.datastructures.peak.Clique

getExpectedBBHs(int) - Method in class maltcms.datastructures.peak.Clique

getExpectedBBHs() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getExpectedBBHs(int) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getExtension() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

getF() - Method in class smueller.alignment.AlignedPairVector

getF1() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getF1() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getFeature(String) - Method in class maltcms.commands.ArrayStatsMap

getFeature(String) - Method in interface maltcms.datastructures.array.IFeatureVector

Return an Array for a specified feature with name.

getFeature(String) - Method in class maltcms.datastructures.feature.DefaultBinnedMSFeatureVector

getFeature(String) - Method in class maltcms.datastructures.feature.DefaultFeatureVector

getFeature(String) - Method in class maltcms.datastructures.feature.FastBinnedMSFeatureVector

getFeature(String) - Method in class maltcms.datastructures.feature.MaltcmsFeatureVector

getFeature(String) - Method in class maltcms.datastructures.ms.Scan1D

getFeature(String) - Method in class maltcms.datastructures.ms.Scan2D

getFeature(String) - Method in class maltcms.datastructures.peak.Peak

getFeature(String) - Method in class maltcms.datastructures.peak.Peak1D

getFeature(String) - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2D

getFeature() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.FeatureList

Gets the value of the feature property.

getFeature() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Subordinate

Gets the value of the feature property.

getFeature(String) - Method in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumn

getFeature(String) - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVector

getFeature(String) - Method in class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector

getFeature(String) - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getFeatureList() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the featureList property.

getFeatureList(File) - Static method in class net.sf.maltcms.evaluation.spi.caap.PeakFactory

getFeatureList(InputStream) - Static method in class net.sf.maltcms.evaluation.spi.caap.PeakFactory

getFeatureNames() - Method in class maltcms.commands.ArrayStatsMap

getFeatureNames() - Method in interface maltcms.datastructures.array.IFeatureVector

Get a list of available feature names for this FeatureVector.

getFeatureNames() - Method in class maltcms.datastructures.feature.DefaultBinnedMSFeatureVector

getFeatureNames() - Method in class maltcms.datastructures.feature.DefaultFeatureVector

getFeatureNames() - Method in class maltcms.datastructures.feature.FastBinnedMSFeatureVector

getFeatureNames() - Method in class maltcms.datastructures.feature.MaltcmsFeatureVector

getFeatureNames() - Method in class maltcms.datastructures.ms.Scan1D

getFeatureNames() - Method in class maltcms.datastructures.ms.Scan2D

getFeatureNames() - Method in class maltcms.datastructures.peak.Peak

getFeatureNames() - Method in class maltcms.datastructures.peak.Peak1D

getFeatureNames() - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

getFeatureNames() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

getFeatureNames() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2D

getFeatureNames() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

getFeatureNames() - Method in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumn

getFeatureNames() - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVector

getFeatureNames() - Method in class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector

getFeatureNames() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getFeatureRanks(Rank<? extends T>) - Method in class maltcms.datastructures.rank.Rank

getFeatures() - Method in class maltcms.datastructures.rank.Rank

getFeatureVector() - Method in class net.sf.maltcms.evaluation.api.classification.Entity

getFeatureVector() - Method in class net.sf.maltcms.evaluation.api.Entity

getFeatureVectorList() - Method in class maltcms.datastructures.cluster.Clique

getFeatureVectorList() - Method in interface maltcms.datastructures.cluster.IClique

getFenstergr() - Static method in class smueller.SymbolicRepresentationAlignment

getFf() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getFieldSeparator() - Method in class maltcms.io.csv.CSVReader

getFile() - Method in class maltcms.ui.charts.PlotRunner

getFileDesignation() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getFileFragment() - Method in class maltcms.datastructures.ms.Experiment1D

getFileFragment() - Method in interface maltcms.datastructures.ms.IExperiment

getFileFragment() - Method in interface maltcms.datastructures.warp.IWarpInput

getFileFragment() - Method in class maltcms.datastructures.warp.MZIWarpInput

getFileFragment() - Method in class maltcms.datastructures.warp.TICWarpInput

getFileFragmentsFromStringArray(IFileFragment, String) - Static method in class maltcms.tools.MaltcmsTools

getFileMenu() - Method in class maltcms.ui.charts.JFreeChartViewer

getFilename() - Method in class maltcms.ui.charts.PlotRunner

getFilenames(Workbook) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getFilesFromFile(String) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getFileType() - Method in class maltcms.io.xml.mzData.SourceFileType

Gets the value of the fileType property.

getFiletype() - Method in class maltcms.ui.charts.PlotRunner

getFirstColumnScanAcquisitionTime() - Method in interface maltcms.datastructures.ms.IScan2D

getFirstColumnScanAcquisitionTime() - Method in class maltcms.datastructures.ms.Scan2D

getFirstColumnScanIndex() - Method in interface maltcms.datastructures.ms.IScan2D

getFirstColumnScanIndex() - Method in class maltcms.datastructures.ms.Scan2D

getFirstRetTime() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getFirstScanIndex() - Method in class maltcms.datastructures.peak.Peak2D

getFixedModification() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the fixedModification property.

getFloat(Index) - Method in class maltcms.datastructures.array.Sparse

getFloat() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the float property.

getFn() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getFN() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getFn() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getFn() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getFNR() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getFNR() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getFNWithoutUnmatchedToolEntityGroups() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getFnWithoutUnmatchedToolEntityGroups() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getFontFamily() - Method in class maltcms.ui.charts.PlotRunner

getFormat() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getFormula() - Method in interface maltcms.datastructures.ms.IMetabolite

getFormula() - Method in class maltcms.datastructures.ms.Metabolite

getFp() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getFP() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getFp() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getFp() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getFPR() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getFPR() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getFragments() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getFragments() - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

getFragments(IFileFragment, List<Tuple2DI>, IArrayD2Double) - Static method in class maltcms.tools.PathTools

Adds VariableFragments and arrays corresponding to path to parent FileFragment.

getFullName() - Method in class maltcms.io.xml.mzData.CvLookupType

Gets the value of the fullName property.

getGain() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getGain() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getGapinit() - Static method in class smueller.SymbolicRepresentationAlignment

getGenerator() - Method in class maltcms.io.xml.bindings.alignment.Alignment

Gets the value of the generator property.

getGenerator() - Method in class maltcms.io.xml.bindings.annotation.AnnotationsType

Gets the value of the generator property.

getGetterNames(String[]) - Method in class maltcms.tools.PublicMemberGetters

getGetterNames() - Method in class maltcms.tools.PublicMemberGetters

getGlobalGapPenalty() - Method in class maltcms.commands.distances.DtwRecurrence

getGlobalGapPenalty() - Method in interface maltcms.commands.distances.IRecurrence

getGlobalScanIndex() - Method in class maltcms.datastructures.ridge.Ridge

getGlobalStatsMap() - Method in class maltcms.commands.scanners.ArrayStatsScanner

getGroundTruthEntities() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getGroundTruthEntities() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getGroundTruthEntityGroup() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getGroundTruthEntityGroup() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getGroundTruthToToolMatchResults() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getHeight() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getHeightColumn(Sheet) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getHorizontalList() - Method in class maltcms.commands.fragments2d.testing.AlignmentPath2D

getHorizontalNeighborsInRadius(Point2D, double) - Method in class maltcms.datastructures.quadTree.QuadTree

getHposition() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint

Gets the value of the hposition property.

getHullpoint() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull

Gets the value of the hullpoint property.

getID() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

getID() - Method in class maltcms.datastructures.cluster.ACluster

getID() - Method in class maltcms.datastructures.cluster.Clique

getID() - Method in interface maltcms.datastructures.cluster.IClique

getID() - Method in interface maltcms.datastructures.cluster.ICluster

getID() - Method in class maltcms.datastructures.ms.Experiment1D

getID() - Method in interface maltcms.datastructures.ms.IMetabolite

getID() - Method in class maltcms.datastructures.ms.Metabolite

getID() - Method in class maltcms.datastructures.peak.Clique

getID() - Method in class maltcms.datastructures.peak.Peak2DClique

getID() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getId() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the id property.

getId() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Gets the value of the id property.

getId() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Gets the value of the id property.

getId() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the id property.

getId() - Method in class maltcms.io.xml.mzData.SpectrumType

Gets the value of the id property.

getId() - Method in class maltcms.io.xml.mzData.SupDataBinaryType

Gets the value of the id property.

getId() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the id property.

getIdentificationRun() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the identificationRun property.

getIdentificationRunRef() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the identificationRunRef property.

getIdentificationRunRef() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the identificationRunRef property.

getIDType() - Method in class maltcms.datastructures.ms.Metabolite

getImgheight() - Method in class maltcms.ui.charts.PlotRunner

getImgwidth() - Method in class maltcms.ui.charts.PlotRunner

getImmediateChildren() - Method in class maltcms.datastructures.quadTree.QuadTreeNode

getIndex() - Method in class maltcms.datastructures.array.Sparse

getIndex() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getIndex() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getIndexArray(List<Array>) - Static method in class maltcms.tools.ArrayTools2

getIndexedVars() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

getIndexedVars() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

getIndexedVars() - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

getIndexFor(double) - Method in class maltcms.datastructures.ms.Chromatogram1D

getIndexFor(double) - Method in class maltcms.datastructures.ms.Chromatogram2D

getIndexFor(double) - Method in interface maltcms.datastructures.ms.IChromatogram

getIndexIterator() - Method in class maltcms.datastructures.array.Sparse

getIndexIteratorFast() - Method in class maltcms.datastructures.array.Sparse

getIndexOfMaximum() - Method in class maltcms.datastructures.ridge.Ridge

getIndexOfMaxIntensity(Array, int[]) - Static method in class maltcms.tools.MaltcmsTools

Returns the index of the element with highest value in array intens.

getIndexOfMaxIntensity(Array) - Static method in class maltcms.tools.MaltcmsTools

getIndexVar() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

getIndexVar() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

getIndexVar() - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

getInputFiles() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getInputFiles() - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

getInputFiles() - Method in class maltcms.ui.wizard.FileInputOutputPane

getInputFilesAsStringArray(File[]) - Method in class maltcms.ui.wizard.AnchorDefinitionPane

getInstance() - Static method in class maltcms.datastructures.constraint.ConstraintFactory

getInstance() - Static method in class maltcms.datastructures.feature.FeatureVectorFactory

getInstance(MetaboliteViewModel) - Static method in class maltcms.db.ui.MetaboliteSearchPreferences

Returns an instance of this class, if there is not an instance yet

getInstance() - Static method in class net.sf.maltcms.apps.Maltcms

Allow only one running instance of Maltcms (per VM)

getInstitution() - Method in class maltcms.io.xml.mzData.PersonType

Gets the value of the institution property.

getInstrument() - Method in class maltcms.io.xml.mzData.MzData.Description

Gets the value of the instrument property.

getInstrumentName() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Gets the value of the instrumentName property.

getInt(Index) - Method in class maltcms.datastructures.array.Sparse

getInt() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the int property.

getIntenArrayBinary() - Method in class maltcms.io.xml.mzData.SpectrumType

Gets the value of the intenArrayBinary property.

getIntensities() - Method in interface maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing

getIntensities() - Method in class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing

getIntensities() - Method in class maltcms.datastructures.ms.Chromatogram1D

getIntensities() - Method in class maltcms.datastructures.ms.Chromatogram2D

getIntensities(int, int) - Method in class maltcms.datastructures.ms.Chromatogram2D

getIntensities() - Method in interface maltcms.datastructures.ms.IChromatogram

getIntensities() - Method in interface maltcms.datastructures.ms.IScan

getIntensities() - Method in interface maltcms.datastructures.ms.IScan1D

getIntensities() - Method in class maltcms.datastructures.ms.Scan1D

getIntensity() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the intensity property.

getIntensityValuesVarName() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getIntensityValuesVarName() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getInterppath() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getIonSelection() - Method in class maltcms.io.xml.mzData.PrecursorType

Gets the value of the ionSelection property.

getIsothermalKovatsIndex(double) - Method in class maltcms.datastructures.peak.RetentionIndexCalculator

getJfc() - Method in class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

getJmb() - Method in class maltcms.ui.charts.JFreeChartViewer

getJPanel() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

getJtp() - Method in class maltcms.ui.charts.JFreeChartViewer

getL() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getLabelString() - Method in class maltcms.datastructures.cluster.ACluster

getLabelString() - Method in interface maltcms.datastructures.cluster.ICluster

getLastIndex() - Method in class maltcms.datastructures.caches.AScanLineCache

Getter.

getLastIndex() - Method in interface maltcms.datastructures.caches.IScanLine

Getter.

getLastIndex() - Method in class maltcms.datastructures.caches.ScanLineCache

Getter.

getLastIndex() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter.

getLastIndex() - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter.

getLChild() - Method in class maltcms.datastructures.cluster.BinaryCluster

getLChildID() - Method in class maltcms.datastructures.cluster.BinaryCluster

getLeftHandSideId() - Method in class maltcms.commands.distances.dtwng.DTW

getLeftHandSideId() - Method in interface maltcms.commands.distances.dtwng.IAlignment

getLength() - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Gets the value of the length property.

getLength() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the length property.

getLHSPointHorizontal(Integer) - Method in class maltcms.commands.fragments2d.testing.AlignmentPath2D

getLHSPointVertical(Integer) - Method in class maltcms.commands.fragments2d.testing.AlignmentPath2D

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class maltcms.db.ui.MetaboliteListCellRenderer

getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class maltcms.db.ui.QueryResultListCellRenderer

getLocation() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getLong(Index) - Method in class maltcms.datastructures.array.Sparse

getLookupImage() - Method in class maltcms.ui.charts.GradientPaintScale

getLowerBound() - Method in class maltcms.ui.charts.GradientPaintScale

getLowThreshold() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getMaltcmsPeaks(Creator, ObjectContainer, String...) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getMap() - Method in class maltcms.commands.distances.dtwng.DTW

getMap() - Method in interface maltcms.commands.distances.dtwng.IAlignment

getMap() - Method in class maltcms.tools.PathTools

getMappedPoints(Alignment, IFileFragment) - Method in class maltcms.datastructures.alignment.AlignmentFactory

getMappedPoints() - Method in class maltcms.io.xml.bindings.alignment.Alignment

Gets the value of the mappedPoints property.

getMasses() - Method in class maltcms.datastructures.ms.Chromatogram1D

getMasses() - Method in class maltcms.datastructures.ms.Chromatogram2D

getMasses(int, int) - Method in class maltcms.datastructures.ms.Chromatogram2D

getMasses() - Method in interface maltcms.datastructures.ms.IChromatogram

getMasses() - Method in interface maltcms.datastructures.ms.IScan

getMasses() - Method in interface maltcms.datastructures.ms.IScan1D

getMasses() - Method in class maltcms.datastructures.ms.Scan1D

getMassesToFilterByCoefficientOfVariation(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getMassesToFilterByCoefficientOfVariation2(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getMassRangeMax() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getMassRangeMax() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getMassRangeMin() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getMassRangeMin() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getMassSpectra(Point) - Method in class maltcms.datastructures.caches.AScanLineCache

This Method is a wrapper for getMassPectra(int, int).

getMassSpectra(int, int) - Method in class maltcms.datastructures.caches.CachedScanLineList

Getter for one mass spectra.

getMassSpectra(int, int) - Method in interface maltcms.datastructures.caches.IScanLine

Getter for one mass spectra.

getMassSpectra(Point) - Method in interface maltcms.datastructures.caches.IScanLine

This Method is a wrapper for getMassPectra(int, int).

getMassSpectra(int, int) - Method in class maltcms.datastructures.caches.ScanLineCache

Getter for one mass spectra.

getMassSpectra(Point) - Method in class maltcms.datastructures.caches.ScanLineCache

This Method is a wrapper for getMassPectra(int, int).

getMassSpectra(int, int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter for one mass spectra.

getMassSpectra(Point) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

This Method is a wrapper for getMassPectra(int, int).

getMassSpectra(int, int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter for one mass spectra.

getMassSpectra(Point) - Method in class maltcms.datastructures.caches.SparseScanLineCache

This Method is a wrapper for getMassPectra(int, int).

getMassSpectra() - Method in class maltcms.datastructures.peak.Peak1DGroup

getMassSpectrum() - Method in interface maltcms.datastructures.ms.IMetabolite

getMassSpectrum() - Method in class maltcms.datastructures.ms.Metabolite

getMassSpectrum(int) - Method in class maltcms.datastructures.peak.Peak1DGroup

getMassSpectrum() - Method in class maltcms.datastructures.peak.Peak1DGroup

getMassType() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the massType property.

getMassValuesVarName() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getMassValuesVarName() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getMatches() - Method in class maltcms.db.predicates.metabolite.MetaboliteSimilarity

getMatchWeight() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

getMatrix() - Method in class smueller.alignment.Alignment

getMax() - Method in class maltcms.commands.fragments2d.peakfinding.Reliability

getMax() - Method in class smueller.tools.Standardizer

getMaxAnnotations() - Method in class maltcms.ui.charts.MassSpectrumPlot

Getter.

getMaxBBHErrors() - Method in class maltcms.datastructures.peak.Clique

getMaxBBHErrors() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getMaxFirstDelta() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMaxHeight() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getMaximumSize() - Method in class maltcms.ui.TabbedPanel

getMaxIndex() - Method in class maltcms.datastructures.array.Sparse

getMaxIntensity() - Method in interface maltcms.datastructures.ms.IMetabolite

getMaxIntensity() - Method in class maltcms.datastructures.ms.Metabolite

getMaxMass() - Method in interface maltcms.datastructures.ms.IMetabolite

getMaxMass() - Method in class maltcms.datastructures.ms.Metabolite

getMaxMass(Array, Array) - Static method in class maltcms.tools.MaltcmsTools

Returns mass of signal with maximum intensity.

getMaxMassIntensity(Array) - Static method in class maltcms.tools.MaltcmsTools

Returns maximum intensity in scan.

getMaxMassIntensity(Array, double) - Static method in class maltcms.tools.MaltcmsTools

getMaxSecondDelta() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMaxStringLengthForTuple(Collection<Tuple2D<String, Array>>, Font) - Static method in class maltcms.tools.ImageTools

getMaxWidth() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getMaxX() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMaxY() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMeanFirstScanIndex() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMeanMS() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMeanMS() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getMeanPoint() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMeanSecondScanIndex() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMedian() - Method in class smueller.tools.Standardizer

getMedianRT(IFileFragment, TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

getMessageArea() - Method in class maltcms.ui.wizard.PipelineWizard

getMetaboliteAtRow(int) - Method in class maltcms.db.ui.MetaboliteViewModel

getMetaboliteMembers() - Method in class maltcms.db.ui.MetaboliteView

getMetadata() - Method in class maltcms.datastructures.ms.Experiment1D

getMetadata(String) - Method in class maltcms.datastructures.ms.Experiment1D

getMetadata() - Method in interface maltcms.datastructures.ms.IExperiment

getMetadata(String) - Method in interface maltcms.datastructures.ms.IExperiment

getMethodForGetterName(String) - Method in class maltcms.db.ui.MetaboliteViewModel

getMethodForGetterName(String) - Method in class maltcms.tools.PublicMemberGetters

getMethodOfCombination() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Gets the value of the methodOfCombination property.

getMethodOnTargetType() - Method in interface maltcms.db.predicates.IMatchPredicate

getMethodOnTargetType() - Method in class maltcms.db.predicates.MatchPredicate

getMethodOnTargetType() - Method in class maltcms.db.predicates.metabolite.MetabolitePredicate

getMin() - Method in class maltcms.commands.fragments2d.peakfinding.Reliability

getMin() - Method in class smueller.tools.Standardizer

getMinArrayComp() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getMinDist() - Method in interface maltcms.commands.fragments2d.peakfinding.srg.IRegionGrowing

getMinDist() - Method in class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing

getMinimizingArrayCompVariableName() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getMinIndex() - Method in class maltcms.datastructures.array.Sparse

getMinIntensity() - Method in interface maltcms.datastructures.ms.IMetabolite

getMinIntensity() - Method in class maltcms.datastructures.ms.Metabolite

getMinMass() - Method in interface maltcms.datastructures.ms.IMetabolite

getMinMass() - Method in class maltcms.datastructures.ms.Metabolite

getMinMaxMassRange(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getMinMaxMassRange(Collection<IFileFragment>) - Static method in class maltcms.tools.MaltcmsTools

getMinMaxMassRange(IFileFragment, IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getMinScansBetweenAnchors() - Method in class maltcms.datastructures.alignment.DefaultPairSet

getMinX() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMinY() - Method in class maltcms.ui.charts.XYBPlot

Getter.

getMissedCleavages() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the missedCleavages property.

getMissingChromatogramList() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

getMissingPeaks(List<List<Point>>, List<List<Peak2D>>, int) - Static method in class maltcms.commands.fragments2d.peakfinding.bbh.BBHTools

getModel() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the model property.

getModulationDuration() - Method in class maltcms.datastructures.ms.Chromatogram2D

getModulationDuration() - Method in interface maltcms.datastructures.ms.IChromatogram2D

getMS(IFileFragment, int) - Static method in class maltcms.tools.MaltcmsTools

getMsLevel() - Method in class maltcms.io.xml.mzData.PrecursorType

Gets the value of the msLevel property.

getMsLevel() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

Gets the value of the msLevel property.

getMW() - Method in interface maltcms.datastructures.ms.IMetabolite

getMw() - Method in interface maltcms.datastructures.ms.IMetabolite

getMW() - Method in class maltcms.datastructures.ms.Metabolite

getMw() - Method in class maltcms.datastructures.ms.Metabolite

getMw() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getMZ() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the mz property.

getMZ() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the mz property.

getMz(FeatureType) - Static method in class net.sf.maltcms.evaluation.spi.caap.PeakFactory

getMzArrayBinary() - Method in class maltcms.io.xml.mzData.SpectrumType

Gets the value of the mzArrayBinary property.

getMZIs(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getMzRangeStart() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

Gets the value of the mzRangeStart property.

getMzRangeStop() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

Gets the value of the mzRangeStop property.

getMzVariableName() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getName() - Method in class maltcms.datastructures.cluster.ACluster

getName() - Method in interface maltcms.datastructures.cluster.ICluster

getName() - Method in class maltcms.datastructures.ms.Experiment1D

getName() - Method in interface maltcms.datastructures.ms.IAnchor

getName() - Method in interface maltcms.datastructures.ms.ITreatmentGroup

getName() - Method in class maltcms.datastructures.ms.Metabolite

getName() - Method in class maltcms.datastructures.ms.RetentionInfo

getName() - Method in class maltcms.datastructures.ms.TreatmentGroup1D

getName() - Method in class maltcms.datastructures.ms.TreatmentGroup2D

getName() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getName() - Method in class maltcms.io.xml.bindings.alignment.PointType.Dimension

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.annotation.AnnotationType

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.annotation.AttributeType

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.ProcessingAction

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.Software

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.FixedModification

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.VariableModification

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model.Param

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.bindings.openms.featurexml.UserParam

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.mzData.CvParamType

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.mzData.PersonType

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.mzData.SoftwareType

Gets the value of the name property.

getName() - Method in class maltcms.io.xml.mzData.UserParamType

Gets the value of the name property.

getName() - Method in class net.sf.maltcms.evaluation.api.Category

getName() - Method in class net.sf.maltcms.evaluation.api.classification.Category

getName() - Method in class net.sf.maltcms.evaluation.spi.tasks.execution.APipeline

getName() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Chromatogram

getName() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Creator

getName() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Group

getName() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getNameOfFile() - Method in class maltcms.io.xml.mzData.SourceFileType

Gets the value of the nameOfFile property.

getNames() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getNames() - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

getNames() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getNcomp() - Method in class maltcms.tools.PathTools

getNdiag() - Method in class maltcms.tools.PathTools

getNeighborhoods() - Method in class maltcms.datastructures.array.PartitionedArray

getNeighborsInRadius(Point2D, double) - Method in class maltcms.datastructures.quadTree.QuadTree

getNewIndexOnLHS(int, List<Tuple2DI>) - Static method in class maltcms.tools.ArrayTools

getNewIndexOnRHS(int, List<Tuple2DI>) - Static method in class maltcms.tools.ArrayTools

getNexp() - Method in class maltcms.tools.PathTools

getNodes() - Method in class maltcms.commands.distances.dtwng.NodeBuilder

getNodesByDimension(int, double[]) - Method in class maltcms.commands.distances.dtwng.NodeBuilder

getNormalization() - Method in class maltcms.commands.filters.array.NormalizationFilter

getNormalizationFactor(IFileFragment, Peak1D) - Method in interface maltcms.datastructures.peak.normalization.IPeakNormalizer

getNormalizationFactor(IFileFragment, Peak1D) - Method in class maltcms.datastructures.peak.normalization.TicAreaNormalizer

getNormalizationName() - Method in interface maltcms.datastructures.peak.normalization.IPeakNormalizer

getNormalizationName() - Method in class maltcms.datastructures.peak.normalization.TicAreaNormalizer

getNr() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull

Gets the value of the nr property.

getNumberOf2DScans() - Method in class maltcms.datastructures.ms.Chromatogram2D

getNumberOf2DScans() - Method in interface maltcms.datastructures.ms.IChromatogram2D

getNumberOfBinnedScans(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getNumberOfIntegerMassBins(double, double, double) - Static method in class maltcms.tools.MaltcmsTools

getNumberOfMaps() - Method in class maltcms.io.xml.bindings.alignment.Alignment

Gets the value of the numberOfMaps property.

getNumberOfModulations() - Method in class maltcms.datastructures.ms.Chromatogram2D

getNumberOfModulations() - Method in interface maltcms.datastructures.ms.IChromatogram2D

getNumberOfPeaks() - Method in interface maltcms.datastructures.peak.IPeakGroup1DProvider

getNumberOfPeaksWithinCliques(IFileFragment) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.CliqueTable

getNumberOfPeaksWithinCliques(IFileFragment, List<Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

getNumberOfPeaksWithinCliques(IFileFragment) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueTable

getNumberOfScans() - Method in class maltcms.datastructures.ms.Chromatogram1D

getNumberOfScans() - Method in class maltcms.datastructures.ms.Chromatogram2D

getNumberOfScans() - Method in interface maltcms.datastructures.ms.IChromatogram

getNumberOfScans() - Method in interface maltcms.datastructures.ms.IScanProvider

getNumberOfScans(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getNumberOfScansPerModulation() - Method in class maltcms.datastructures.ms.Chromatogram2D

getNumberOfScansPerModulation() - Method in interface maltcms.datastructures.ms.IChromatogram2D

getNumberOfStoredElements() - Method in class maltcms.datastructures.array.DenseArray

getNumberOfStoredElements() - Method in interface maltcms.datastructures.array.IArrayD2Byte

getNumberOfStoredElements() - Method in interface maltcms.datastructures.array.IArrayD2Double

getNumberOfStoredElements() - Method in class maltcms.datastructures.array.PartitionedArray

getNumberOfStoredElements() - Method in class maltcms.datastructures.array.SparseArray

getNumberOfStoredElements() - Method in class maltcms.datastructures.array.TiledArray

getNumKeys() - Method in class maltcms.datastructures.array.Sparse

getNumPartitions() - Method in class maltcms.datastructures.array.PartitionedArray

getObjectContainer() - Method in class maltcms.db.ui.MetaboliteViewModel

getObjectContainer(MetaboliteBrowser.Credentials) - Static method in class net.sf.maltcms.apps.MetaboliteBrowser

getOffset() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the offset property.

getOldScanLineCache(IFileFragment) - Static method in class maltcms.datastructures.caches.ScanLineCacheFactory

getOptimalOperationSequenceString() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

getOptimalOperationSequenceString() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

getOptimalValue() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

getOptimalValue() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

getOptimizationFunction() - Method in class maltcms.commands.distances.dtwng.DTW

getOptimizationFunction() - Method in interface maltcms.commands.distances.dtwng.IAlignment

getOutputDirectory() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITask

getOutputDirectory() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

getOverallquality() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the overallquality property.

getPaint(double) - Method in class maltcms.ui.charts.GradientPaintScale

getPairwiseAlignment(IFileFragment, IFileFragment, IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getPairwiseAlignment(TupleND<IFileFragment>, IFileFragment, IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getPairwiseAlignments(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getPairwiseDistance() - Method in class smueller.alignment.Alignment

getPairwiseDistanceFragment(IFileFragment, String) - Static method in class maltcms.tools.MaltcmsTools

getPairwiseDistanceFragment(TupleND<IFileFragment>) - Static method in class maltcms.tools.MaltcmsTools

getPairwiseDistanceFragment(TupleND<IFileFragment>, String) - Static method in class maltcms.tools.MaltcmsTools

getPairwiseDistanceMatrixVariableName() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getPairwiseDistanceNamesVariableName() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getPairwiseDistances() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getPairwiseFeatureSimilarity() - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

getPairwiseFeatureVectorOperation() - Method in class maltcms.commands.distances.dtwng.DTW

getPairwiseFeatureVectorOperation() - Method in interface maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation

getParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model

Gets the value of the param property.

getParent() - Method in class maltcms.datastructures.ms.Chromatogram1D

getParent() - Method in class maltcms.datastructures.ms.Chromatogram2D

getParent() - Method in class maltcms.datastructures.ms.Experiment1D

getParent() - Method in interface maltcms.datastructures.ms.IChromatogram

getParent() - Method in class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

getParent() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getPartitionIterator() - Method in class maltcms.datastructures.array.PartitionedArray

getPath() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getPath() - Method in interface maltcms.datastructures.warp.IWarpInput

getPath() - Method in class maltcms.datastructures.warp.MZIWarpInput

getPath() - Method in class maltcms.datastructures.warp.TICWarpInput

getPathToFile() - Method in class maltcms.io.xml.mzData.SourceFileType

Gets the value of the pathToFile property.

getPathway() - Method in class smueller.alignment.Alignment

getPeak(int) - Method in interface maltcms.datastructures.peak.IPeakGroup1DProvider

getPeak1D(MaltcmsAnnotation) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

getPeak2DCliqueList(Collection<IFileFragment>, List<List<Point>>, List<List<Peak2D>>) - Static method in class maltcms.commands.fragments2d.peakfinding.bbh.BBHTools

getPeakAnnotation(AnnotationType) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

getPeakArea() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getPeakForChromatogramByCreatorByName(ObjectContainer, Chromatogram, String, String) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getPeakingMasses(IFileFragment, int, int, int, double) - Static method in class maltcms.tools.MaltcmsTools

Returns a list of pairs, where the first element corresponds to the intensity, and the second to the associated mass channel.

getPeakList() - Method in class maltcms.datastructures.peak.Clique

getPeakList() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getPeakLists() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

Getter.

getPeakMassTolerance() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the peakMassTolerance property.

getPeakPositions() - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet

getPeaks(IFileFragment) - Method in interface maltcms.experimental.bipace.api.IPeakListProvider

getPeaks(IFileFragment) - Method in class maltcms.experimental.bipace.spi.PeakList1DProvider

getPeaks(IFileFragment) - Method in class maltcms.experimental.bipace.spi.PeakList2DProvider

getPeaks(ObjectContainer) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getPeaks(Workbook, int, Creator, ObjectContainer) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getPeaksByCreator(ObjectContainer, String) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getPeaksForChromatogram(ObjectContainer, Chromatogram) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getPeaksForChromatogramByCreator(ObjectContainer, Chromatogram, String) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getPeaksSortedBySimilarity(String) - Method in class maltcms.datastructures.peak.Peak

Only call this method, after having added all similarities!

getPeakWithHighestSimilarity(String) - Method in class maltcms.datastructures.peak.Peak

getPeptideHit() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the peptideHit property.

getPeptideHit() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the peptideHit property.

getPeptideIdentification() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the peptideIdentification property.

getPipelines() - Method in class net.sf.maltcms.evaluation.spi.tasks.execution.APipeline

getPlainVars() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

getPlainVars() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

getPlainVars() - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

getPlot() - Method in class maltcms.ui.charts.PlotRunner

getPoint() - Method in class maltcms.io.xml.bindings.alignment.PointMapType

Gets the value of the point property.

getPointFor(int) - Method in class maltcms.datastructures.ms.Chromatogram2D

getPointFor(double) - Method in class maltcms.datastructures.ms.Chromatogram2D

getPointFor(int) - Method in interface maltcms.datastructures.ms.IChromatogram2D

getPointFor(double) - Method in interface maltcms.datastructures.ms.IChromatogram2D

getPointList(List<double[]>) - Method in class maltcms.commands.distances.dtwng.NodeBuilder

getPointMap() - Method in class maltcms.io.xml.bindings.alignment.MappedPointsType

Gets the value of the pointMap property.

getPointNumber() - Method in class maltcms.io.xml.bindings.alignment.PointMapType

Gets the value of the pointNumber property.

getPosition() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the position property.

getPostProcessors() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITask

getPostProcessors() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

getPrecision() - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Gets the value of the precision property.

getPrecision() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getPrecision() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getPrecursor() - Method in class maltcms.io.xml.mzData.SpectrumDescType.PrecursorList

Gets the value of the precursor property.

getPrecursorList() - Method in class maltcms.io.xml.mzData.SpectrumDescType

Gets the value of the precursorList property.

getPrecursorPeakTolerance() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the precursorPeakTolerance property.

getPredecessors() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getPreferredSize() - Method in class maltcms.ui.TabbedPanel

getProcess() - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

getProcessingAction() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

Gets the value of the processingAction property.

getProcessingMethod() - Method in class maltcms.io.xml.mzData.DataProcessingType

Gets the value of the processingMethod property.

getProgress() - Method in class maltcms.mpaxs.MaltcmsConfigurableRunnable

getProgress() - Method in class maltcms.mpaxs.TestConfigurableCallable

getProteinHit() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Gets the value of the proteinHit property.

getProteinIdentification() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Gets the value of the proteinIdentification property.

getProteinRefs() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the proteinRefs property.

getProteinRefs() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the proteinRefs property.

getPwd() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getPwDistAlignmentsVarName() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getPwDistMatrixVariableName() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getPwDistVariableName() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getQuality() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the quality property.

getQuantilValue(IFileFragment, Array, double[], boolean, AFragmentCommand) - Static method in class maltcms.commands.fragments2d.tools.ArrayTools

Visualization of the sorted standard deviation.

getQuery() - Method in class smueller.alignment.Alignment

getQueryFileFragment() - Method in interface maltcms.datastructures.warp.IWarpInput

getQueryFileFragment() - Method in class maltcms.datastructures.warp.MZIWarpInput

getQueryFileFragment() - Method in class maltcms.datastructures.warp.TICWarpInput

getQueryPanel(MetaboliteViewModel) - Method in class net.sf.maltcms.apps.MetaboliteBrowser

getQuerysize() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getRamp() - Method in class maltcms.ui.charts.GradientPaintScale

getRank(String) - Method in class maltcms.datastructures.rank.Rank

getRatio(String, String) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

getRatio(String, String) - Method in class maltcms.datastructures.peak.Peak2DClique

getRChild() - Method in class maltcms.datastructures.cluster.BinaryCluster

getRChildID() - Method in class maltcms.datastructures.cluster.BinaryCluster

getRecall() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getRecall() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getRecurrence() - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

getRef() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getRef() - Method in class smueller.alignment.Alignment

getReference() - Method in class maltcms.datastructures.peak.Peak2D

getReferenceFileFragment() - Method in interface maltcms.datastructures.warp.IWarpInput

getReferenceFileFragment() - Method in class maltcms.datastructures.warp.MZIWarpInput

getReferenceFileFragment() - Method in class maltcms.datastructures.warp.TICWarpInput

getRefsize() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getRegionPoints() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getReliability() - Method in class maltcms.commands.fragments2d.peakfinding.Reliability

getRequiredSize(List<Sparse>) - Static method in class maltcms.tools.ArrayTools

Compute total number of elements for all Sparse arrays in list.

getResource() - Method in class maltcms.io.xml.bindings.alignment.MappedPointsType

Gets the value of the resource property.

getResource() - Method in class maltcms.io.xml.bindings.annotation.MaltcmsAnnotation

Gets the value of the resource property.

getResult() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

getResult() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getResult() - Method in class smueller.datastructure.AlignmentOutput

getResultFileFragment() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

getResultFileFragment() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

getResultVector() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

getResultVector() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getRetentionIndex() - Method in interface maltcms.datastructures.ms.IRetentionInfo

getRetentionIndex() - Method in class maltcms.datastructures.ms.Metabolite

getRetentionIndex() - Method in class maltcms.datastructures.ms.RetentionInfo

getRetentionIndex2D() - Method in interface maltcms.datastructures.ms.IRetentionInfo2D

getRetentionIndex2D() - Method in class maltcms.datastructures.ms.Metabolite2D

getRetentionTime() - Method in interface maltcms.datastructures.ms.IRetentionInfo

getRetentionTime() - Method in class maltcms.datastructures.ms.Metabolite

getRetentionTime() - Method in class maltcms.datastructures.ms.RetentionInfo

getRetentionTime() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getRetentionTime2D() - Method in interface maltcms.datastructures.ms.IRetentionInfo2D

getRetentionTime2D() - Method in class maltcms.datastructures.ms.Metabolite2D

getRetentionTimeUnit() - Method in interface maltcms.datastructures.ms.IRetentionInfo

getRetentionTimeUnit() - Method in class maltcms.datastructures.ms.Metabolite

getRetentionTimeUnit() - Method in class maltcms.datastructures.ms.RetentionInfo

getRetentionTimeUnit2D() - Method in interface maltcms.datastructures.ms.IRetentionInfo2D

getRetentionTimeUnit2D() - Method in class maltcms.datastructures.ms.Metabolite2D

getRHSPointHorizontal(Integer) - Method in class maltcms.commands.fragments2d.testing.AlignmentPath2D

getRHSPointVerticals(Integer) - Method in class maltcms.commands.fragments2d.testing.AlignmentPath2D

getRidge() - Method in class maltcms.datastructures.rank.Rank

getRidgeCost() - Method in class maltcms.datastructures.ridge.Ridge

getRidgeCosts() - Method in class maltcms.datastructures.ridge.Ridge

getRidgePoints() - Method in class maltcms.datastructures.ridge.Ridge

getRightHandSideId() - Method in class maltcms.commands.distances.dtwng.DTW

getRightHandSideId() - Method in interface maltcms.commands.distances.dtwng.IAlignment

getRowCount() - Method in class maltcms.db.ui.MetaboliteViewModel

getRowLength() - Method in class maltcms.datastructures.array.PartitionedArray

getRowOffset() - Method in class maltcms.datastructures.array.PartitionedArray

getRT() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the rt property.

getRT() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the rt property.

getRT() - Method in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumn

getRT() - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVector

getRt(FeatureType) - Static method in class net.sf.maltcms.evaluation.spi.caap.PeakFactory

getRT() - Method in class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector

getRt() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getRTColumn(Sheet) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getRtstart() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getRtstop() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

getSample(double[], double[], double) - Static method in class maltcms.tools.ImageTools

getSampleDescription() - Method in class maltcms.io.xml.mzData.AdminType

Gets the value of the sampleDescription property.

getSampleName() - Method in class maltcms.io.xml.mzData.AdminType

Gets the value of the sampleName property.

getSampleSize() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getScalarSimilarities() - Method in interface maltcms.math.functions.IScalarArraySimilarity

getScan(int) - Method in class maltcms.datastructures.ms.Chromatogram1D

getScan(int) - Method in class maltcms.datastructures.ms.Chromatogram2D

getScan(int) - Method in interface maltcms.datastructures.ms.IScanProvider

getScan2D(int, int) - Method in class maltcms.datastructures.ms.Chromatogram2D

getScan2D(int, int) - Method in interface maltcms.datastructures.ms.IChromatogram2D

getScanAcquisitionTime() - Method in class maltcms.datastructures.ms.Chromatogram1D

getScanAcquisitionTime() - Method in class maltcms.datastructures.ms.Chromatogram2D

getScanAcquisitionTime() - Method in interface maltcms.datastructures.ms.IChromatogram

getScanAcquisitionTime() - Method in interface maltcms.datastructures.ms.IScan

getScanAcquisitionTime() - Method in interface maltcms.datastructures.ms.IScan1D

getScanAcquisitionTime() - Method in class maltcms.datastructures.ms.Scan1D

getScanAcquisitionTime() - Method in class maltcms.datastructures.peak.Peak

getScanAcquisitionTime(IFileFragment, int) - Static method in class maltcms.tools.MaltcmsTools

getScanAcquisitionTimeUnit() - Method in class maltcms.datastructures.ms.Chromatogram1D

getScanAcquisitionTimeUnit() - Method in class maltcms.datastructures.ms.Chromatogram2D

getScanAcquisitionTimeUnit() - Method in interface maltcms.datastructures.ms.IChromatogram

getScanAcquisitionTimeVariableName() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

getScanAcquisitionTimeVariableName() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getScanAcquisitionTimeVarName() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getScanAcquisitionTimeVarName() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getScanIndex() - Method in interface maltcms.datastructures.ms.IAnchor

getScanIndex() - Method in interface maltcms.datastructures.ms.IScan

getScanIndex() - Method in interface maltcms.datastructures.ms.IScan1D

getScanIndex() - Method in class maltcms.datastructures.ms.Metabolite

getScanIndex() - Method in class maltcms.datastructures.ms.RetentionInfo

getScanIndex() - Method in class maltcms.datastructures.ms.Scan1D

getScanIndex() - Method in class maltcms.datastructures.peak.Peak

getScanIndex() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getScanIndexVarName() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getScanIndexVarName() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getScanLineCache(IFileFragment) - Static method in class maltcms.datastructures.caches.ScanLineCacheFactory

This method will automatically create a new IScanLine for the given IFileFragment if no one is cached.

getScanLineCount() - Method in class maltcms.datastructures.caches.AScanLineCache

Getter.

getScanLineCount() - Method in interface maltcms.datastructures.caches.IScanLine

Getter.

getScanLineCount() - Method in class maltcms.datastructures.caches.ScanLineCache

Getter.

getScanLineCount() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter.

getScanLineCount() - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter.

getScanLineImpl() - Method in class maltcms.datastructures.ms.Chromatogram2D

Call for explicit access to the underlying IScanLine implementation.

getScanlineMS(int) - Method in class maltcms.datastructures.caches.CachedScanLineList

This method will create a List of Array containing the mass spectra of scanline x.

getScanlineMS(int) - Method in interface maltcms.datastructures.caches.IScanLine

This method will create a List of Array containing the mass spectra of scanline x.

getScanlineMS(int) - Method in class maltcms.datastructures.caches.ScanLineCache

Getter.

getScanlineMS(int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter.

getScanlineMS(int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter.

getScanlineSparseMS(int) - Method in class maltcms.datastructures.caches.CachedScanLineList

getScanlineSparseMS(int) - Method in interface maltcms.datastructures.caches.IScanLine

getScanlineSparseMS(int) - Method in class maltcms.datastructures.caches.ScanLineCache

getScanlineSparseMS(int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

getScanlineSparseMS(int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

getScans() - Method in class maltcms.datastructures.ms.Chromatogram1D

getScans() - Method in class maltcms.datastructures.ms.Chromatogram2D

getScansPerModulation() - Method in class maltcms.datastructures.caches.AScanLineCache

Getter.

getScansPerModulation() - Method in interface maltcms.datastructures.caches.IScanLine

Getter.

getScansPerModulation() - Method in class maltcms.datastructures.caches.ScanLineCache

Getter.

getScansPerModulation() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Getter.

getScansPerModulation() - Method in class maltcms.datastructures.caches.SparseScanLineCache

Getter.

getScore() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Gets the value of the score property.

getScore() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the score property.

getScore() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the score property.

getScoreType() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Gets the value of the scoreType property.

getScoreType() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the scoreType property.

getScoreType() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the scoreType property.

getSearchEngine() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Gets the value of the searchEngine property.

getSearchEngineVersion() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Gets the value of the searchEngineVersion property.

getSearchParameters() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Gets the value of the searchParameters property.

getSecondColumnScanAcquisitionTime() - Method in interface maltcms.datastructures.ms.IScan2D

getSecondColumnScanAcquisitionTime() - Method in class maltcms.datastructures.ms.Scan2D

getSecondColumnScanAcquisitionTimeUnit() - Method in class maltcms.datastructures.ms.Chromatogram2D

getSecondColumnScanAcquisitionTimeUnit() - Method in interface maltcms.datastructures.ms.IChromatogram2D

getSecondColumnScanIndex() - Method in interface maltcms.datastructures.ms.IScan2D

getSecondColumnScanIndex() - Method in class maltcms.datastructures.ms.Scan2D

getSecondRetTime() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getSecondScanIndex() - Method in class maltcms.datastructures.peak.Peak2D

getSeedIntensity() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getSeedMS() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getSeedPoint() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

getSelectedDomainVariable() - Method in class maltcms.ui.charts.VariableSelectionPanel

getSelectedValuesVariable() - Method in class maltcms.ui.charts.VariableSelectionPanel

getSensitivity() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getSensitivity() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getSeq1() - Method in class smueller.alignment.Alignment

getSeq2() - Method in class smueller.alignment.Alignment

getSequence() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Gets the value of the sequence property.

getSequence() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the sequence property.

getSequence() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the sequence property.

getShape() - Method in class maltcms.datastructures.array.DenseArray

getShape() - Method in interface maltcms.datastructures.array.IArrayD2Byte

getShape() - Method in interface maltcms.datastructures.array.IArrayD2Double

getShape() - Method in class maltcms.datastructures.array.PartitionedArray

getShape() - Method in class maltcms.datastructures.array.Sparse

getShape() - Method in class maltcms.datastructures.array.SparseArray

getShape() - Method in class maltcms.datastructures.array.TiledArray

getShortName() - Method in interface maltcms.datastructures.ms.IMetabolite

getShortName() - Method in class maltcms.datastructures.ms.Metabolite

getSignificanceThreshold() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Gets the value of the significanceThreshold property.

getSignificanceThreshold() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the significanceThreshold property.

getSignificanceThreshold() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the significanceThreshold property.

getSim() - Method in class maltcms.datastructures.peak.Peak2D

Getter.

getSimilaritiesAboveThreshold() - Method in class maltcms.db.predicates.metabolite.MSimilarityPredicate

getSimilarity(Peak) - Method in class maltcms.datastructures.peak.Peak

getSimilarityForPeaks(String, String) - Method in class maltcms.datastructures.peak.Clique

getSimilarityForPeaks(IFileFragment, IFileFragment) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getSimilarityForPeaks(String, String) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

getSize() - Method in class maltcms.datastructures.alignment.DefaultPairSet

getSize() - Method in class maltcms.datastructures.array.Sparse

getSize() - Method in class maltcms.datastructures.cluster.ACluster

getSize() - Method in interface maltcms.datastructures.cluster.ICluster

getSize() - Method in class maltcms.datastructures.ms.Experiment1D

getSize() - Method in class maltcms.datastructures.ridge.Ridge

getSizeForFlattenedArray(Array) - Static method in class maltcms.tools.ArrayTools

Returns the number of elements required for a one-dimensional representation of multidimensional array.

getSkip() - Method in class maltcms.io.csv.CSVReader

getSkippedLines() - Method in class maltcms.io.csv.CSVReader

getSnrValues() - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet

getSoftware() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

Gets the value of the software property.

getSoftware() - Method in class maltcms.io.xml.mzData.DataProcessingType

Gets the value of the software property.

getSortedjavarray1() - Method in class smueller.datastructure.SortedJavArrays

getSortedjavarray2() - Method in class smueller.datastructure.SortedJavArrays

getSorti() - Static method in class smueller.SymbolicRepresentationAlignment

getSource() - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Gets the value of the source property.

getSourceFile() - Method in class maltcms.io.xml.mzData.AdminType

Gets the value of the sourceFile property.

getSourceFiles() - Method in class maltcms.datastructures.ms.Experiment1D

getSourceFilesVarName() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getSourceFilesVarName() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getSP() - Method in interface maltcms.datastructures.ms.IMetabolite

getSP() - Method in class maltcms.datastructures.ms.Metabolite

getSparseMassSpectra(int, int) - Method in class maltcms.datastructures.caches.CachedScanLineList

getSparseMassSpectra(Point) - Method in class maltcms.datastructures.caches.CachedScanLineList

getSparseMassSpectra(int, int) - Method in interface maltcms.datastructures.caches.IScanLine

getSparseMassSpectra(Point) - Method in interface maltcms.datastructures.caches.IScanLine

getSparseMassSpectra(int, int) - Method in class maltcms.datastructures.caches.ScanLineCache

getSparseMassSpectra(Point) - Method in class maltcms.datastructures.caches.ScanLineCache

getSparseMassSpectra(int, int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

getSparseMassSpectra(Point) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

getSparseMassSpectra(int, int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

getSparseMassSpectra(Point) - Method in class maltcms.datastructures.caches.SparseScanLineCache

getSparseScanLineCache(IFileFragment) - Static method in class maltcms.datastructures.caches.ScanLineCacheFactory

getSpecificity() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getSpecificity() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getSpectrum() - Method in class maltcms.io.xml.mzData.MzData.SpectrumList

Gets the value of the spectrum property.

getSpectrumDesc() - Method in class maltcms.io.xml.mzData.SpectrumType

Gets the value of the spectrumDesc property.

getSpectrumInstrument() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType

Gets the value of the spectrumInstrument property.

getSpectrumList() - Method in class maltcms.io.xml.mzData.MzData

Gets the value of the spectrumList property.

getSpectrumRef() - Method in class maltcms.io.xml.mzData.PrecursorType

Gets the value of the spectrumRef property.

getSpectrumReference() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the spectrumReference property.

getSpectrumReference() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the spectrumReference property.

getSpectrumSettings() - Method in class maltcms.io.xml.mzData.SpectrumDescType

Gets the value of the spectrumSettings property.

getSpectrumType() - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Gets the value of the spectrumType property.

getSquaredDiff(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator

getSquaredDiff(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator

NaN's are treated as 0, giving a large distance for x!

getSquaredDiff(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.IFeatureVectorComparator

getSquaredDiff(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator

NaN's are treated as 0, giving a large distance for x!

getStand() - Static method in class smueller.SymbolicRepresentationAlignment

getStartTimeColumn(Sheet) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getStates() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

getStates() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

getStats() - Method in class maltcms.datastructures.ms.Experiment1D

getStatsMap() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

getStatus() - Method in class maltcms.ui.charts.JFreeChartViewer

getStdDevOfDistanceToCentroid(Peak) - Method in class maltcms.datastructures.peak.Clique

getString() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the string property.

getStringFromFile(File) - Static method in class net.sf.maltcms.apps.DTWNew

getSubordinate() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the subordinate property.

getSupDataArrayBinaryOrSupDataArray() - Method in class maltcms.io.xml.mzData.SpectrumType

Gets the value of the supDataArrayBinaryOrSupDataArray property.

getSupDataArrayRef() - Method in class maltcms.io.xml.mzData.SupDescType

Gets the value of the supDataArrayRef property.

getSupDataDesc() - Method in class maltcms.io.xml.mzData.SupDescType

Gets the value of the supDataDesc property.

getSupDesc() - Method in class maltcms.io.xml.mzData.SpectrumType

Gets the value of the supDesc property.

getSupSourceFile() - Method in class maltcms.io.xml.mzData.SupDescType

Gets the value of the supSourceFile property.

getSymbolicPath() - Method in class maltcms.tools.PathTools

getTableHeader() - Method in class maltcms.db.ui.MetaboliteViewModel

getTarget() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getTargetContainer() - Method in class maltcms.ui.charts.PlotRunner

getTaskId() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITask

getTaskId() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

getTaskInputs() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITaskResult

getTaskInputs() - Method in class net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult

getTaskOutputs() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITaskResult

getTaskOutputs() - Method in class net.sf.maltcms.evaluation.spi.tasks.maltcms.DefaultTaskResult

getTaxonomy() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the taxonomy property.

getTemperatureProgrammedKovatsIndex(double) - Method in class maltcms.datastructures.peak.RetentionIndexCalculator

getTIC(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getTIC(IFileFragment, int) - Static method in class maltcms.tools.MaltcmsTools

getTile(int, int) - Method in class maltcms.datastructures.array.TiledArray

getTime() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the time property.

getTimeUnit() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

getTimeUnit() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getTitle() - Method in class maltcms.ui.charts.AChart

getTitle() - Method in class maltcms.ui.charts.AlignmentMapChart

getTitle() - Method in class maltcms.ui.charts.BHeatMapChart

getTitle() - Method in class maltcms.ui.charts.CombinedDomainXYChart

getTitle() - Method in class maltcms.ui.charts.HeatMapChart

getTitle() - Method in class maltcms.ui.charts.MassSpectrumPlot

getTitle() - Method in class maltcms.ui.charts.PlotRunner

getTitle() - Method in class maltcms.ui.charts.SpiderWebChart

getTitle() - Method in class maltcms.ui.charts.XYChart

getTitle() - Method in class maltcms.ui.charts.XYZChart

getTn() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getTN() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getTn() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getTn() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getToolEntities() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getToolEntities() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getToolEntityGroup() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getToolEntityGroup() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getToolname() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getToolName() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getTopKIndicesOfMaxIntensity(Array, int) - Static method in class maltcms.tools.MaltcmsTools

getTotalIntensity() - Method in interface maltcms.datastructures.ms.IScan

getTotalIntensity() - Method in interface maltcms.datastructures.ms.IScan1D

getTotalIntensity() - Method in class maltcms.datastructures.ms.Scan1D

getTotalIntensityVarName() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

getTotalIntensityVarName() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

getTotalNumElements() - Method in class maltcms.datastructures.array.PartitionedArray

getTp() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

getTP() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getTp() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

getTp() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getTrace() - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

getTrace() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

getTs() - Method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet

getType() - Method in class maltcms.io.xml.bindings.alignment.Alignment

Gets the value of the type property.

getType() - Method in class maltcms.io.xml.bindings.annotation.AnnotationsType

Gets the value of the type property.

getType() - Method in class maltcms.io.xml.bindings.annotation.AnnotationType

Gets the value of the type property.

getType() - Method in class maltcms.io.xml.bindings.openms.featurexml.UserParam

Gets the value of the type property.

getUnassignedPeptideIdentification() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the unassignedPeptideIdentification property.

getUniqueMasses(Array) - Static method in class maltcms.tools.ArrayTools2

Sorts.

getUnit() - Method in class maltcms.io.xml.bindings.alignment.PointType.Dimension

Gets the value of the unit property.

getUnit() - Method in class maltcms.io.xml.bindings.annotation.AttributeType

Gets the value of the unit property.

getUnmatchedGroundTruthEntities() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getUnmatchedGroundTruthEntities() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getUnmatchedToolEntities() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

getUnmatchedToolEntities() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

getUpperBound() - Method in class maltcms.ui.charts.GradientPaintScale

getUri() - Method in class maltcms.io.xml.bindings.alignment.ResourceType

Gets the value of the uri property.

getUri() - Method in class maltcms.io.xml.bindings.annotation.ResourceType

Gets the value of the uri property.

getURI() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the uri property.

getUsedIndices() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getUsedMasses(IFileFragment, String) - Static method in class maltcms.tools.ArrayTools2

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.FixedModification

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.VariableModification

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the userParam property.

getUserParam() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Gets the value of the userParam property.

getValue() - Method in class maltcms.io.xml.bindings.alignment.PointType.Dimension

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.bindings.annotation.AttributeType

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint.Hposition

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model.Param

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Position

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Quality

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.bindings.openms.featurexml.UserParam

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.mzData.CvParamType

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Gets the value of the value property.

getValue() - Method in class maltcms.io.xml.mzData.UserParamType

Gets the value of the value property.

getValueAt(int, int) - Method in class maltcms.db.ui.MetaboliteViewModel

getVariableModification() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Gets the value of the variableModification property.

getVariableName() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

getVariance() - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

getVersion() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.Software

Gets the value of the version property.

getVersion() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Gets the value of the version property.

getVersion() - Method in class maltcms.io.xml.mzData.CvLookupType

Gets the value of the version property.

getVersion() - Method in class maltcms.io.xml.mzData.MzData

Gets the value of the version property.

getVersion() - Method in class maltcms.io.xml.mzData.SoftwareType

Gets the value of the version property.

getVerticalNeighborsInRadius(Point2D, double) - Method in class maltcms.datastructures.quadTree.QuadTree

getVisibleTableHeader() - Method in class maltcms.db.ui.MetaboliteViewModel

getWarpPath(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

getWeight(String) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

getWeight(String) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

getWorkbook(File) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

getWorkflow() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

getWorkflow() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getWorkflow() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getWorkflow() - Method in class maltcms.io.misc.StatsWriter

getWorkflow() - Method in class maltcms.statistics.LogDeltaEvaluation

getWorkflow() - Method in class maltcms.statistics.OneWayPeakAnova

getWorkflowSlot() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

getWorkflowSlot() - Method in class maltcms.commands.fragments.alignment.CenterStarAlignment

getWorkflowSlot() - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

getWorkflowSlot() - Method in class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment

getWorkflowSlot() - Method in class maltcms.commands.fragments.assignment.EIMSDBMetaboliteAssignment

getWorkflowSlot() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

getWorkflowSlot() - Method in class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.ANDIChromImporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.ANDIMSExporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.MSPExporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.ObiWarplmataExporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.PeakAreaTableExporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.TICPeakListImporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.io.VariableDataExporter

getWorkflowSlot() - Method in class maltcms.commands.fragments.peakfinding.CwtEicPeakFinder

getWorkflowSlot() - Method in class maltcms.commands.fragments.peakfinding.CwtTicPeakFinder

getWorkflowSlot() - Method in class maltcms.commands.fragments.peakfinding.EICPeakFinder

getWorkflowSlot() - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

getWorkflowSlot() - Method in class maltcms.commands.fragments.preprocessing.DefaultVarLoader

getWorkflowSlot() - Method in class maltcms.commands.fragments.preprocessing.DenseArrayProducer

getWorkflowSlot() - Method in class maltcms.commands.fragments.preprocessing.MassFilter

getWorkflowSlot() - Method in class maltcms.commands.fragments.spectratyping.VBetaFamilyComparison

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.EICHeatmapCoplot

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.MZIDistributionVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments.visualization.TICHeatmapCoplot

getWorkflowSlot() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

getWorkflowSlot() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

getWorkflowSlot() - Method in class maltcms.commands.fragments.warp.PathWarp

getWorkflowSlot() - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarProducer

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarVis

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.ModulationExtractor

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator

Deprecated.

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.testing.Alignment2D

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.visualization.DeltaMasses

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.visualization.GradientVisualizer

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.warp.CreateHorizontalTicVector

getWorkflowSlot() - Method in class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer

getWorkflowSlot() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

getWorkflowSlot() - Method in class maltcms.datastructures.fragments.PairwiseDistances

getWorkflowSlot() - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

getWorkflowSlot() - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

getWorkflowSlot() - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.AnchorExporter

getWorkflowSlot() - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter

getWorkflowSlot() - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.XmlAlignmentWriter

getWorkflowSlot() - Method in class maltcms.experimental.bipace.peakCliqueAlignment.PeakSimilarityVisualizer

getWorkflowSlot() - Method in class maltcms.io.csv.CSVWriter

getWorkflowSlot() - Method in class maltcms.io.misc.StatsWriter

getWorkflowSlot() - Method in class maltcms.statistics.LogDeltaEvaluation

getWorkflowSlot() - Method in class maltcms.statistics.OneWayPeakAnova

getWorkflowSlot() - Method in class smueller.SymbolicRepresentationAlignment

getWorkingDirectory() - Method in interface net.sf.maltcms.evaluation.api.tasks.ITask

getWorkingDirectory() - Method in class net.sf.maltcms.evaluation.spi.tasks.Task

getXAxisLabel() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

getXcaliburPeaks(Creator, ObjectContainer, String...) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

getXYDataSeries(double[]) - Static method in class maltcms.tools.JFreeChartTools

getXYDataset(double[], String) - Static method in class maltcms.tools.JFreeChartTools

getXYZDataset(List<double[]>, String) - Static method in class maltcms.tools.JFreeChartTools

getYaxis_max() - Method in class maltcms.ui.charts.AChart

getYaxis_min() - Method in class maltcms.ui.charts.AChart

getYAxisLabel() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

glue(List<Tuple2D<Array, Array>>, int) - Static method in class maltcms.tools.ArrayTools2

GradientPaintScale - Class in maltcms.ui.charts

GradientPaintScale(double[], double, double, Color[]) - Constructor for class maltcms.ui.charts.GradientPaintScale

GradientVisualizer - Class in maltcms.commands.fragments2d.visualization

Creates a gradient image of an chromatogramm using a specific distance function.

GradientVisualizer() - Constructor for class maltcms.commands.fragments2d.visualization.GradientVisualizer

Group - Class in net.sf.maltcms.evaluation.spi.xcalibur

Group(String, List<Chromatogram>) - Constructor for class net.sf.maltcms.evaluation.spi.xcalibur.Group

H

handleComments(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleData(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleDBNo(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleFileFragments(int, int, int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

handleFormula(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleLine(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleMW(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleName(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleNumPeaks(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleOneInfinite(int, double, double, double, double, Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

handleSynon(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonDate(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonID(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonMATCH(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonMPIMPID(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonName(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonRI(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonRT(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleSynonSP(String) - Method in class maltcms.db.MSPFormatMetaboliteParser

handleThreeEqual(double, double, double, Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

handleTwoEqual(double, double, double, Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

handleTwoInfinites(double, double, double, Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

handleZeroEqual(double, double, double, double, Integer, Integer, List<Tuple2DI>, StringBuffer) - Method in class maltcms.tools.PathTools

Deprecated.

hasActivePoints() - Method in class maltcms.datastructures.peak.PeakArea2D

Checks, if this snake has an not empty list of active points.

hasAttribute(Attribute) - Method in class maltcms.datastructures.ms.Experiment1D

hasAttribute(String) - Method in class maltcms.datastructures.ms.Experiment1D

hasChild(IVariableFragment) - Method in class maltcms.datastructures.ms.Experiment1D

hasChild(String) - Method in class maltcms.datastructures.ms.Experiment1D

hasChildren(IVariableFragment...) - Method in class maltcms.datastructures.ms.Experiment1D

hasChildren(String...) - Method in class maltcms.datastructures.ms.Experiment1D

hashCode() - Method in class maltcms.datastructures.cluster.Clique

hashCode() - Method in class maltcms.datastructures.peak.Clique

hashCode() - Method in class maltcms.datastructures.peak.Peak

hashCode() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

hashCode() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

hashCode() - Method in class net.sf.maltcms.evaluation.api.Category

hashCode() - Method in class net.sf.maltcms.evaluation.api.classification.Category

hashCode() - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

hashCode() - Method in class net.sf.maltcms.evaluation.api.EntityGroup

hashCode() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

hashCode() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

hasNext() - Method in class net.sf.maltcms.evaluation.spi.BeansXmlGenerator

HeatMapChart - Class in maltcms.ui.charts

Creates a chart with labeled domain axis, displaying a heatmap.

HeatMapChart(BufferedImage, String, String, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>, String) - Constructor for class maltcms.ui.charts.HeatMapChart

HEIGHT_DEFAULT - Static variable in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

hyperlinkUpdate(HyperlinkEvent) - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

hyperlinkUpdate(HyperlinkEvent) - Method in class maltcms.ui.wizard.PipelineWizard

I

IAggregatePredicateFactory<T> - Interface in maltcms.db.predicates.metabolite

IAlignment - Interface in maltcms.commands.distances.dtwng

IAnchor - Interface in maltcms.datastructures.ms

Interface for alignment anchors.

IArrayD2Byte - Interface in maltcms.datastructures.array

Interface abstraction of 2-dimensional arrays storing double values.

IArrayD2Double - Interface in maltcms.datastructures.array

Interface abstraction of 2-dimensional arrays storing double values.

IArraySimilarity - Interface in maltcms.math.functions

Interface to define classes, comparing arrays, especially mass spectra by some function and returning a generic type as result.

IBaselineEstimator - Interface in maltcms.commands.fragments.peakfinding.ticPeakFinder

IBidirectionalBestHit - Interface in maltcms.commands.fragments2d.peakfinding.bbh

Interface for an BBH algorithm used by SeededRegionGrowing.

IChromatogram - Interface in maltcms.datastructures.ms

Interface representing a Chromatogram.

IChromatogram1D - Interface in maltcms.datastructures.ms

Interface representing a 1-dimensional chromatogram.

IChromatogram2D - Interface in maltcms.datastructures.ms

Interface representing a 2-dimensional chromatogram.

IClique<T extends IFeatureVector> - Interface in maltcms.datastructures.cluster

ICliqueMemberCriterion<T extends IFeatureVector> - Interface in maltcms.datastructures.cluster

ICliqueUpdater<T extends IFeatureVector> - Interface in maltcms.datastructures.cluster

ICluster - Interface in maltcms.datastructures.cluster

Interface for general, n-ary clusters.

IClusteringAlgorithm - Interface in maltcms.commands.fragments.cluster

ID - Variable in class maltcms.db.ui.MetaboliteViewModel

IDBQuery<T extends com.db4o.query.Predicate<G>,G> - Interface in maltcms.db

Ident2DTWVisualizer - Class in maltcms.commands.fragments2d.warp.visualization

Basically the same as Default2DTWVisualizer but dont uses the warp path.

Ident2DTWVisualizer() - Constructor for class maltcms.commands.fragments2d.warp.visualization.Ident2DTWVisualizer

IdentityNodeBuilder - Class in maltcms.commands.distances.dtwng

IdentityNodeBuilder() - Constructor for class maltcms.commands.distances.dtwng.IdentityNodeBuilder

IDtwSimilarityFunction - Interface in maltcms.commands.distances

Interface to define classes, comparing arrays, especially mass spectra by some function and returning a double value as result.

IDynamicTimeWarp - Interface in maltcms.commands.distances.dtw

Refinement of PairwiseFeatureSequenceSimilarity, adding necessary methods for alignment with DTW.

IExperiment - Interface in maltcms.datastructures.ms

Interface representing an experiment.

IExperiment1D - Interface in maltcms.datastructures.ms

Interface representing an experiment containing a 1-dimensional chromatogram.

IExperiment2D - Interface in maltcms.datastructures.ms

Interface representing a 2-dimensional chromatogram.

IFeatureVector - Interface in maltcms.datastructures.array

IFeatureVectorComparator - Interface in net.sf.maltcms.evaluation.api.classification

IFeatureVectorComparator - Interface in net.sf.maltcms.evaluation.api

IFileFragmentModifier - Interface in maltcms.datastructures

ImagePanel - Class in maltcms.experimental.ui

ImagePanel() - Constructor for class maltcms.experimental.ui.ImagePanel

ImageTools - Class in maltcms.tools

Utility class concerned with creation and saving of images.

ImageTools() - Constructor for class maltcms.tools.ImageTools

IMatchPredicate<T> - Interface in maltcms.db.predicates

IMetabolite - Interface in maltcms.datastructures.ms

Interface representing a Metabolite.

ImpaxsExecution - Class in maltcms.mpaxs

ImpaxsExecution() - Constructor for class maltcms.mpaxs.ImpaxsExecution

importXLS(File, int) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

IMutableFeatureVector - Interface in maltcms.datastructures.array

indexArray(int, int) - Static method in class maltcms.tools.ArrayTools

Create an index array with given size, whose integer indexing begins at begin_index.

init(List<IFeatureVector>, List<IFeatureVector>, IArrayD2Double, IArrayD2Double, TwoFeatureVectorOperation) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

init(List<IFeatureVector>, List<IFeatureVector>, IArrayD2Double, IArrayD2Double, TwoFeatureVectorOperation) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

init(double[][], String[], TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

init(IFileFragment, TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

init(IFileFragment, TupleND<IFileFragment>) - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

init(double[][], String[], TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

initArrays(int, int, Area, ArrayInt.D1, ArrayInt.D1, ArrayInt.D1) - Static method in class maltcms.datastructures.array.PartitionedArray

initClassLoader(String[]) - Method in class net.sf.maltcms.apps.Maltcms

initRandom() - Static method in class maltcms.tools.ArrayTools

initRandom(long) - Static method in class maltcms.tools.ArrayTools

inRange(int, int) - Method in class maltcms.datastructures.array.DenseArray

inRange(int, int) - Method in interface maltcms.datastructures.array.IArrayD2Byte

inRange(int, int) - Method in interface maltcms.datastructures.array.IArrayD2Double

inRange(int, int) - Method in class maltcms.datastructures.array.PartitionedArray

inRange(int, int) - Method in class maltcms.datastructures.array.SparseArray

inRange(int, int) - Method in class maltcms.datastructures.array.TiledArray

insertRandomGauss(List<Array>, int, int, int) - Static method in class maltcms.tools.ArrayTools

InstrumentDescriptionType - Class in maltcms.io.xml.mzData

Description of the components of the mass spectrometer used Java class for instrumentDescriptionType complex type.

InstrumentDescriptionType() - Constructor for class maltcms.io.xml.mzData.InstrumentDescriptionType

InstrumentDescriptionType.AnalyzerList - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

InstrumentDescriptionType.AnalyzerList() - Constructor for class maltcms.io.xml.mzData.InstrumentDescriptionType.AnalyzerList

integrate(Peak2D, IFileFragment, List<Array>, IWorkflow) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakIntegration

Integrate the peak area and adds the sum to the PeakArea.

integrate(Peak2D, IFileFragment, List<Array>, IWorkflow) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakIntegration

Integrate the peak area and adds the sum to the PeakArea.

integrate(Array) - Static method in class maltcms.tools.ArrayTools

integrate(List<Array>) - Static method in class maltcms.tools.ArrayTools

Sum over all values of all arrays within a list.

intervalAdded(ListDataEvent) - Method in class maltcms.ui.wizard.AnchorDefinitionPane

intervalRemoved(ListDataEvent) - Method in class maltcms.ui.wizard.AnchorDefinitionPane

invoke(QueryCallable<T>) - Method in class maltcms.db.QueryDB

Submits the QueryCallable qf to the ExecutorService es and returns a Future to retrieve results.

invoke() - Method in class maltcms.db.QueryDB

Submits the QueryCallable constructed according to current settings and returns Future to retrieve results.

IOptimizationFunction - Interface in maltcms.commands.distances.dtwng

IPairwiseFeatureVectorSequenceOperation<RESULT> - Interface in maltcms.commands.distances.dtwng

IPeakExporter - Interface in maltcms.commands.fragments2d.peakfinding.output

Provides some methods to export relevant peak information.

IPeakFinder - Interface in maltcms.commands.fragments.peakfinding.ticPeakFinder

IPeakGroup1DProvider<T extends Peak1D> - Interface in maltcms.datastructures.peak

IPeakIdentification - Interface in maltcms.commands.fragments2d.peakfinding.output

Supports a method to identify a peak.

IPeakIntegration - Interface in maltcms.commands.fragments2d.peakfinding.output

Provides some methods to do a peak integration.

IPeakIntegrator - Interface in maltcms.commands.fragments.peakfinding.ticPeakFinder

IPeakListProvider<T extends Peak> - Interface in maltcms.experimental.bipace.api

IPeakNormalizer - Interface in maltcms.datastructures.peak.normalization

IPeakPicking - Interface in maltcms.commands.fragments2d.peakfinding.picking

IPipeline<T extends Serializable> - Interface in net.sf.maltcms.evaluation.spi.tasks.execution

IPostProcessor - Interface in net.sf.maltcms.evaluation.api

IPostProcessor - Interface in net.sf.maltcms.evaluation.api.tasks

IRecurrence - Interface in maltcms.commands.distances

Interface for classes performing a recurring operation, e.g. dynamic programming.

IRegionGrowing - Interface in maltcms.commands.fragments2d.peakfinding.srg

IRetentionInfo - Interface in maltcms.datastructures.ms

Interface extending a simple anchor, adding retention index and time info.

IRetentionInfo2D - Interface in maltcms.datastructures.ms

Interface adding retention index 2d and time 2d info.

IRidgeCost - Interface in maltcms.datastructures.ridge

isAboveThreshold(double, double) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

isAllInOneChart() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

isBidiBestHitFor(Peak) - Method in class maltcms.datastructures.peak.Peak

isBidiBestHitForAll(List<Peak>, int) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

isBidiBestHitForAll(List<Peak>, int) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder

isBidiBestHitForK(List<Peak>, int, int) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

isBidiBestHitForK(List<Peak>, int, int) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder

isBidirectionalBestHit(int, int) - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

IScalarArraySimilarity - Interface in maltcms.math.functions

IScalarSimilarity - Interface in maltcms.math.functions

The implemented similarity function should have the following properties: The maximal function value must be greater than the minimal function value, assuming that a similarity between two scalars is maximal iff both entities are identical/equal and minimal iff they are completely unrelated and that increasing similarity is reflected by a greater value of the function.

IScan - Interface in maltcms.datastructures.ms

Interface representing a Scan (usually an MS scan).

IScan1D - Interface in maltcms.datastructures.ms

IScan1DProvider - Interface in maltcms.datastructures.ms

IScan2D - Interface in maltcms.datastructures.ms

IScan2DProvider - Interface in maltcms.datastructures.ms

isCandidate(int, double[], int) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

isCandidate(double, double, double) - Method in class maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask

IScanLine - Interface in maltcms.datastructures.caches

Interface for all scan line data holder.

IScanProvider<T extends IScan> - Interface in maltcms.datastructures.ms

Interface giving access to specific scans within an experiment.

isCaseInsensitiveMatching() - Method in class maltcms.db.predicates.metabolite.MStringMatchPredicate

isDone() - Method in class smueller.alignment.AlignedPairVector

isEmpty() - Method in class maltcms.datastructures.peak.FiFoQueue

isEmpty() - Method in class maltcms.datastructures.quadTree.QuadTree

isEmpty() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

isExitOnException() - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

isFirstBidiBestHitForRest(List<Peak>, int) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

isFirstBidiBestHitForRest(List<Peak>, int) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder

isFirstLineHeaders() - Method in class maltcms.io.csv.CSVReader

isFN(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator

isFN(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator

isFN(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.IFeatureVectorComparator

isFN(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator

isFP(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator

isFP(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator

isFP(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.IFeatureVectorComparator

isFP(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator

isHeadless() - Method in class maltcms.ui.charts.PlotRunner

isHigherScoreBetter() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Gets the value of the higherScoreBetter property.

isHigherScoreBetter() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Gets the value of the higherScoreBetter property.

isHigherScoreBetter() - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Gets the value of the higherScoreBetter property.

isIgnoreNegativeInfinity() - Method in class maltcms.commands.scanners.ArrayStatsScanner

isIgnorePositiveInfinity() - Method in class maltcms.commands.scanners.ArrayStatsScanner

isIndexed() - Method in class maltcms.io.xml.mzData.SupDataType

Gets the value of the indexed property.

isIsAlignmentReference() - Method in class maltcms.io.xml.bindings.alignment.MappedPointsType

Gets the value of the isAlignmentReference property.

isIsCompleteMap() - Method in class maltcms.io.xml.bindings.alignment.Alignment

Gets the value of the isCompleteMap property.

isLog() - Method in class maltcms.commands.filters.array.NormalizationFilter

isMassWithinEpsilon(double, double, double) - Static method in class maltcms.tools.MaltcmsTools

isMaxMass(Array, Array, double, double) - Static method in class maltcms.tools.MaltcmsTools

Determine, whether the mass with maximum intensity within this scan is the same (within epsilon) of maxMass.

isMerged() - Method in class maltcms.datastructures.peak.PeakArea2D

isMinCandidate(int, double[], int) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

isMinimize() - Method in class maltcms.commands.distances.dtwng.FeatureVectorDtwSimilarity

isMinimize() - Method in class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation

isMinimize() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

isMinimize() - Method in class maltcms.datastructures.fragments.PairwiseDistances

isMinimize() - Method in class maltcms.experimental.operations.MSPeaklistAlignment

isMinimizeDist() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

isMinimizing() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

isMinimum(double, double, double) - Static method in class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

isModified() - Method in class maltcms.datastructures.ms.Experiment1D

isNavigateToResults() - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

isNormalizeByMapWeights() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

isNormalizeGlobal() - Method in class maltcms.commands.filters.array.NormalizationFilter

isPairwise() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

isPairwiseWithFirst() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

isRunGui() - Method in class net.sf.maltcms.apps.Maltcms

isSaveCDM() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

isSaveGraphics() - Method in class maltcms.ui.charts.PlotRunner

isSavePWDM() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

isSerializeJFreeChart() - Method in class maltcms.ui.charts.PlotRunner

isSizeOverride() - Method in class maltcms.ui.charts.PlotRunner

isSkipCommentLines() - Method in class maltcms.io.csv.CSVReader

isStop() - Method in class maltcms.ui.charts.PlotRunner

isSubstractStartTime() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

isSubstractStartTime() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

isTN(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator

isTN(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator

isTN(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.IFeatureVectorComparator

isTN(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator

isTP(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.classification.IFeatureVectorComparator

isTP(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator

isTP(IFeatureVector, IFeatureVector) - Method in interface net.sf.maltcms.evaluation.api.IFeatureVectorComparator

isTP(IFeatureVector, IFeatureVector) - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator

ITask<T extends Serializable> - Interface in net.sf.maltcms.evaluation.api.tasks

ITaskResult - Interface in net.sf.maltcms.evaluation.api.tasks

Created by IntelliJ IDEA.

iterator() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

iterator() - Method in class maltcms.datastructures.alignment.DefaultPairSet

iterator() - Method in class maltcms.datastructures.array.PartitionedArray

iterator() - Method in class maltcms.datastructures.ms.Chromatogram1D

This iterator acts on the underlying collection of scans in Chromatogram1D, so be careful with concurrent access / modification!

iterator() - Method in class maltcms.datastructures.ms.Chromatogram2D

This iterator acts on the underlying collection of scans in Chromatogram1D, so be careful with concurrent access / modification!

iterator() - Method in class maltcms.datastructures.ms.Experiment1D

iterator() - Method in class maltcms.datastructures.peak.FiFoQueue

iterator() - Method in class maltcms.datastructures.peak.Peak1D

iterator() - Method in class maltcms.datastructures.peak.Peak1DGroup

iterator() - Method in class maltcms.datastructures.quadTree.QuadTree

iterator() - Method in class net.sf.maltcms.evaluation.spi.BeansXmlGenerator

ITreatmentGroup<T extends IChromatogram> - Interface in maltcms.datastructures.ms

IVisualization - Interface in maltcms.commands.fragments2d.warp.visualization

This interface provies all method to be an visualization for the 2d time warp path.

IWarpInput - Interface in maltcms.datastructures.warp

Parameter Object encapsulating required data for Warp after alignment.

IWavelet - Interface in maltcms.commands.filters.array.wavelet

Interface for Wavelet implementations.

J

JFreeChartTools - Class in maltcms.tools

JFreeChartTools() - Constructor for class maltcms.tools.JFreeChartTools

JFreeChartViewer - Class in maltcms.ui.charts

JFreeChartViewer() - Constructor for class maltcms.ui.charts.JFreeChartViewer

JFreeChartViewer.ChartPanelMouseListener - Class in maltcms.ui.charts

JFreeChartViewer.ChartPanelMouseListener(ChartPanel) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartPanelMouseListener

JFreeChartViewer.ChartSerializeAction - Class in maltcms.ui.charts

JFreeChartViewer.ChartSerializeAction() - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

JFreeChartViewer.ChartSerializeAction(String, Icon) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

JFreeChartViewer.ChartSerializeAction(String) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

JFreeChartViewer.ChromatogramOpenAction - Class in maltcms.ui.charts

JFreeChartViewer.ChromatogramOpenAction() - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

JFreeChartViewer.ChromatogramOpenAction(String, Icon) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

JFreeChartViewer.ChromatogramOpenAction(String) - Constructor for class maltcms.ui.charts.JFreeChartViewer.ChromatogramOpenAction

JFreeChartViewer.FileOpenAction - Class in maltcms.ui.charts

JFreeChartViewer.FileOpenAction() - Constructor for class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

JFreeChartViewer.FileOpenAction(String, Icon) - Constructor for class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

JFreeChartViewer.FileOpenAction(String) - Constructor for class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

JFreeChartViewer.XYAnnotationAdder - Class in maltcms.ui.charts

JFreeChartViewer.XYAnnotationAdder() - Constructor for class maltcms.ui.charts.JFreeChartViewer.XYAnnotationAdder

joinFeatures(File, String, FeatureMap.FeatureList) - Static method in class net.sf.maltcms.evaluation.spi.caap.PeakFactory

joinIJtoK(int, int, int, double[]) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

joinIJtoK(int, int, int, double[]) - Method in class maltcms.commands.fragments.cluster.CompleteLinkageAlgorithm

joinIJtoK(int, int, int, double[]) - Method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

joinIJtoK(int, int, int, double[]) - Method in class maltcms.commands.fragments.cluster.SingleLinkageAlgorithm

joinIJtoK(int, int, int, double[]) - Method in class maltcms.commands.fragments.cluster.UPGMAAlgorithm

JoinScans - Class in net.sf.maltcms.apps

JoinScans() - Constructor for class net.sf.maltcms.apps.JoinScans

K

keyPressed(KeyEvent) - Method in class maltcms.db.ui.MetaboliteQueryPanel

keyReleased(KeyEvent) - Method in class maltcms.db.ui.MetaboliteQueryPanel

keySet() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

keySet() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

keyTyped(KeyEvent) - Method in class maltcms.db.ui.MetaboliteQueryPanel

L

LineVectorRenderer - Class in maltcms.ui.renderer

Extension of default VectorRenderer, omitting heads / tails of vectors.

LineVectorRenderer() - Constructor for class maltcms.ui.renderer.LineVectorRenderer

listen(IEvent<IWorkflowResult>) - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

listen(IEvent<IWorkflowResult>) - Method in class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated. Relay method, calling all registered Listeners, if an event is received from a Workflow.

load(File) - Method in class maltcms.datastructures.alignment.AlignmentFactory

load(File) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

loadAnchorsFromFiles() - Method in class maltcms.ui.wizard.AnchorDefinitionPane

LocalHostLauncher - Class in maltcms.runtime

Deprecated.

LocalHostLauncher(PropertiesConfiguration, Container, boolean) - Constructor for class maltcms.runtime.LocalHostLauncher

Deprecated.

LocalHostMaltcmsProcess - Class in maltcms.runtime

Deprecated.

LocalHostMaltcmsProcess() - Constructor for class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated.

LoessMinimaBaselineEstimator - Class in maltcms.commands.fragments.peakfinding.ticPeakFinder

Estimates a baseline from a an array of function values using local minima to fit a Loess polynomial spline function.

LoessMinimaBaselineEstimator() - Constructor for class maltcms.commands.fragments.peakfinding.ticPeakFinder.LoessMinimaBaselineEstimator

log - Static variable in class maltcms.tools.MaltcmsTools

logData(Array) - Method in class smueller.tools.Standardizer

LogDeltaEvaluation - Class in maltcms.statistics

LogDeltaEvaluation() - Constructor for class maltcms.statistics.LogDeltaEvaluation

LogFilter - Class in maltcms.commands.filters.array

Applies log10 or ln to all elements of an array.

LogFilter() - Constructor for class maltcms.commands.filters.array.LogFilter

LogFilter(boolean) - Constructor for class maltcms.commands.filters.array.LogFilter

M

MAggregatePredicate - Class in maltcms.db.predicates.metabolite

Implementation of a combined Predicate for IMetabolite instances.

MAggregatePredicate(Collection<MetabolitePredicate>) - Constructor for class maltcms.db.predicates.metabolite.MAggregatePredicate

MAggregatePredicate() - Constructor for class maltcms.db.predicates.metabolite.MAggregatePredicate

MAggregatePredicateFactory - Class in maltcms.db.predicates.metabolite

MAggregatePredicateFactory(Predicate<IMetabolite>) - Constructor for class maltcms.db.predicates.metabolite.MAggregatePredicateFactory

main(String[]) - Static method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

main(String[]) - Static method in class maltcms.commands.fragments.cluster.UPGMAAlgorithm

main(String[]) - Static method in class maltcms.commands.fragments.io.CSVAnchorReader

main(String[]) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

main(String[]) - Static method in class maltcms.commands.fragments2d.testing.DTWTest

main(String[]) - Static method in class maltcms.datastructures.caches.RingBuffer

main(String[]) - Static method in class maltcms.datastructures.peak.Peak2D

main(String[]) - Static method in class maltcms.datastructures.peak.RetentionIndexCalculator

main(String[]) - Static method in class maltcms.datastructures.quadTree.QuadTree

main(String[]) - Static method in class maltcms.db.connection.DB4oServer

main(String[]) - Static method in class maltcms.db.MetaboliteQueryDB

main(String[]) - Static method in class maltcms.db.MSPFormatMetaboliteParser

main(String[]) - Static method in class maltcms.db.RawMSQuery

main(String[]) - Static method in class maltcms.io.csv.CSVReader

main(String[]) - Static method in class maltcms.mpaxs.ImpaxsExecution

main(String[]) - Static method in class maltcms.tools.ImageTools

main(String[]) - Static method in class maltcms.tools.MaltcmsTools

main(String[]) - Static method in class maltcms.ui.charts.GradientPaintScale

main(String[]) - Static method in class maltcms.ui.charts.JFreeChartViewer

Main - Class in maltcms.ui.wizard

Main() - Constructor for class maltcms.ui.wizard.Main

main(String[]) - Static method in class maltcms.ui.wizard.Main

main(String[]) - Static method in class maltcms.ui.wizard.PipelineWizard

Goals for v0.1 Configure a pipeline for anchor finding/loading binning, preprocessing alignment visualization and allow the user to decide on the first pane, whether an existing pipeline configuration should be loaded, or if a new one should be created.

main(String[]) - Static method in class net.sf.maltcms.apps.DTWNew

main(String[]) - Static method in class net.sf.maltcms.apps.FileCopy

main(String[]) - Static method in class net.sf.maltcms.apps.JoinScans

main(String[]) - Static method in class net.sf.maltcms.apps.Maltcms

Application's main procedure.

main(String[]) - Static method in class net.sf.maltcms.apps.MetaboliteBrowser

main(String[]) - Static method in class net.sf.maltcms.apps.MSScanVisualizer

main(String[]) - Static method in class net.sf.maltcms.apps.MultipleAlignmentColumnEvaluation

main(String[]) - Static method in class net.sf.maltcms.apps.MultipleAlignmentRowEvaluation

main(String[]) - Static method in class net.sf.maltcms.evaluation.api.ClassificationPerformanceTest

main(String[]) - Static method in class net.sf.maltcms.evaluation.spi.caap.PeakFactory

main(String[]) - Static method in class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest

main(String[]) - Static method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

main(String[]) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

main(String[]) - Static method in class net.sf.maltcms.tutorials.MyWorkflow

main(String[]) - Static method in class smueller.SymbolicRepresentationAlignment

makeComparativeTICChart(AChart<XYPlot>, AChart<XYPlot>, IFileFragment, IFileFragment, String, String, Collection<XYAnnotation>, Collection<XYAnnotation>, double, double) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

makeDifferentialTICChart(List<Tuple2DI>, IFileFragment, IFileFragment, Array, Array, Array, String, String, Collection<XYAnnotation>, Collection<XYAnnotation>) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

makeImage(WritableRaster, List<Array>, int, int[][], double) - Static method in class maltcms.tools.ImageTools

makeImage(WritableRaster, List<Array>, int, int[][], double, double[]) - Static method in class maltcms.tools.ImageTools

makeImage2D(Array, int, double) - Static method in class maltcms.tools.ImageTools

makeImage2D(WritableRaster, Array, int, int[][], double, double[]) - Static method in class maltcms.tools.ImageTools

makeImage2D(Array, int) - Static method in class maltcms.tools.ImageTools

makeMapChart(AChart<XYPlot>, AChart<XYPlot>, IFileFragment, Array, Array, String, IFileFragment, IFileFragment, Collection<XYAnnotation>, Collection<XYAnnotation>) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

makeRatioTICChart(List<Tuple2DI>, IFileFragment, IFileFragment, Array, Array, Array, String, String, Collection<XYAnnotation>, Collection<XYAnnotation>) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

makeSuperimposedChart(List<Tuple2DI>, IFileFragment, IFileFragment, Array, Array, Array, String, String, Collection<XYAnnotation>, Collection<XYAnnotation>) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

Maltcms - Class in net.sf.maltcms.apps

Main Application Hook, starts with setting allowed command-line parameters.

maltcms.commands - package maltcms.commands

maltcms.commands.distances - package maltcms.commands.distances

maltcms.commands.distances.dtw - package maltcms.commands.distances.dtw

maltcms.commands.distances.dtwng - package maltcms.commands.distances.dtwng

maltcms.commands.filters - package maltcms.commands.filters

maltcms.commands.filters.array - package maltcms.commands.filters.array

maltcms.commands.filters.array.wavelet - package maltcms.commands.filters.array.wavelet

maltcms.commands.fragments.alignment - package maltcms.commands.fragments.alignment

maltcms.commands.fragments.alignment.peakCliqueAlignment - package maltcms.commands.fragments.alignment.peakCliqueAlignment

maltcms.commands.fragments.assignment - package maltcms.commands.fragments.assignment

maltcms.commands.fragments.cluster - package maltcms.commands.fragments.cluster

maltcms.commands.fragments.cluster.pairwiseDistanceCalculator - package maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

maltcms.commands.fragments.io - package maltcms.commands.fragments.io

maltcms.commands.fragments.peakfinding - package maltcms.commands.fragments.peakfinding

maltcms.commands.fragments.peakfinding.cwtEicPeakFinder - package maltcms.commands.fragments.peakfinding.cwtEicPeakFinder

maltcms.commands.fragments.peakfinding.ticPeakFinder - package maltcms.commands.fragments.peakfinding.ticPeakFinder

maltcms.commands.fragments.preprocessing - package maltcms.commands.fragments.preprocessing

maltcms.commands.fragments.preprocessing.defaultVarLoader - package maltcms.commands.fragments.preprocessing.defaultVarLoader

maltcms.commands.fragments.preprocessing.denseArrayProducer - package maltcms.commands.fragments.preprocessing.denseArrayProducer

maltcms.commands.fragments.spectratyping - package maltcms.commands.fragments.spectratyping

maltcms.commands.fragments.visualization - package maltcms.commands.fragments.visualization

maltcms.commands.fragments.warp - package maltcms.commands.fragments.warp

maltcms.commands.fragments2d.peakfinding - package maltcms.commands.fragments2d.peakfinding

maltcms.commands.fragments2d.peakfinding.bbh - package maltcms.commands.fragments2d.peakfinding.bbh

maltcms.commands.fragments2d.peakfinding.output - package maltcms.commands.fragments2d.peakfinding.output

maltcms.commands.fragments2d.peakfinding.picking - package maltcms.commands.fragments2d.peakfinding.picking

maltcms.commands.fragments2d.peakfinding.srg - package maltcms.commands.fragments2d.peakfinding.srg

maltcms.commands.fragments2d.preprocessing - package maltcms.commands.fragments2d.preprocessing

maltcms.commands.fragments2d.preprocessing.default2dVarLoader - package maltcms.commands.fragments2d.preprocessing.default2dVarLoader

maltcms.commands.fragments2d.testing - package maltcms.commands.fragments2d.testing

maltcms.commands.fragments2d.tools - package maltcms.commands.fragments2d.tools

maltcms.commands.fragments2d.visualization - package maltcms.commands.fragments2d.visualization

maltcms.commands.fragments2d.warp - package maltcms.commands.fragments2d.warp

maltcms.commands.fragments2d.warp.visualization - package maltcms.commands.fragments2d.warp.visualization

maltcms.commands.scanners - package maltcms.commands.scanners

maltcms.datastructures - package maltcms.datastructures

maltcms.datastructures.alignment - package maltcms.datastructures.alignment

maltcms.datastructures.array - package maltcms.datastructures.array

maltcms.datastructures.caches - package maltcms.datastructures.caches

maltcms.datastructures.cluster - package maltcms.datastructures.cluster

maltcms.datastructures.constraint - package maltcms.datastructures.constraint

maltcms.datastructures.feature - package maltcms.datastructures.feature

maltcms.datastructures.fragments - package maltcms.datastructures.fragments

maltcms.datastructures.ms - package maltcms.datastructures.ms

maltcms.datastructures.peak - package maltcms.datastructures.peak

maltcms.datastructures.peak.annotations - package maltcms.datastructures.peak.annotations

maltcms.datastructures.peak.normalization - package maltcms.datastructures.peak.normalization

maltcms.datastructures.quadTree - package maltcms.datastructures.quadTree

maltcms.datastructures.rank - package maltcms.datastructures.rank

maltcms.datastructures.ridge - package maltcms.datastructures.ridge

maltcms.datastructures.warp - package maltcms.datastructures.warp

maltcms.db - package maltcms.db

maltcms.db.connection - package maltcms.db.connection

maltcms.db.predicates - package maltcms.db.predicates

maltcms.db.predicates.metabolite - package maltcms.db.predicates.metabolite

maltcms.db.ui - package maltcms.db.ui

maltcms.experimental.bipace - package maltcms.experimental.bipace

maltcms.experimental.bipace.api - package maltcms.experimental.bipace.api

maltcms.experimental.bipace.datastructures.api - package maltcms.experimental.bipace.datastructures.api

maltcms.experimental.bipace.datastructures.spi - package maltcms.experimental.bipace.datastructures.spi

maltcms.experimental.bipace.peakCliqueAlignment - package maltcms.experimental.bipace.peakCliqueAlignment

maltcms.experimental.bipace.peakCliqueAlignment.io - package maltcms.experimental.bipace.peakCliqueAlignment.io

maltcms.experimental.bipace.spi - package maltcms.experimental.bipace.spi

maltcms.experimental.operations - package maltcms.experimental.operations

maltcms.experimental.ui - package maltcms.experimental.ui

maltcms.io - package maltcms.io

maltcms.io.andims - package maltcms.io.andims

maltcms.io.csv - package maltcms.io.csv

maltcms.io.misc - package maltcms.io.misc

maltcms.io.xml.bindings.alignment - package maltcms.io.xml.bindings.alignment

maltcms.io.xml.bindings.annotation - package maltcms.io.xml.bindings.annotation

maltcms.io.xml.bindings.openms.featurexml - package maltcms.io.xml.bindings.openms.featurexml

maltcms.io.xml.mzData - package maltcms.io.xml.mzData

maltcms.io.xml.mzML - package maltcms.io.xml.mzML

maltcms.io.xml.mzXML - package maltcms.io.xml.mzXML

maltcms.math.functions - package maltcms.math.functions

maltcms.math.functions.similarities - package maltcms.math.functions.similarities

maltcms.mpaxs - package maltcms.mpaxs

maltcms.runtime - package maltcms.runtime

maltcms.statistics - package maltcms.statistics

maltcms.test - package maltcms.test

maltcms.tools - package maltcms.tools

maltcms.ui - package maltcms.ui

maltcms.ui.charts - package maltcms.ui.charts

maltcms.ui.renderer - package maltcms.ui.renderer

maltcms.ui.wizard - package maltcms.ui.wizard

MaltcmsAnnotation - Class in maltcms.io.xml.bindings.annotation

Java class for anonymous complex type.

MaltcmsAnnotation() - Constructor for class maltcms.io.xml.bindings.annotation.MaltcmsAnnotation

MaltcmsAnnotationFactory - Class in maltcms.datastructures.peak

MaltcmsAnnotationFactory() - Constructor for class maltcms.datastructures.peak.MaltcmsAnnotationFactory

MaltcmsConfigurableRunnable - Class in maltcms.mpaxs

MaltcmsConfigurableRunnable() - Constructor for class maltcms.mpaxs.MaltcmsConfigurableRunnable

MaltcmsFeatureVector - Class in maltcms.datastructures.feature

FeatureVector implementation, which directly accesses the IFileFragment required at construction time.

MaltcmsFeatureVector() - Constructor for class maltcms.datastructures.feature.MaltcmsFeatureVector

MaltcmsTaskResult - Class in net.sf.maltcms.evaluation.spi.tasks.maltcms

MaltcmsTaskResult(File) - Constructor for class net.sf.maltcms.evaluation.spi.tasks.maltcms.MaltcmsTaskResult

MaltcmsTools - Class in maltcms.tools

Utility class providing many comfort methods, providing more direct access to andims compatible variables.

MaltcmsTools() - Constructor for class maltcms.tools.MaltcmsTools

MaltcmsWorkflow - Class in net.sf.maltcms.evaluation.spi.tasks.maltcms

MaltcmsWorkflow() - Constructor for class net.sf.maltcms.evaluation.spi.tasks.maltcms.MaltcmsWorkflow

mapIndex(int) - Method in class maltcms.datastructures.caches.AScanLineCache

mapIndex(int) - Method in interface maltcms.datastructures.caches.IScanLine

Map a global scan index to a Point of x,y coordinates.

mapIndex(int) - Method in class maltcms.datastructures.caches.ScanLineCache

mapIndex(int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

mapIndex(int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

MappedPointsType - Class in maltcms.io.xml.bindings.alignment

Java class for mappedPointsType complex type.

MappedPointsType() - Constructor for class maltcms.io.xml.bindings.alignment.MappedPointsType

mapPoint(int, int) - Method in class maltcms.datastructures.caches.AScanLineCache

mapPoint(Point) - Method in class maltcms.datastructures.caches.AScanLineCache

mapPoint(Point) - Method in interface maltcms.datastructures.caches.IScanLine

Map a Point to a global scan index.

mapPoint(int, int) - Method in interface maltcms.datastructures.caches.IScanLine

Map two coordinates x,y to a global scan index.

mapPoint(int, int) - Method in class maltcms.datastructures.caches.ScanLineCache

mapPoint(Point) - Method in class maltcms.datastructures.caches.ScanLineCache

mapPoint(int, int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

mapPoint(Point) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

mapPoint(int, int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

mapPoint(Point) - Method in class maltcms.datastructures.caches.SparseScanLineCache

mapSampleTable(double[], double, double) - Static method in class maltcms.tools.ImageTools

mapSampleTable(double[]) - Static method in class maltcms.tools.ImageTools

mapTanH(double, double, double) - Static method in class maltcms.tools.ImageTools

MassFilter - Class in maltcms.commands.fragments.preprocessing

MassFilter() - Constructor for class maltcms.commands.fragments.preprocessing.MassFilter

MASSSPECTRUM - Variable in class maltcms.db.ui.MetaboliteViewModel

MassSpectrumPlot - Class in maltcms.ui.charts

Will create a XYPlot bar chart.

MassSpectrumPlot(String, boolean, boolean) - Constructor for class maltcms.ui.charts.MassSpectrumPlot

Constructor to create an empty plot.

MassSpectrumPlot(String, String, Array, boolean, boolean) - Constructor for class maltcms.ui.charts.MassSpectrumPlot

Default constructor.

MassSpectrumVisualization - Class in maltcms.commands.fragments2d.visualization

Visualization for one mass spectra.

MassSpectrumVisualization() - Constructor for class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization

MassType - Enum in maltcms.io.xml.bindings.openms.featurexml

Java class for MassType.

MASSWEIGHT - Variable in class maltcms.db.ui.MetaboliteViewModel

match(IMetabolite) - Method in class maltcms.db.predicates.metabolite.MAggregatePredicate

match(IMetabolite) - Method in class maltcms.db.predicates.metabolite.MetaboliteSimilarity

match(IMetabolite) - Method in class maltcms.db.predicates.metabolite.MNumRangePredicate

match(IMetabolite) - Method in class maltcms.db.predicates.metabolite.MSimilarityPredicate

match(IMetabolite) - Method in class maltcms.db.predicates.metabolite.MStringContainsPredicate

match(IMetabolite) - Method in class maltcms.db.predicates.metabolite.MStringMatchPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.AggregatePeakPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNameFilenameRTPeakPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakNamePredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ByCreatorNamePeakPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakNamePeakPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramCreatorPeakPredicate

match(Chromatogram) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramNamePredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPeakPredicate

match(Chromatogram) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.ChromatogramPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPeakPredicate

match(Creator) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.CreatorPredicate

match(Peak) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval.PeakPredicate

matchMass(double, double, double) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

MatchPredicate<T> - Class in maltcms.db.predicates

MatchPredicate() - Constructor for class maltcms.db.predicates.MatchPredicate

matrix(int, int) - Static method in class maltcms.tools.ArrayTools

max(Array, Array) - Static method in class maltcms.tools.ArrayTools2

Return a new array where each dimension is the maximum between a and b.

max(List<Array>, List<Array>) - Static method in class maltcms.tools.ArrayTools2

Return a new list where each array is the max(a.get(i), b.get(i)).

MAXINTENSITY - Variable in class maltcms.db.ui.MetaboliteViewModel

MAXINTNORM - Variable in class maltcms.db.ui.MetaboliteViewModel

MAXMASS - Variable in class maltcms.db.ui.MetaboliteViewModel

MaxSortPeakPicking - Class in maltcms.commands.fragments2d.peakfinding.picking

MaxSortPeakPicking() - Constructor for class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking

MaxSortPeakPicking.PointComparator - Class in maltcms.commands.fragments2d.peakfinding.picking

MaxSortPeakPicking.PointComparator() - Constructor for class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking.PointComparator

mean(List<Array>) - Static method in class maltcms.tools.ArrayTools2

Computes a mean Array from the given list.

mean(Array) - Method in class smueller.tools.Standardizer

MeanStdDevNormalizationFilter - Class in maltcms.commands.filters.array

Normalize all values of an array given a normalization string.

MeanStdDevNormalizationFilter() - Constructor for class maltcms.commands.filters.array.MeanStdDevNormalizationFilter

MeanStdDevNormalizationFilter(double, double) - Constructor for class maltcms.commands.filters.array.MeanStdDevNormalizationFilter

MeanVarProducer - Class in maltcms.commands.fragments2d.preprocessing

Will iterate over all mass spectra and calculates mean and variance.

MeanVarProducer() - Constructor for class maltcms.commands.fragments2d.preprocessing.MeanVarProducer

MeanVarVis - Class in maltcms.commands.fragments2d.preprocessing

This class will visualize the computed mean, variance and standard deviation of every chromatogram.

MeanVarVis() - Constructor for class maltcms.commands.fragments2d.preprocessing.MeanVarVis

MedianBaselineFilter - Class in maltcms.commands.filters.array

Estimate a local baseline using a windowed median and perform baseline subtraction.

MedianBaselineFilter() - Constructor for class maltcms.commands.filters.array.MedianBaselineFilter

merge() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

merge() - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

merge(List<TreeMap<Double, Integer>>, boolean) - Static method in class maltcms.tools.ArrayTools

merge2(List<Array>, List<Array>, List<Array>, List<Array>, List<Tuple2DI>, boolean) - Static method in class maltcms.tools.ArrayTools

mergeCliques(Clique<T>, Clique<T>, HashMap<T, Clique<T>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CliqueFinder

mergePeaks(List<PeakArea2D>, IScanLine, List<ArrayDouble.D1>) - Method in class maltcms.commands.fragments2d.peakfinding.PeakSeparator

Metabolite - Class in maltcms.datastructures.ms

Concrete implementation of a Metabolite.

Metabolite() - Constructor for class maltcms.datastructures.ms.Metabolite

Metabolite(String, String, String, int, String, String, String, double, double, String, int, String, String, ArrayDouble.D1, ArrayInt.D1) - Constructor for class maltcms.datastructures.ms.Metabolite

Metabolite2D - Class in maltcms.datastructures.ms

Metabolite2D(String, String, String, int, String, String, String, double, double, String, int, String, String, ArrayDouble.D1, ArrayInt.D1, double, double, String) - Constructor for class maltcms.datastructures.ms.Metabolite2D

MetaboliteBrowser - Class in net.sf.maltcms.apps

MetaboliteBrowser() - Constructor for class net.sf.maltcms.apps.MetaboliteBrowser

MetaboliteListCellRenderer - Class in maltcms.db.ui

MetaboliteListCellRenderer() - Constructor for class maltcms.db.ui.MetaboliteListCellRenderer

MetaboliteListSelectionListener - Class in maltcms.db.ui

MetaboliteListSelectionListener(MetaboliteView, MetaboliteViewModel, JTable) - Constructor for class maltcms.db.ui.MetaboliteListSelectionListener

MetabolitePredicate - Class in maltcms.db.predicates.metabolite

MetabolitePredicate() - Constructor for class maltcms.db.predicates.metabolite.MetabolitePredicate

MetaboliteQueryAction - Class in maltcms.db.ui

MetaboliteQueryAction(String, Icon, JTextField, MetaboliteViewModel) - Constructor for class maltcms.db.ui.MetaboliteQueryAction

MetaboliteQueryAction(String, Icon, String, MetaboliteViewModel) - Constructor for class maltcms.db.ui.MetaboliteQueryAction

MetaboliteQueryDB - Class in maltcms.db

MetaboliteQueryDB(String) - Constructor for class maltcms.db.MetaboliteQueryDB

MetaboliteQueryDB(String, Predicate<IMetabolite>) - Constructor for class maltcms.db.MetaboliteQueryDB

MetaboliteQueryDB(String, String[], MAggregatePredicateFactory) - Constructor for class maltcms.db.MetaboliteQueryDB

MetaboliteQueryPanel - Class in maltcms.db.ui

MetaboliteQueryPanel(MetaboliteViewModel) - Constructor for class maltcms.db.ui.MetaboliteQueryPanel

MetaboliteSearchPreferences - Class in maltcms.db.ui

MetaboliteSimilarity - Class in maltcms.db.predicates.metabolite

MetaboliteSimilarity(IScan, double, int, boolean) - Constructor for class maltcms.db.predicates.metabolite.MetaboliteSimilarity

MetaboliteSimilarity(Array, Array, double, int, boolean) - Constructor for class maltcms.db.predicates.metabolite.MetaboliteSimilarity

MetaboliteSimilarity(IMetabolite, double, int, boolean) - Constructor for class maltcms.db.predicates.metabolite.MetaboliteSimilarity

MetaboliteView - Class in maltcms.db.ui

MetaboliteView(MetaboliteViewModel) - Constructor for class maltcms.db.ui.MetaboliteView

MetaboliteViewModel - Class in maltcms.db.ui

MetaboliteViewModel(ObjectContainer) - Constructor for class maltcms.db.ui.MetaboliteViewModel

MexicanHatWavelet - Class in maltcms.commands.filters.array.wavelet

MexicanHatWavelet() - Constructor for class maltcms.commands.filters.array.wavelet.MexicanHatWavelet

MexicanHatWaveletFilter - Class in maltcms.commands.filters.array.wavelet

MexicanHatWaveletFilter() - Constructor for class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

min(Array, Array) - Static method in class maltcms.tools.ArrayTools2

Return a new array where each dimension is the minimum between a and b.

min(List<Array>, List<Array>) - Static method in class maltcms.tools.ArrayTools2

Return a new list where each array is the min(a.get(i), b.get(i)).

mini(double, double, double) - Method in class smueller.alignment.Alignment

minimize() - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

minimize() - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

minimize() - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

Returns true, if this LDF is a distance between Arrays, false if LDF is a similarity.

minimize() - Method in class maltcms.math.functions.DtwPairwiseSimilarity

minimize() - Method in class maltcms.math.functions.DtwTimePenalizedPairwiseSimilarity

MinimumFilter - Class in maltcms.commands.filters.array

This class will set all elements smaller than minimum to zero.

MinimumFilter() - Constructor for class maltcms.commands.filters.array.MinimumFilter

MinimumFilter(double) - Constructor for class maltcms.commands.filters.array.MinimumFilter

Default constructor.

MININTENSITY - Variable in class maltcms.db.ui.MetaboliteViewModel

MININTNORM - Variable in class maltcms.db.ui.MetaboliteViewModel

MINMASS - Variable in class maltcms.db.ui.MetaboliteViewModel

MinMaxMassFinderWorker - Class in maltcms.commands.fragments.preprocessing.denseArrayProducer

MinMaxMassFinderWorker() - Constructor for class maltcms.commands.fragments.preprocessing.denseArrayProducer.MinMaxMassFinderWorker

MinMaxNormalizationFilter - Class in maltcms.commands.filters.array

Normalize all values of an array given a normalization string.

MinMaxNormalizationFilter() - Constructor for class maltcms.commands.filters.array.MinMaxNormalizationFilter

MinMaxNormalizationFilter(double, double) - Constructor for class maltcms.commands.filters.array.MinMaxNormalizationFilter

MissingPeak2D - Class in maltcms.commands.fragments2d.peakfinding.bbh

MissingPeak2D() - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

MissingPeak2D(int, int, int, int) - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

MNumRangePredicate - Class in maltcms.db.predicates.metabolite

MNumRangePredicate(Number, Number, Method) - Constructor for class maltcms.db.predicates.metabolite.MNumRangePredicate

modify(IFileFragment) - Method in class maltcms.commands.distances.dtwng.DTW

modify(IFileFragment) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

modify(IFileFragment) - Method in class maltcms.datastructures.feature.FeatureVectorList

modify(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseDistances

modify(IFileFragment) - Method in interface maltcms.datastructures.IFileFragmentModifier

modifyImageLookupTable(BufferedImage, int[][], double[], double, double, int, float) - Static method in class maltcms.tools.ImageTools

ModulationExtractor - Class in maltcms.commands.fragments2d.preprocessing

ModulationExtractor allows to subset the modulations contained in a GCxGC-MS file, by setting the global scan_index variable and the second_column_scan_index variables to their appropriate values.

ModulationExtractor() - Constructor for class maltcms.commands.fragments2d.preprocessing.ModulationExtractor

ModulationTimeEstimator - Class in maltcms.commands.fragments2d.preprocessing

Deprecated.

ModulationTimeEstimator() - Constructor for class maltcms.commands.fragments2d.preprocessing.ModulationTimeEstimator

Deprecated.

ModulationTimeEstimatorTask - Class in maltcms.commands.fragments2d.preprocessing.default2dVarLoader

ModulationTimeEstimatorTask() - Constructor for class maltcms.commands.fragments2d.preprocessing.default2dVarLoader.ModulationTimeEstimatorTask

mouseClicked(MouseEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

mouseEntered(MouseEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

mouseExited(MouseEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

mousePressed(MouseEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

mouseReleased(MouseEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

MovingAverageFilter - Class in maltcms.commands.filters.array

MovingAverageFilter() - Constructor for class maltcms.commands.filters.array.MovingAverageFilter

MovingMedianFilter - Class in maltcms.commands.filters.array

MovingMedianFilter() - Constructor for class maltcms.commands.filters.array.MovingMedianFilter

MSimilarityPredicate - Class in maltcms.db.predicates.metabolite

MSimilarityPredicate(MetaboliteSimilarity) - Constructor for class maltcms.db.predicates.metabolite.MSimilarityPredicate

MSPeaklistAlignment - Class in maltcms.experimental.operations

MSPeaklistAlignment() - Constructor for class maltcms.experimental.operations.MSPeaklistAlignment

MSPExporter - Class in maltcms.commands.fragments.io

MSPExporter() - Constructor for class maltcms.commands.fragments.io.MSPExporter

MSPFormatMetaboliteParser - Class in maltcms.db

MSPFormatMetaboliteParser() - Constructor for class maltcms.db.MSPFormatMetaboliteParser

MSScanVisualizer - Class in net.sf.maltcms.apps

MSScanVisualizer() - Constructor for class net.sf.maltcms.apps.MSScanVisualizer

MStringContainsPredicate - Class in maltcms.db.predicates.metabolite

MStringContainsPredicate(String) - Constructor for class maltcms.db.predicates.metabolite.MStringContainsPredicate

MStringMatchPredicate - Class in maltcms.db.predicates.metabolite

MStringMatchPredicate(String) - Constructor for class maltcms.db.predicates.metabolite.MStringMatchPredicate

mult(Array, Array) - Static method in class maltcms.tools.ArrayTools

Calculates A*B elementwise.

mult(Array, double) - Static method in class maltcms.tools.ArrayTools

mult(Sparse, double) - Static method in class maltcms.tools.SparseTools

Deprecated.

MultipleAlignment - Class in net.sf.maltcms.evaluation.api.alignment

MultipleAlignment() - Constructor for class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

MultipleAlignmentColumnEvaluation - Class in net.sf.maltcms.apps

MultipleAlignmentColumnEvaluation(File, File, File...) - Constructor for class net.sf.maltcms.apps.MultipleAlignmentColumnEvaluation

Creates a new Eval object given a ground truth file and an array of tool result files.

MultipleAlignmentRowEvaluation - Class in net.sf.maltcms.apps

MultipleAlignmentRowEvaluation(File, File, File...) - Constructor for class net.sf.maltcms.apps.MultipleAlignmentRowEvaluation

Creates a new Eval object given a ground truth file and an array of tool result files.

MultipleAlignmentWriter - Class in maltcms.experimental.bipace.peakCliqueAlignment.io

MultipleAlignmentWriter() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter

MultiplicationFilter - Class in maltcms.commands.filters.array

Multiply a value with all values of an array.

MultiplicationFilter() - Constructor for class maltcms.commands.filters.array.MultiplicationFilter

MultiplicationFilter(double) - Constructor for class maltcms.commands.filters.array.MultiplicationFilter

MyWorkflow - Class in net.sf.maltcms.tutorials

MyWorkflow() - Constructor for class net.sf.maltcms.tutorials.MyWorkflow

MzData - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

MzData() - Constructor for class maltcms.io.xml.mzData.MzData

MzData.Description - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

MzData.Description() - Constructor for class maltcms.io.xml.mzData.MzData.Description

MzData.SpectrumList - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

MzData.SpectrumList() - Constructor for class maltcms.io.xml.mzData.MzData.SpectrumList

MzData.SpectrumList.Spectrum - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

MzData.SpectrumList.Spectrum() - Constructor for class maltcms.io.xml.mzData.MzData.SpectrumList.Spectrum

MZDataDataSource - Class in maltcms.io.xml.mzData

MZDataDataSource() - Constructor for class maltcms.io.xml.mzData.MZDataDataSource

MZIDistributionVisualizer - Class in maltcms.commands.fragments.visualization

Plot the distribution of values looking at mz bin values.

MZIDistributionVisualizer() - Constructor for class maltcms.commands.fragments.visualization.MZIDistributionVisualizer

MziDtwWorkerFactory - Class in maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

MziDtwWorkerFactory() - Constructor for class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.MziDtwWorkerFactory

MZIDynamicTimeWarp - Class in maltcms.commands.distances.dtw

Implementation of Pairwise Dynamic-Time-Warping for time-series data with an evenly gridded array of mass over charge (mz) vs intensity for each time-point (scan).

MZIDynamicTimeWarp() - Constructor for class maltcms.commands.distances.dtw.MZIDynamicTimeWarp

MZIWarpInput - Class in maltcms.datastructures.warp

Specialization for MZIWarp, using mass spectra.

MZIWarpInput(IFileFragment, IWorkflow) - Constructor for class maltcms.datastructures.warp.MZIWarpInput

MZIWarpInput(List<Tuple2DI>, Tuple2D<List<Array>, List<Array>>, IFileFragment, IFileFragment, IFileFragment) - Constructor for class maltcms.datastructures.warp.MZIWarpInput

MZMLDataSource - Class in maltcms.io.xml.mzML

MZMLDataSource() - Constructor for class maltcms.io.xml.mzML.MZMLDataSource

MZXMLDataSource - Class in maltcms.io.xml.mzXML

MZXMLDataSource() - Constructor for class maltcms.io.xml.mzXML.MZXMLDataSource

MZXMLSaxDataSource - Class in maltcms.io.xml.mzXML

Implements IDataSource for mzXML Files.

MZXMLSaxDataSource() - Constructor for class maltcms.io.xml.mzXML.MZXMLSaxDataSource

MZXMLStaxDataSource - Class in maltcms.io.xml.mzXML

Implements IDataSource for mzXML Files.

MZXMLStaxDataSource() - Constructor for class maltcms.io.xml.mzXML.MZXMLStaxDataSource

N

NAME - Variable in class maltcms.db.ui.MetaboliteViewModel

names - Static variable in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

NeighborJoinAlgorithm - Class in maltcms.commands.fragments.cluster

Implementation of NeighborJoining by Saitou and Nei (cite...)

NeighborJoinAlgorithm() - Constructor for class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

NeighborJoinAlgorithm(double[][], String[]) - Constructor for class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

NeighborJoinAlgorithm(double[][], TupleND<IFileFragment>, PairwiseFeatureSequenceSimilarity) - Constructor for class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

nequal(double, double, double) - Static method in class maltcms.tools.PathTools

net.sf.maltcms.apps - package net.sf.maltcms.apps

net.sf.maltcms.evaluation.api - package net.sf.maltcms.evaluation.api

net.sf.maltcms.evaluation.api.alignment - package net.sf.maltcms.evaluation.api.alignment

net.sf.maltcms.evaluation.api.classification - package net.sf.maltcms.evaluation.api.classification

net.sf.maltcms.evaluation.api.tasks - package net.sf.maltcms.evaluation.api.tasks

net.sf.maltcms.evaluation.spi - package net.sf.maltcms.evaluation.spi

net.sf.maltcms.evaluation.spi.alignment - package net.sf.maltcms.evaluation.spi.alignment

net.sf.maltcms.evaluation.spi.caap - package net.sf.maltcms.evaluation.spi.caap

net.sf.maltcms.evaluation.spi.classification - package net.sf.maltcms.evaluation.spi.classification

net.sf.maltcms.evaluation.spi.hohenheim - package net.sf.maltcms.evaluation.spi.hohenheim

net.sf.maltcms.evaluation.spi.tasks - package net.sf.maltcms.evaluation.spi.tasks

net.sf.maltcms.evaluation.spi.tasks.execution - package net.sf.maltcms.evaluation.spi.tasks.execution

net.sf.maltcms.evaluation.spi.tasks.maltcms - package net.sf.maltcms.evaluation.spi.tasks.maltcms

net.sf.maltcms.evaluation.spi.xcalibur - package net.sf.maltcms.evaluation.spi.xcalibur

net.sf.maltcms.tutorials - package net.sf.maltcms.tutorials

NetcdfDataSource - Class in maltcms.io.andims

Implementation of IDataSource for Netcdf files, following the ANDI-MS/AIA standard.

NetcdfDataSource() - Constructor for class maltcms.io.andims.NetcdfDataSource

NewDistanceMatrix - Class in smueller.datastructure

NewDistanceMatrix(double[]) - Constructor for class smueller.datastructure.NewDistanceMatrix

newRowsAdded(TableModelEvent) - Method in class maltcms.db.ui.MetaboliteView

next() - Method in class net.sf.maltcms.evaluation.spi.BeansXmlGenerator

nextGaussian() - Static method in class maltcms.tools.ArrayTools

nextGID() - Method in class maltcms.datastructures.ms.Experiment1D

nextUniform() - Static method in class maltcms.tools.ArrayTools

ninf(double, double, double) - Static method in class maltcms.tools.PathTools

NodeBuilder - Class in maltcms.commands.distances.dtwng

NodeBuilder() - Constructor for class maltcms.commands.distances.dtwng.NodeBuilder

NormalizationFilter - Class in maltcms.commands.filters.array

Normalize all values of given arrays to the interval of 0..1, given min and max values.

NormalizationFilter() - Constructor for class maltcms.commands.filters.array.NormalizationFilter

NormalizationFilter(String, boolean, boolean) - Constructor for class maltcms.commands.filters.array.NormalizationFilter

normalize(Array, StatsMap, String, boolean) - Static method in class maltcms.commands.filters.array.NormalizationFilter

normalize(List<Array>, String) - Static method in class maltcms.commands.filters.array.NormalizationFilter

normalize(List<Peak2D>, Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakNormalization

normalize(List<List<Peak2D>>, List<List<Point>>, Collection<IFileFragment>) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakNormalization

normalize(Array, Array, int, Logger) - Static method in class maltcms.tools.ArrayTools2

Will create a new Array containing all missing mass bins.

normalize(List<Array>, String, boolean) - Method in class maltcms.ui.charts.AChart

normalized - Static variable in class maltcms.tools.SparseTools

Deprecated.

normalizeGlobal(List<Array>) - Static method in class maltcms.commands.filters.array.NormalizationFilter

normalizeLocalToUnitLength(List<Array>) - Static method in class maltcms.commands.filters.array.NormalizationFilter

normalizeTo(Peak2D) - Method in class maltcms.datastructures.peak.Peak2D

normalizeTo(Peak2D) - Method in class maltcms.datastructures.peak.PeakArea2D

norms - Static variable in class maltcms.commands.filters.array.SavitzkyGolayFilter

nullData(Array) - Method in class smueller.tools.Standardizer

O

ObiWarplmataExporter - Class in maltcms.commands.fragments.io

ObiWarplmataExporter() - Constructor for class maltcms.commands.fragments.io.ObiWarplmataExporter

ObjectFactory - Class in maltcms.io.xml.bindings.alignment

This object contains factory methods for each Java content interface and Java element interface generated in the maltcms.io.xml.bindings.alignment package.

ObjectFactory() - Constructor for class maltcms.io.xml.bindings.alignment.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: maltcms.io.xml.bindings.alignment

ObjectFactory - Class in maltcms.io.xml.bindings.annotation

This object contains factory methods for each Java content interface and Java element interface generated in the maltcms.io.xml.bindings.annotation package.

ObjectFactory() - Constructor for class maltcms.io.xml.bindings.annotation.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: maltcms.io.xml.bindings.annotation

ObjectFactory - Class in maltcms.io.xml.bindings.openms.featurexml

This object contains factory methods for each Java content interface and Java element interface generated in the maltcms.io.xml.bindings.openms.featurexml package.

ObjectFactory() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: maltcms.io.xml.bindings.openms.featurexml

ObjectFactory - Class in maltcms.io.xml.mzData

This object contains factory methods for each Java content interface and Java element interface generated in the maltcms.io.xml.mzData package.

ObjectFactory() - Constructor for class maltcms.io.xml.mzData.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: maltcms.io.xml.mzData

offer(E) - Method in class maltcms.datastructures.peak.FiFoQueue

oldest() - Method in class maltcms.datastructures.caches.RingBuffer

OneAffineAlignment - Class in smueller.alignment

OneAffineAlignment(IFileFragment, IFileFragment) - Constructor for class smueller.alignment.OneAffineAlignment

OneByOneRegionGrowing - Class in maltcms.commands.fragments2d.peakfinding.srg

OneByOneRegionGrowing() - Constructor for class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing

OneWayPeakAnova - Class in maltcms.statistics

OneWayPeakAnova() - Constructor for class maltcms.statistics.OneWayPeakAnova

OptimalAlignmentVector - Class in smueller.alignment

OptimalAlignmentVector() - Constructor for class smueller.alignment.OptimalAlignmentVector

P

paa(Array, int) - Static method in class smueller.tools.DimensionReduce

pairedEICs(List<Tuple2D<Double, Double>>, List<Tuple2D<Double, Double>>) - Static method in class maltcms.tools.MaltcmsTools

PairwiseAlignment - Class in maltcms.datastructures.fragments

Implementation of IFileFragmentProvider for PairwiseAlignment.

PairwiseAlignment() - Constructor for class maltcms.datastructures.fragments.PairwiseAlignment

PairwiseAlignmentMatrixVisualizer - Class in maltcms.commands.fragments.visualization

Draw the pairwise distance and/or cumulative distance matrix used for alignment.

PairwiseAlignmentMatrixVisualizer() - Constructor for class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer

PairwiseAlignmentVisualizer - Class in maltcms.commands.fragments.visualization

Plots a pairwise alignment, by displaying both time series' tics, connected by lines depicting the path obtained from alignment.

PairwiseAlignmentVisualizer() - Constructor for class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

PairwiseDistanceCalculator - Class in maltcms.commands.fragments.cluster

Calculates pariwise scores or costs between time series of possibly different lengths.

PairwiseDistanceCalculator() - Constructor for class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator

PairwiseDistanceResult - Class in maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

PairwiseDistanceResult() - Constructor for class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceResult

PairwiseDistances - Class in maltcms.datastructures.fragments

PairwiseDistances() - Constructor for class maltcms.datastructures.fragments.PairwiseDistances

PairwiseDistanceWorker - Class in maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

PairwiseDistanceWorker() - Constructor for class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.PairwiseDistanceWorker

PairwiseFeatureSequenceSimilarity - Interface in maltcms.commands.distances

Interface to allow the values of comparison of multiple arrays to also be used as a cost/score measure.

PairwiseFeatureSimilarity - Class in maltcms.commands.distances

Class used to calculate a pairwise score or cost between mass-spectra.

PairwiseFeatureSimilarity() - Constructor for class maltcms.commands.distances.PairwiseFeatureSimilarity

PairwisePeakListSimilarities - Class in maltcms.experimental.bipace.datastructures.spi

PairwisePeakListSimilarities() - Constructor for class maltcms.experimental.bipace.datastructures.spi.PairwisePeakListSimilarities

PairwiseSimilarityWorker - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

PairwiseSimilarityWorker() - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.PairwiseSimilarityWorker

ParamType - Class in maltcms.io.xml.mzData

Structure allowing the use of controlled or uncontrolled vocabulary Java class for paramType complex type.

ParamType() - Constructor for class maltcms.io.xml.mzData.ParamType

parse(File) - Method in class maltcms.db.MSPFormatMetaboliteParser

parseCommandLine(String[]) - Method in class net.sf.maltcms.apps.Maltcms

Builds the final composite configuration from all available configuration sources.

parseDouble(String) - Method in class net.sf.maltcms.evaluation.spi.hohenheim.Eval

parseMaskedMassesList(List<?>) - Static method in class maltcms.tools.MaltcmsTools

PartitionCalculator - Class in maltcms.commands.distances

PartitionCalculator(Rectangle, IArrayD2Double, ArrayDouble.D1, ArrayDouble.D1, List<Array>, List<Array>) - Constructor for class maltcms.commands.distances.PartitionCalculator

PartitionedArray - Class in maltcms.datastructures.array

Array, which has been partitioned into rectangular areas, e.g. by anchors.

PartitionedArray(int, int, ArrayInt.D1, ArrayInt.D1, ArrayInt.D1, ArrayDouble.D1, double, Area) - Constructor for class maltcms.datastructures.array.PartitionedArray

PathTools - Class in maltcms.tools

Utility class providing methods for handling of the path obtained from alignment.

PathTools() - Constructor for class maltcms.tools.PathTools

PathTools.Direction - Enum in maltcms.tools

PathWarp - Class in maltcms.commands.fragments.warp

Instead of warping one time series to the time scale of another one, warp both to their common time, given by the steps of the alignment map.

PathWarp() - Constructor for class maltcms.commands.fragments.warp.PathWarp

Peak - Class in maltcms.datastructures.peak

Shorthand class for peaks.

Peak() - Constructor for class maltcms.datastructures.peak.Peak

Peak - Class in net.sf.maltcms.evaluation.spi.xcalibur

Peak(Creator, Chromatogram, String, double, double, double, double[], double, double, RTUnit) - Constructor for class net.sf.maltcms.evaluation.spi.xcalibur.Peak

Peak1D - Class in maltcms.datastructures.peak

Peak1D() - Constructor for class maltcms.datastructures.peak.Peak1D

Peak1D(int, int, int) - Constructor for class maltcms.datastructures.peak.Peak1D

Peak1DBidiBestHitsCriterion - Class in maltcms.datastructures.cluster

Peak1DBidiBestHitsCriterion() - Constructor for class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion

Peak1DBidiBestHitsCriterion.Peak1DSimilarities - Class in maltcms.datastructures.cluster

Peak1DBidiBestHitsCriterion.Peak1DSimilarities(List<Peak1D>, IArrayD2Double) - Constructor for class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion.Peak1DSimilarities

Peak1DCliqueStatistics - Class in maltcms.experimental.bipace.datastructures.spi

Peak1DCliqueStatistics() - Constructor for class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

Peak1DGroup - Class in maltcms.datastructures.peak

Peak1DGroup(IFileFragment, int, boolean) - Constructor for class maltcms.datastructures.peak.Peak1DGroup

Peak1DGroup(Peak1D...) - Constructor for class maltcms.datastructures.peak.Peak1DGroup

Peak1DSimilarityCalculator - Class in maltcms.experimental.bipace.spi

Peak1DSimilarityCalculator() - Constructor for class maltcms.experimental.bipace.spi.Peak1DSimilarityCalculator

Peak2D - Class in maltcms.datastructures.peak

Dataholder for all important information about a peak.

Peak2D() - Constructor for class maltcms.datastructures.peak.Peak2D

Default constructor.

Peak2D - Class in maltcms.experimental.bipace.datastructures.spi

Peak2D(String, IFileFragment, int, Array, double) - Constructor for class maltcms.experimental.bipace.datastructures.spi.Peak2D

Peak2D(String, IFileFragment, int, Array, double, double, double) - Constructor for class maltcms.experimental.bipace.datastructures.spi.Peak2D

Peak2DClique - Class in maltcms.commands.fragments2d.peakfinding.bbh

Peak2DClique(String) - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

Peak2DClique(String, Collection<IFileFragment>, List<Peak2D>) - Constructor for class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

Peak2DClique - Class in maltcms.datastructures.peak

Peak2DClique(String) - Constructor for class maltcms.datastructures.peak.Peak2DClique

Peak2DClique(String, Collection<IFileFragment>, List<Peak2D>) - Constructor for class maltcms.datastructures.peak.Peak2DClique

Peak2DCliqueStatistics - Class in maltcms.experimental.bipace.datastructures.spi

Peak2DCliqueStatistics() - Constructor for class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

Peak2DSimilarityCalculator - Class in maltcms.experimental.bipace.spi

Peak2DSimilarityCalculator() - Constructor for class maltcms.experimental.bipace.spi.Peak2DSimilarityCalculator

PeakAnnotation - Class in maltcms.datastructures.peak.annotations

PeakAnnotation() - Constructor for class maltcms.datastructures.peak.annotations.PeakAnnotation

PeakArea2D - Class in maltcms.datastructures.peak

Reprensents a singel snake.

PeakArea2D(Point, Array, double, int, int) - Constructor for class maltcms.datastructures.peak.PeakArea2D

Default constructor.

PeakAreaTableExporter - Class in maltcms.commands.fragments.io

Exports aligned peak area table.

PeakAreaTableExporter() - Constructor for class maltcms.commands.fragments.io.PeakAreaTableExporter

PeakCliqueAlignment - Class in maltcms.commands.fragments.alignment

For every peak in each chromatogram, its bi-directional best hits are determined, and all bi-directional best hits are merged.

PeakCliqueAlignment() - Constructor for class maltcms.commands.fragments.alignment.PeakCliqueAlignment

peakCntAlignment(double[], double[], double[], double[]) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

PeakComparator - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

PeakComparator() - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakComparator

PeakComparator - Class in maltcms.experimental.bipace.peakCliqueAlignment

PeakComparator() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.PeakComparator

PeakExporter - Class in maltcms.commands.fragments2d.peakfinding.output

Implementation of an peak exporter.

PeakExporter() - Constructor for class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

PeakFactory - Class in maltcms.datastructures.peak

PeakFactory() - Constructor for class maltcms.datastructures.peak.PeakFactory

PeakFactory - Class in net.sf.maltcms.evaluation.spi.caap

PeakFactory() - Constructor for class net.sf.maltcms.evaluation.spi.caap.PeakFactory

PeakFileFragmentComparator - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

PeakFileFragmentComparator() - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakFileFragmentComparator

PeakFileFragmentComparator - Class in maltcms.experimental.bipace.peakCliqueAlignment

PeakFileFragmentComparator() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.PeakFileFragmentComparator

PeakFinderUtils - Class in maltcms.commands.fragments.peakfinding.ticPeakFinder

PeakFinderUtils() - Constructor for class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakFinderUtils

PeakIdentification - Class in maltcms.commands.fragments2d.peakfinding.output

Will do the identification.

PeakIdentification() - Constructor for class maltcms.commands.fragments2d.peakfinding.output.PeakIdentification

PeakIntegration - Class in maltcms.commands.fragments2d.peakfinding.output

Does the Peak Integration on basis of the unique masses.

PeakIntegration() - Constructor for class maltcms.commands.fragments2d.peakfinding.output.PeakIntegration

PeakIntegration - Enum in maltcms.datastructures.peak

PeakList<T extends Peak> - Class in maltcms.experimental.bipace

PeakList() - Constructor for class maltcms.experimental.bipace.PeakList

PeakList1DProvider - Class in maltcms.experimental.bipace.spi

PeakList1DProvider() - Constructor for class maltcms.experimental.bipace.spi.PeakList1DProvider

PeakList2DProvider - Class in maltcms.experimental.bipace.spi

PeakList2DProvider(List<Tuple2D<IFileFragment, List<Peak2D>>>) - Constructor for class maltcms.experimental.bipace.spi.PeakList2DProvider

PeakListBinaryType - Class in maltcms.io.xml.mzData

Extension of binary data group for m/z and intensity values Java class for peakListBinaryType complex type.

PeakListBinaryType() - Constructor for class maltcms.io.xml.mzData.PeakListBinaryType

PeakListBinaryType.Data - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

PeakListBinaryType.Data() - Constructor for class maltcms.io.xml.mzData.PeakListBinaryType.Data

PeakNormalization - Class in maltcms.commands.fragments2d.peakfinding.output

PeakNormalization() - Constructor for class maltcms.commands.fragments2d.peakfinding.output.PeakNormalization

PeakPositionsResultSet - Class in maltcms.commands.fragments.peakfinding.ticPeakFinder

PeakPositionsResultSet(Array, ArrayInt.D1, double[], List<Integer>, PolynomialSplineFunction) - Constructor for class maltcms.commands.fragments.peakfinding.ticPeakFinder.PeakPositionsResultSet

PeakRTFeatureVector - Class in net.sf.maltcms.evaluation.api

PeakRTFeatureVector(double) - Constructor for class net.sf.maltcms.evaluation.api.PeakRTFeatureVector

PeakRTFeatureVector - Class in net.sf.maltcms.evaluation.spi.classification

PeakRTFeatureVector(double) - Constructor for class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector

PeakRTFeatureVectorComparator - Class in net.sf.maltcms.evaluation.api.classification

PeakRTFeatureVectorComparator(double) - Constructor for class net.sf.maltcms.evaluation.api.classification.PeakRTFeatureVectorComparator

PeakRTFeatureVectorComparator - Class in net.sf.maltcms.evaluation.api

PeakRTFeatureVectorComparator(double) - Constructor for class net.sf.maltcms.evaluation.api.PeakRTFeatureVectorComparator

PeakSeparator - Class in maltcms.commands.fragments2d.peakfinding

PeakSeparator() - Constructor for class maltcms.commands.fragments2d.peakfinding.PeakSeparator

PeakSimilarityCalculator<T extends Peak> - Class in maltcms.experimental.bipace.api

PeakSimilarityCalculator() - Constructor for class maltcms.experimental.bipace.api.PeakSimilarityCalculator

PeakSimilarityVisualizer - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

PeakSimilarityVisualizer() - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakSimilarityVisualizer

PeakSimilarityVisualizer - Class in maltcms.experimental.bipace.peakCliqueAlignment

PeakSimilarityVisualizer() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.PeakSimilarityVisualizer

PeakType - Enum in maltcms.datastructures.peak

peek() - Method in class maltcms.datastructures.peak.FiFoQueue

PerformanceMetrics - Class in net.sf.maltcms.evaluation.api

PerformanceMetrics(String, int, int, int, int, int, int, int, double, HashSet<EntityGroup>, HashSet<EntityGroup>) - Constructor for class net.sf.maltcms.evaluation.api.PerformanceMetrics

PerformanceMetrics - Class in net.sf.maltcms.evaluation.spi.classification

PerformanceMetrics(String, int, int, int, int, int, int, int, double, HashSet<EntityGroup>, HashSet<EntityGroup>, HashMap<EntityGroup, EntityGroupClassificationResult>) - Constructor for class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

performTest(String, List<EntityGroup>) - Method in class net.sf.maltcms.evaluation.api.ClassificationPerformanceTest

performTest(String, List<EntityGroup>) - Method in class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformanceTest

PersonType - Class in maltcms.io.xml.mzData

Data type for operator identification information.

PersonType() - Constructor for class maltcms.io.xml.mzData.PersonType

PipelineWizard - Class in maltcms.ui.wizard

PipelineWizard() - Constructor for class maltcms.ui.wizard.PipelineWizard

PipelineWizard.CreateConfigurationAction - Class in maltcms.ui.wizard

PipelineWizard.CreateConfigurationAction() - Constructor for class maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction

PipelineWizard.CreateConfigurationAction(String, Icon) - Constructor for class maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction

PipelineWizard.CreateConfigurationAction(String) - Constructor for class maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction

PipelineWizard.EditConfigurationAction - Class in maltcms.ui.wizard

PipelineWizard.EditConfigurationAction() - Constructor for class maltcms.ui.wizard.PipelineWizard.EditConfigurationAction

PipelineWizard.EditConfigurationAction(String, Icon) - Constructor for class maltcms.ui.wizard.PipelineWizard.EditConfigurationAction

PipelineWizard.EditConfigurationAction(String) - Constructor for class maltcms.ui.wizard.PipelineWizard.EditConfigurationAction

PipelineWizard.LoadConfigurationAction - Class in maltcms.ui.wizard

PipelineWizard.LoadConfigurationAction() - Constructor for class maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction

PipelineWizard.LoadConfigurationAction(String, Icon) - Constructor for class maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction

PipelineWizard.LoadConfigurationAction(String) - Constructor for class maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction

PipelineWizard.RunConfigurationAction - Class in maltcms.ui.wizard

PipelineWizard.RunConfigurationAction() - Constructor for class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction

PipelineWizard.RunConfigurationAction(String, Icon) - Constructor for class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction

PipelineWizard.RunConfigurationAction(String) - Constructor for class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction

PlotRunner - Class in maltcms.ui.charts

Callable which returns a JFreeChart object.

PlotRunner(Plot, String, String, File) - Constructor for class maltcms.ui.charts.PlotRunner

pointListFromArrays(Array, Array) - Static method in class maltcms.tools.PathTools

Constructs List of pairs of indices from array representation.

pointListToArrays(List<Point>) - Static method in class maltcms.tools.PathTools

Constructs array representation from List of pairs of indices.

PointMapType - Class in maltcms.io.xml.bindings.alignment

Java class for pointMapType complex type.

PointMapType() - Constructor for class maltcms.io.xml.bindings.alignment.PointMapType

points - Static variable in class maltcms.commands.filters.array.SavitzkyGolayFilter

PointType - Class in maltcms.io.xml.bindings.alignment

Java class for pointType complex type.

PointType() - Constructor for class maltcms.io.xml.bindings.alignment.PointType

PointType.Dimension - Class in maltcms.io.xml.bindings.alignment

Java class for anonymous complex type.

PointType.Dimension() - Constructor for class maltcms.io.xml.bindings.alignment.PointType.Dimension

poll() - Method in class maltcms.datastructures.peak.FiFoQueue

popActivePoint() - Method in class maltcms.datastructures.peak.PeakArea2D

Pops the first active point in the active list.

pow(Array, double) - Static method in class maltcms.tools.ArrayTools

PrecursorType - Class in maltcms.io.xml.mzData

The method of precursor ion selection and activation Java class for precursorType complex type.

PrecursorType() - Constructor for class maltcms.io.xml.mzData.PrecursorType

prepareAnchors(IFileFragment) - Static method in class maltcms.tools.MaltcmsTools

prepareArraysMZIasList(IFileFragment, String, String, String, String, String) - Static method in class maltcms.tools.MaltcmsTools

prepareDenseArraysMZI(IFileFragment, IFileFragment, String, String, String, String, String, String, Double, Double, File) - Static method in class maltcms.tools.MaltcmsTools

prepareDenseArraysMZI(IFileFragment, String, String, String, String, String, String, Double, Double, File) - Static method in class maltcms.tools.MaltcmsTools

prepareEICFragments(TupleND<IFileFragment>, Class<?>, File) - Static method in class maltcms.tools.MaltcmsTools

prepareInputArraysTICasList(Tuple2D<IFileFragment, IFileFragment>) - Static method in class maltcms.tools.MaltcmsTools

prepareRow(int, int, int, int, ArrayInt.D1, ArrayInt.D1, ArrayInt.D1) - Static method in class maltcms.datastructures.array.PartitionedArray

prepareSparseMZI(IFileFragment, String, String, String, Double, Double) - Static method in class maltcms.tools.MaltcmsTools

PreprocessingPane - Class in maltcms.ui.wizard

PreprocessingPane() - Constructor for class maltcms.ui.wizard.PreprocessingPane

Creates new form PreprocessingPane

previous() - Method in class maltcms.datastructures.caches.RingBuffer

printAlignment(String, String, String) - Method in class maltcms.experimental.operations.EditDistance

Prints the alignment of Strings a and b, given an edit sequence.

printBugTrackMessage(Logger) - Static method in class net.sf.maltcms.apps.Maltcms

printCluster() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

printDistances() - Method in class maltcms.datastructures.cluster.ACluster

printDistanceToNewCluster(int, int, int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

printDistMatrix() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

printMap(String, HashMap<Integer, Integer>) - Static method in class net.sf.maltcms.apps.JoinScans

printMatrix(double[][], double[], double[]) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

printNamesMatrix() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

printPercentDone(double, long, long, Logger) - Static method in class maltcms.tools.ArrayTools

printPercentDone(double, long, long, OutputStream) - Static method in class maltcms.tools.ArrayTools

printRMatrix() - Method in class maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

printSet(Set<Integer>) - Static method in class net.sf.maltcms.apps.JoinScans

process(ITask) - Method in interface net.sf.maltcms.evaluation.api.tasks.IPostProcessor

process(ITask) - Method in class net.sf.maltcms.evaluation.spi.classification.ClassificationPerformancePostProcessor

processArrays(MZIWarpInput, IFileFragment) - Method in class maltcms.commands.fragments.warp.PathWarp

processIndexedArrays(MZIWarpInput, IFileFragment) - Method in class maltcms.commands.fragments.warp.PathWarp

processRIs(MZIWarpInput, IFileFragment, int, int, int) - Method in class maltcms.commands.fragments.warp.PathWarp

processVariables(String[], Configuration) - Method in class net.sf.maltcms.apps.Maltcms

Prepares the String[] for input to processVariableFragments.

ProductSimilarity - Class in maltcms.math.functions

ProductSimilarity() - Constructor for class maltcms.math.functions.ProductSimilarity

ProfileChromatogram1D - Class in maltcms.datastructures.ms

ProfileChromatogram1D(IFileFragment) - Constructor for class maltcms.datastructures.ms.ProfileChromatogram1D

ProgressiveTreeAlignment - Class in maltcms.commands.fragments.alignment

Implementation of progressive, tree based multiple alignment.

ProgressiveTreeAlignment() - Constructor for class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment

project2(boolean, List<Array>, List<Array>, List<Tuple2DI>, List<Array>, List<Array>, boolean) - Static method in class maltcms.tools.ArrayTools

projectToLHS(Array, List<Tuple2DI>, Array, boolean) - Static method in class maltcms.commands.fragments.warp.ChromatogramWarp2

projectToLHS(Array, List<Tuple2DI>, Array, boolean) - Static method in class maltcms.tools.ArrayTools

projectToRHS(Array, List<Tuple2DI>, Array, boolean) - Static method in class maltcms.commands.fragments.warp.ChromatogramWarp2

projectToRHS(Array, List<Tuple2DI>, Array, boolean) - Static method in class maltcms.tools.ArrayTools

propertyChange(PropertyChangeEvent) - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

provideFileFragment() - Method in class maltcms.datastructures.fragments.PairwiseAlignment

PublicMemberGetters<T> - Class in maltcms.tools

PublicMemberGetters(Class<?>) - Constructor for class maltcms.tools.PublicMemberGetters

PublicMemberGetters(Class<?>, String...) - Constructor for class maltcms.tools.PublicMemberGetters

PublicMemberGetters(T) - Constructor for class maltcms.tools.PublicMemberGetters

push(T) - Method in class maltcms.datastructures.caches.RingBuffer

put(Point2D, T) - Method in class maltcms.datastructures.quadTree.QuadTree

put(Category, AlignmentColumn) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

putAll(Map<? extends Category, ? extends AlignmentColumn>) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

putCluster(int, BinaryCluster) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

Q

Quad - Enum in maltcms.datastructures.quadTree

QuadTree<T> - Class in maltcms.datastructures.quadTree

QuadTree(Rectangle2D) - Constructor for class maltcms.datastructures.quadTree.QuadTree

QuadTree(double, double, double, double, int) - Constructor for class maltcms.datastructures.quadTree.QuadTree

QuadTreeNode<T> - Class in maltcms.datastructures.quadTree

QuadTreeNode(double, double, double, double, Tuple2D<Point2D, T>, int, int) - Constructor for class maltcms.datastructures.quadTree.QuadTreeNode

QuadTreeNodeDepthFirstVisitor<T> - Class in maltcms.datastructures.quadTree

QuadTreeNodeDepthFirstVisitor(QuadTreeNode<T>) - Constructor for class maltcms.datastructures.quadTree.QuadTreeNodeDepthFirstVisitor

QuadTreeNodeVisitor<T> - Interface in maltcms.datastructures.quadTree

QualityControl - Class in maltcms.commands.fragments2d.peakfinding

QualityControl() - Constructor for class maltcms.commands.fragments2d.peakfinding.QualityControl

QuantileSnrPeakFinder - Class in maltcms.commands.fragments.peakfinding.ticPeakFinder

QuantileSnrPeakFinder() - Constructor for class maltcms.commands.fragments.peakfinding.ticPeakFinder.QuantileSnrPeakFinder

query(Predicate<IMetabolite>) - Method in class maltcms.db.ui.MetaboliteViewModel

QueryCallable<T> - Class in maltcms.db

QueryCallable(String, Predicate<T>) - Constructor for class maltcms.db.QueryCallable

QueryDB<T> - Class in maltcms.db

QueryDB(String) - Constructor for class maltcms.db.QueryDB

QueryDB(String, Predicate<T>) - Constructor for class maltcms.db.QueryDB

QueryDB(String, String[], IAggregatePredicateFactory<T>) - Constructor for class maltcms.db.QueryDB

QueryResultListCellRenderer - Class in maltcms.db.ui

QueryResultListCellRenderer() - Constructor for class maltcms.db.ui.QueryResultListCellRenderer

R

rampToColorArray(int[][]) - Static method in class maltcms.tools.ImageTools

randomGaussian(int, double, double) - Static method in class maltcms.tools.ArrayTools

randomGaussian(int, int, double, double) - Static method in class maltcms.tools.SparseTools

Deprecated.

randomUniform(int, double, double) - Static method in class maltcms.tools.ArrayTools

randomUniform(int, int, double, double) - Static method in class maltcms.tools.SparseTools

Deprecated.

Rank<T extends Ridge> - Class in maltcms.datastructures.rank

Rank(T) - Constructor for class maltcms.datastructures.rank.Rank

Rank.ResponseComparator<T extends Ridge> - Class in maltcms.datastructures.rank

Rank.ResponseComparator() - Constructor for class maltcms.datastructures.rank.Rank.ResponseComparator

RankComparator - Class in maltcms.datastructures.rank

RankComparator(String) - Constructor for class maltcms.datastructures.rank.RankComparator

rankEICsByVariance(IFileFragment, List<Array>, int, Class<?>, File) - Static method in class maltcms.tools.MaltcmsTools

ranksByIntensity(Array) - Static method in class maltcms.tools.MaltcmsTools

ranksByIntensity(Array, double) - Static method in class maltcms.tools.MaltcmsTools

Expects intensities to be sorted in ascending order of masses.

RankSorter - Class in maltcms.datastructures.rank

RankSorter(List<Rank<Ridge>>) - Constructor for class maltcms.datastructures.rank.RankSorter

RawMSQuery - Class in maltcms.db

RawMSQuery(Tuple2D<Array, Array>) - Constructor for class maltcms.db.RawMSQuery

read(InputStream) - Method in class maltcms.io.csv.CSVReader

read(String) - Method in class maltcms.io.csv.CSVReader

readAll(IFileFragment) - Method in class maltcms.io.andims.NetcdfDataSource

readAll(IFileFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

readAll(IFileFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

readAll(IFileFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

readAll(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

readAll(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

readAll(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

readColorRamp(String) - Method in class maltcms.io.csv.ColorRampReader

readExternal(ObjectInput) - Method in class maltcms.datastructures.ms.Experiment1D

readIndexed(IVariableFragment) - Method in class maltcms.io.andims.NetcdfDataSource

readIndexed(IVariableFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

readIndexed(IVariableFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

readIndexed(IVariableFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

readIndexed(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

readIndexed(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

readIndexed(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

readIndexed2(IVariableFragment) - Method in class maltcms.io.andims.NetcdfDataSource

ReadIndexed: Read a number of (sparse) arrays written in row-compressed-storage (1D-array of values >0) Row-Compressed-Array: DATA Index array: INDEX with length k=|INDEX| => Number of arrays NOTATION: DATA[FROM,TO,STRIDE], NOTE: TO is inclusive, not up to Require: Index containing offsets into DATA, such that INDEX[0]=DATA[0] and INDEX[i]=start index of array i with 0<=i=k INDEX[i+1] = |DATA|-1 ELSE a[i] = DATA[INDEX[i],INDEX[i+1]-1] ENDIF If we only want to read a subsection of DATA, say j scans starting from scan i, we use Require: NEW_INDEX with length j FOR a=0;a= k SCAN[a] = DATA[INDEX[a],|DATA|-1] ELSE SCAN[a] = DATA[INDEX[a],INDEX[a+1]-1] ENDIF NEW_INDEX[a] = DATA[INDEX[a]]; ENDFOR

readSingle(IVariableFragment) - Method in class maltcms.io.andims.NetcdfDataSource

readSingle(IVariableFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

readSingle(IVariableFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

readSingle(IVariableFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

readSingle(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

readSingle(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

Reads a single array referenced by a IVariableFragment.

readSingle(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

Reads a single array referenced by a IVariableFragment.

readStructure(IFileFragment) - Method in class maltcms.io.andims.NetcdfDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.andims.NetcdfDataSource

readStructure(IFileFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

readStructure(IFileFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

readStructure(IFileFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

readStructure(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

readStructure(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

readStructure(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

readStructure(IVariableFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

ReBuild - Class in smueller.datastructure

ReBuild() - Constructor for class smueller.datastructure.ReBuild

recurse(double[][], int, int, double, double, double, double, Point[][]) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

regionContains(Point) - Method in class maltcms.datastructures.peak.PeakArea2D

Contains.

Reliability - Class in maltcms.commands.fragments2d.peakfinding

Reliability(double) - Constructor for class maltcms.commands.fragments2d.peakfinding.Reliability

remove() - Method in class maltcms.datastructures.peak.FiFoQueue

remove(Object) - Method in class maltcms.datastructures.peak.FiFoQueue

remove(Point2D) - Method in class maltcms.datastructures.quadTree.QuadTree

remove(Point2D) - Method in class maltcms.datastructures.quadTree.QuadTreeNode

remove(Object) - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

remove() - Method in class net.sf.maltcms.evaluation.spi.BeansXmlGenerator

removeAll(Collection<?>) - Method in class maltcms.datastructures.peak.FiFoQueue

removeChild(IVariableFragment) - Method in class maltcms.datastructures.ms.Experiment1D

removeListener(IListener<IEvent<IWorkflowResult>>) - Method in class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated.

removeListener(IListener<IEvent<Configuration>>) - Method in class maltcms.ui.wizard.PipelineWizard

removePeak(Peak) - Method in class maltcms.datastructures.peak.Clique

removePeak(T) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

removePeakSimilaritiesWhichHaveNoBestHits(TupleND<IFileFragment>, HashMap<String, List<Peak>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.BBHFinder

removeSourceFile(IFileFragment) - Method in class maltcms.datastructures.ms.Experiment1D

removeSourceFiles() - Method in class maltcms.datastructures.ms.Experiment1D

resetResultList() - Method in class maltcms.db.predicates.metabolite.MSimilarityPredicate

ResourceType - Class in maltcms.io.xml.bindings.alignment

Java class for resourceType complex type.

ResourceType() - Constructor for class maltcms.io.xml.bindings.alignment.ResourceType

ResourceType - Class in maltcms.io.xml.bindings.annotation

Java class for resourceType complex type.

ResourceType() - Constructor for class maltcms.io.xml.bindings.annotation.ResourceType

Result<T extends Serializable> - Class in maltcms.experimental.bipace.datastructures.api

Result() - Constructor for class maltcms.experimental.bipace.datastructures.api.Result

retainAll(Collection<?>) - Method in class maltcms.datastructures.peak.FiFoQueue

retainSimilarityRemoveRest(Peak) - Method in class maltcms.datastructures.peak.Peak

RetentionIndexCalculator - Class in maltcms.datastructures.peak

RetentionIndexCalculator(int[], Peak1D...) - Constructor for class maltcms.datastructures.peak.RetentionIndexCalculator

RetentionIndexCalculator(int[], double...) - Constructor for class maltcms.datastructures.peak.RetentionIndexCalculator

RetentionIndexPeakAnnotation - Class in maltcms.datastructures.peak.annotations

RetentionIndexPeakAnnotation() - Constructor for class maltcms.datastructures.peak.annotations.RetentionIndexPeakAnnotation

RetentionInfo - Class in maltcms.datastructures.ms

Concrete implementation of IRetentionInfo.

RetentionInfo() - Constructor for class maltcms.datastructures.ms.RetentionInfo

RETINDEX - Variable in class maltcms.db.ui.MetaboliteViewModel

RETTIME - Variable in class maltcms.db.ui.MetaboliteViewModel

RETTIMEUNIT - Variable in class maltcms.db.ui.MetaboliteViewModel

revalidate() - Method in class maltcms.ui.wizard.AnchorDefinitionPane

Ridge - Class in maltcms.datastructures.ridge

Ridge(Point2D, double) - Constructor for class maltcms.datastructures.ridge.Ridge

RidgeCost0 - Class in maltcms.datastructures.ridge

RidgeCost0() - Constructor for class maltcms.datastructures.ridge.RidgeCost0

RidgeCost1 - Class in maltcms.datastructures.ridge

RidgeCost1() - Constructor for class maltcms.datastructures.ridge.RidgeCost1

RidgeCost2 - Class in maltcms.datastructures.ridge

RidgeCost2() - Constructor for class maltcms.datastructures.ridge.RidgeCost2

RingBuffer<T> - Class in maltcms.datastructures.caches

Implementation of a RingBuffer datastructure e.g. for caches with fixed capacity and automatic remove oldest entry semantics.

RingBuffer(int) - Constructor for class maltcms.datastructures.caches.RingBuffer

rootMeanSquareError(List<Tuple2DI>, List<Array>, List<Array>) - Static method in class maltcms.tools.ArrayTools

rows() - Method in class maltcms.datastructures.array.DenseArray

rows() - Method in interface maltcms.datastructures.array.IArrayD2Byte

rows() - Method in interface maltcms.datastructures.array.IArrayD2Double

rows() - Method in class maltcms.datastructures.array.PartitionedArray

rows() - Method in class maltcms.datastructures.array.SparseArray

rows() - Method in class maltcms.datastructures.array.TiledArray

RT_DEFAULT - Static variable in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

RT_START_DEFAULT - Static variable in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

RT_STOP_DEFAULT - Static variable in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

RTGroupCorrectionWarp - Class in maltcms.commands.fragments.warp

Use Objects of this class to apply an alignment, warping a source chromatogram to the time/scans of reference chromatogram.

RTGroupCorrectionWarp() - Constructor for class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

RTUnit - Enum in net.sf.maltcms.evaluation.spi.xcalibur

run() - Method in class maltcms.db.connection.DB4oServer

run() - Method in class maltcms.mpaxs.MaltcmsConfigurableRunnable

run() - Method in class maltcms.mpaxs.TestConfigurableCallable

run() - Method in class maltcms.mpaxs.TestRunnable

run() - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

S

save(Alignment, File) - Method in class maltcms.datastructures.alignment.AlignmentFactory

save() - Method in class maltcms.datastructures.ms.Experiment1D

save(MaltcmsAnnotation, File) - Method in class maltcms.datastructures.peak.MaltcmsAnnotationFactory

saveAnchorsToFiles() - Method in class maltcms.ui.wizard.AnchorDefinitionPane

saveImage(RenderedImage, String, String, File, IWorkflowElement, IFileFragment...) - Static method in class maltcms.tools.ImageTools

saveImages(File, String, List<JFreeChart>) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

saveImages(String, String, List<JFreeChart>) - Static method in class maltcms.commands.fragments2d.peakfinding.CwtChartFactory

savePathCSV(IFileFragment, IArrayD2Double, IArrayD2Double, List<Tuple2DI>, IWorkflow, boolean) - Method in class maltcms.tools.PathTools

savePeakAnnotations(List<Peak1D>, IFileFragment) - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

savePeakMatchRTTable(HashMap<String, Integer>, List<List<Peak>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter

savePeakMatchTable(HashMap<String, Integer>, List<List<Peak>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.MultipleAlignmentWriter

saveSimilarityMatrix(TupleND<IFileFragment>, HashMap<String, List<Peak>>) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

saveToCSV(ArrayDouble.D2, ArrayChar.D2) - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

saveToCSV(IFileFragment, ArrayDouble.D2, ArrayChar.D2) - Method in class maltcms.commands.fragments.cluster.PairwiseDistanceCalculator

saveToCSV(ArrayDouble.D2, ArrayChar.D2) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.CenterFinder

saveToCSV(IFileFragment, ArrayDouble.D2, ArrayChar.D2) - Method in class smueller.SymbolicRepresentationAlignment

saveToXMLAlignment(TupleND<IFileFragment>, List<List<Peak>>) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.io.XmlAlignmentWriter

SavitzkyGolayFilter - Class in maltcms.commands.filters.array

Implementation of the Savitzky-Golay Filter.

SavitzkyGolayFilter() - Constructor for class maltcms.commands.filters.array.SavitzkyGolayFilter

scalar(double) - Static method in class maltcms.tools.ArrayTools

scale(Array) - Method in class smueller.tools.Standardizer

Scan1D - Class in maltcms.datastructures.ms

Implementation of a 1-dimensional scan.

Scan1D(Array, Array, int, double) - Constructor for class maltcms.datastructures.ms.Scan1D

Scan2D - Class in maltcms.datastructures.ms

Specialization of Scan1D, adding second column times and indices, indicating the modulation periods scans belong to.

Scan2D(Array, Array, int, double) - Constructor for class maltcms.datastructures.ms.Scan2D

Scan2D(Array, Array, int, double, int, int, double, double) - Constructor for class maltcms.datastructures.ms.Scan2D

SCANINDEX - Variable in class maltcms.db.ui.MetaboliteViewModel

ScanLineCache - Class in maltcms.datastructures.caches

This class is a dataholder for mass spectra.

ScanLineCacheFactory - Class in maltcms.datastructures.caches

This Factory creates all IScanLine caches and hold an reference to support multiple usage.

ScanLineCacheFactory() - Constructor for class maltcms.datastructures.caches.ScanLineCacheFactory

ScanLineCacheOld - Class in maltcms.datastructures.caches

This class is a dataholder for mass spectra.

ScanlineFilterTicWarp - Class in maltcms.commands.fragments2d.warp

Implementation of Pairwise Dynamic-Time-Warping for time-series data.

ScanlineFilterTicWarp() - Constructor for class maltcms.commands.fragments2d.warp.ScanlineFilterTicWarp

ScanlineHorizontalTicWarp - Class in maltcms.commands.fragments2d.warp

Implementation of pairwise Dynamic-Time-Warping for time-series data.

ScanlineHorizontalTicWarp() - Constructor for class maltcms.commands.fragments2d.warp.ScanlineHorizontalTicWarp

ScanlineMaxMSWarp - Class in maltcms.commands.fragments2d.warp

Warps two chromatogramms according to their mean mass spectra of the scan lines.

ScanlineMaxMSWarp() - Constructor for class maltcms.commands.fragments2d.warp.ScanlineMaxMSWarp

ScanlineMeanMSWarp - Class in maltcms.commands.fragments2d.warp

Warps two chromatogramms according to their mean mass spectra of the scan lines.

ScanlineMeanMSWarp() - Constructor for class maltcms.commands.fragments2d.warp.ScanlineMeanMSWarp

ScanlineTicWarp - Class in maltcms.commands.fragments2d.warp

Implementation of Pairwise Dynamic-Time-Warping for time-series data.

ScanlineTicWarp() - Constructor for class maltcms.commands.fragments2d.warp.ScanlineTicWarp

ScoreDistributionVisualizer - Class in maltcms.commands.fragments.visualization

ScoreDistributionVisualizer() - Constructor for class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer

SeededRegionGrowing - Class in maltcms.commands.fragments2d.peakfinding

Peakpicking + integration + identification + normalization + evaluation...

SeededRegionGrowing() - Constructor for class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing

SeededRegionGrowing.PeakAreaComparator - Class in maltcms.commands.fragments2d.peakfinding

SeededRegionGrowing.PeakAreaComparator() - Constructor for class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing.PeakAreaComparator

SeededRegionGrowing.PeakComparator - Class in maltcms.commands.fragments2d.peakfinding

SeededRegionGrowing.PeakComparator() - Constructor for class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing.PeakComparator

selectCentroid() - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

selectCentroid() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

selectCentroid() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

separatePeaks(List<PeakArea2D>, IScalarArraySimilarity, IScanLine, List<ArrayDouble.D1>) - Method in class maltcms.commands.fragments2d.peakfinding.PeakSeparator

set(double, double, double) - Method in class maltcms.commands.distances.DtwRecurrence

set(double, double, double) - Method in interface maltcms.commands.distances.IRecurrence

set(int, int, double) - Method in class maltcms.datastructures.array.DenseArray

set(int, int, byte) - Method in interface maltcms.datastructures.array.IArrayD2Byte

set(int, int, double) - Method in interface maltcms.datastructures.array.IArrayD2Double

set(int, int, double) - Method in class maltcms.datastructures.array.PartitionedArray

set(int, double) - Method in class maltcms.datastructures.array.Sparse

set(int, int, double) - Method in class maltcms.datastructures.array.SparseArray

set(int, int, double) - Method in class maltcms.datastructures.array.TiledArray

setA(char) - Method in class smueller.alignment.AlignedPairVector

setAaAfter(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Sets the value of the aaAfter property.

setAaAfter(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Sets the value of the aaAfter property.

setAaBefore(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Sets the value of the aaBefore property.

setAaBefore(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Sets the value of the aaBefore property.

setAccession(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Sets the value of the accession property.

setAccession(String) - Method in class maltcms.io.xml.mzData.CvParamType

Sets the value of the accession property.

setAccessionNumber(String) - Method in class maltcms.io.xml.mzData.MzData

Sets the value of the accessionNumber property.

setAcqNumber(int) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification.Acquisition

Sets the value of the acqNumber property.

setAcqSpecification(SpectrumSettingsType.AcqSpecification) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType

Sets the value of the acqSpecification property.

setActivation(ParamType) - Method in class maltcms.io.xml.mzData.PrecursorType

Sets the value of the activation property.

setAdditional(ParamType) - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Sets the value of the additional property.

setAddress(String) - Method in class maltcms.io.xml.mzData.CvLookupType

Sets the value of the address property.

setAdmin(AdminType) - Method in class maltcms.io.xml.mzData.MzData.Description

Sets the value of the admin property.

setAlignment(IArrayD2Double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setAlignments(TupleND<IFileFragment>) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setAllInOneChart(boolean) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setAlpha(double) - Method in class maltcms.ui.charts.GradientPaintScale

setAlphaBeta(double, double) - Method in class maltcms.ui.charts.GradientPaintScale

setAnalyzerList(InstrumentDescriptionType.AnalyzerList) - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Sets the value of the analyzerList property.

setAnchorNamesVariableName(String) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setAnchorRetentionIndexVariableName(String) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setAnchors(DefaultPairSet<IAnchor>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

Set paired anchors

setAnchors(Tuple2D<Point, Point>...) - Method in class maltcms.datastructures.warp.WarpMap2D

setAnchorScanIndexVariableName(String) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setAnchorTimesVariableName(String) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setApplicationContext(ApplicationContext) - Method in class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.ApplicationContextWorkerFactory

setArea(double) - Method in class maltcms.datastructures.peak.Peak2D

setArrayDistanceClassName(String) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setArrayName(String) - Method in class maltcms.io.xml.mzData.SupDataBinaryType

Sets the value of the arrayName property.

setArrayName(String) - Method in class maltcms.io.xml.mzData.SupDataType

Sets the value of the arrayName property.

setArraySimilarities(IArraySimilarity...) - Method in interface maltcms.math.functions.IScalarArraySimilarity

setAttributes(Attribute...) - Method in class maltcms.datastructures.ms.Experiment1D

setAvailableVariables(String[]) - Method in class maltcms.ui.charts.VariableSelectionPanel

setAverageCount(int) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

setB(char) - Method in class smueller.alignment.AlignedPairVector

setBarDistance(double) - Method in class maltcms.ui.charts.MassSpectrumPlot

Setter.

setBarWidth(double) - Method in class maltcms.ui.charts.MassSpectrumPlot

Setter.

setBasedir(String) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setBeta(double) - Method in class maltcms.ui.charts.GradientPaintScale

setBinMZbyConfig() - Static method in class maltcms.tools.MaltcmsTools

setBinMZDefault(String) - Static method in class maltcms.tools.MaltcmsTools

setBinSize(int) - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Setter.

setBinSize(int) - Method in interface maltcms.commands.fragments2d.warp.visualization.IVisualization

Setter.

setBinSize(int) - Method in class maltcms.datastructures.caches.AScanLineCache

Setter.

setBinSize(int) - Method in interface maltcms.datastructures.caches.IScanLine

Setter.

setBinSize(int) - Method in class maltcms.datastructures.caches.ScanLineCache

Setter.

setBinSize(int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Setter.

setBinSize(int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

Setter.

setC(int) - Method in class smueller.alignment.AlignedPairVector

setCacheModulations(boolean) - Method in class maltcms.datastructures.caches.AScanLineCache

Setter.

setCacheModulations(boolean) - Method in interface maltcms.datastructures.caches.IScanLine

Setter.

setCacheModulations(boolean) - Method in class maltcms.datastructures.caches.ScanLineCache

Setter.

setCacheModulations(boolean) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Setter.

setCacheModulations(boolean) - Method in class maltcms.datastructures.caches.SparseScanLineCache

Setter.

setCaller(Class) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakExporter

Setter.

setCaller(Class) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

Setter.

setCaseInsensitiveMatching(boolean) - Method in class maltcms.db.predicates.metabolite.MStringMatchPredicate

setCd(IRecurrence) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setCentroid(T) - Method in class maltcms.datastructures.cluster.Clique

setCentroid(T) - Method in interface maltcms.datastructures.cluster.IClique

setCentroid(IClique<T>) - Method in interface maltcms.datastructures.cluster.ICliqueUpdater

setCharge(BigInteger) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Sets the value of the charge property.

setCharge(BigInteger) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Sets the value of the charge property.

setCharge(Double) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Sets the value of the charge property.

setCharges(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the charges property.

setChromatogram(IChromatogram1D) - Method in class maltcms.datastructures.ms.Experiment1D

setChromatogram(IChromatogram1D) - Method in interface maltcms.datastructures.ms.IExperiment1D

setChromatogram2D(IChromatogram2D) - Method in class maltcms.datastructures.ms.Experiment2D

setChromatogram2D(IChromatogram2D) - Method in interface maltcms.datastructures.ms.IExperiment2D

setChromatogramDistanceFunction(PairwiseFeatureSequenceSimilarity) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setChromatograms(List<Chromatogram>) - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Group

setChromatogramWarpCommand(AFragmentCommand) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setClassLabel(String) - Method in class maltcms.datastructures.ridge.Ridge

setCliqueStatistics(CliqueStatistics<T>) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

setCluster(HashMap<Integer, BinaryCluster>) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setClusterNames(String[]) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setColorrampLocation(String) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setColStart(ArrayInt.D1) - Method in class maltcms.datastructures.array.PartitionedArray

setComment(String) - Method in class maltcms.io.csv.CSVReader

setComment(String) - Method in class maltcms.io.xml.mzData.DescriptionType

Sets the value of the comment property.

setComments(String) - Method in interface maltcms.datastructures.ms.IMetabolite

setComments(String) - Method in class maltcms.datastructures.ms.Metabolite

setComments(String) - Method in class maltcms.io.xml.mzData.SoftwareType

Sets the value of the comments property.

setCompletionTime(XMLGregorianCalendar) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

Sets the value of the completionTime property.

setCompletionTime(XMLGregorianCalendar) - Method in class maltcms.io.xml.mzData.SoftwareType

Sets the value of the completionTime property.

setCompressionWeight(double) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

setConfiguration(Configuration) - Method in class maltcms.runtime.LocalHostMaltcmsProcess

Deprecated.

setConfiguration(PropertiesConfiguration) - Method in class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction

setConfiguration(PropertiesConfiguration) - Method in class maltcms.ui.wizard.PipelineWizard

setConsensus(IFileFragment) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setConsensus(IFileFragment) - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

setConstraints(Area) - Method in class maltcms.commands.distances.dtwng.DTW

setConstraints(Area) - Method in interface maltcms.commands.distances.dtwng.IAlignment

setContactInfo(String) - Method in class maltcms.io.xml.mzData.PersonType

Sets the value of the contactInfo property.

setContainer(Container) - Method in class maltcms.ui.wizard.PipelineWizard.LoadConfigurationAction

setContainer(Container) - Method in class maltcms.ui.wizard.PipelineWizard.RunConfigurationAction

setCount(BigInteger) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.FeatureList

Sets the value of the count property.

setCount(int) - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType.AnalyzerList

Sets the value of the count property.

setCount(int) - Method in class maltcms.io.xml.mzData.MzData.SpectrumList

Sets the value of the count property.

setCount(int) - Method in class maltcms.io.xml.mzData.SpectrumDescType.PrecursorList

Sets the value of the count property.

setCount(int) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Sets the value of the count property.

setCreator(Class<?>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setCreatorVersion(String) - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Creator

setCumulativeDistance(DtwRecurrence) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setCvLabel(String) - Method in class maltcms.io.xml.mzData.CvLookupType

Sets the value of the cvLabel property.

setCvLabel(String) - Method in class maltcms.io.xml.mzData.CvParamType

Sets the value of the cvLabel property.

setd(int, int, double) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setD(int) - Method in class smueller.alignment.AlignedPairVector

setData(double[][], double[], double[]) - Method in class maltcms.experimental.ui.ImagePanel

setData(PeakListBinaryType.Data) - Method in class maltcms.io.xml.mzData.PeakListBinaryType

Sets the value of the data property.

setData(PeakListBinaryType.Data) - Method in class maltcms.io.xml.mzData.SupDataBinaryType

Sets the value of the data property.

setDataProcessing(DataProcessingType) - Method in class maltcms.io.xml.mzData.MzData.Description

Sets the value of the dataProcessing property.

setDate(String) - Method in interface maltcms.datastructures.ms.IMetabolite

setDate(String) - Method in class maltcms.datastructures.ms.Metabolite

setDate(XMLGregorianCalendar) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Sets the value of the date property.

setDB(String) - Method in interface maltcms.db.IDBQuery

setDB(String) - Method in class maltcms.db.RawMSQuery

setDb(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the db property.

setDbVersion(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the dbVersion property.

setDefaultValue(double) - Method in class maltcms.commands.distances.dtwng.DTW

setDefaultValue(double) - Method in interface maltcms.commands.distances.dtwng.IAlignment

setDescription(MzData.Description) - Method in class maltcms.io.xml.mzData.MzData

Sets the value of the description property.

setDetector(ParamType) - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Sets the value of the detector property.

setDim(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint.Hposition

Sets the value of the dim property.

setDim(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Position

Sets the value of the dim property.

setDim(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Quality

Sets the value of the dim property.

setDimNumber(BigInteger) - Method in class maltcms.io.xml.bindings.alignment.PointMapType

Sets the value of the dimNumber property.

setDist(double[][]) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setDistance(IArrayD2Double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setDistances(double[]) - Method in class maltcms.datastructures.cluster.ACluster

setDistances(double[]) - Method in interface maltcms.datastructures.cluster.ICluster

setDistanceTo(ICluster, double) - Method in class maltcms.datastructures.cluster.ACluster

setDistanceTo(int, double) - Method in class maltcms.datastructures.cluster.ACluster

setDistanceToParent(double) - Method in class maltcms.datastructures.cluster.ACluster

setDistanceToParent(double) - Method in interface maltcms.datastructures.cluster.ICluster

setDocumentId(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Sets the value of the documentId property.

setDone(boolean) - Method in class smueller.alignment.AlignedPairVector

setDouble(Index, double) - Method in class maltcms.datastructures.array.Sparse

setE(int) - Method in class smueller.alignment.AlignedPairVector

setEnabled(boolean) - Method in class maltcms.db.ui.MetaboliteView

setEndian(String) - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Sets the value of the endian property.

setEnzyme(DigestionEnzyme) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the enzyme property.

setExpansionWeight(double) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

setExperiment(IExperiment1D) - Method in class maltcms.datastructures.ms.Chromatogram1D

setExperiment(IExperiment) - Method in class maltcms.datastructures.ms.Chromatogram2D

setExtension(String) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

setF(int) - Method in class smueller.alignment.AlignedPairVector

setFeatureList(FeatureMap.FeatureList) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Sets the value of the featureList property.

setFf(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setFieldSeparator(String) - Method in class maltcms.io.csv.CSVReader

setFile(File) - Method in class maltcms.datastructures.ms.Experiment1D

setFile(String) - Method in class maltcms.datastructures.ms.Experiment1D

setFile(File) - Method in class maltcms.ui.charts.PlotRunner

setFileDesignation(String) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setFileFragment(IFileFragment) - Method in class maltcms.commands.scanners.ArrayStatsScanner

setFileFragment(IFileFragment) - Method in class maltcms.datastructures.ms.Experiment1D

setFileFragment(IFileFragment) - Method in interface maltcms.datastructures.ms.IExperiment

setFileFragments(IFileFragment, IFileFragment) - Method in class maltcms.commands.distances.dtw.ADynamicTimeWarp

setFileFragments(IFileFragment, IFileFragment) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

setFileFragments(IFileFragment, IFileFragment, Class<?>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setFileMenu(JMenu) - Method in class maltcms.ui.charts.JFreeChartViewer

setFilename(String) - Method in class maltcms.ui.charts.PlotRunner

setFileType(String) - Method in class maltcms.io.xml.mzData.SourceFileType

Sets the value of the fileType property.

setFiletype(String) - Method in class maltcms.ui.charts.PlotRunner

setFirstColumnScanAcquisitionTime(double) - Method in interface maltcms.datastructures.ms.IScan2D

setFirstColumnScanAcquisitionTime(double) - Method in class maltcms.datastructures.ms.Scan2D

setFirstColumnScanIndex(int) - Method in interface maltcms.datastructures.ms.IScan2D

setFirstColumnScanIndex(int) - Method in class maltcms.datastructures.ms.Scan2D

setFirstLineHeaders(boolean) - Method in class maltcms.io.csv.CSVReader

setFirstRetTime(double) - Method in class maltcms.datastructures.peak.Peak2D

Setter.

setFloat(Index, float) - Method in class maltcms.datastructures.array.Sparse

setFontFamily(String) - Method in class maltcms.ui.charts.PlotRunner

setFormat(String) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setFormula(String) - Method in interface maltcms.datastructures.ms.IMetabolite

setFormula(String) - Method in class maltcms.datastructures.ms.Metabolite

setFragments(HashMap<Integer, IFileFragment>) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setFragments(IFileFragment, IFileFragment, IFileFragment) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

setFullName(String) - Method in class maltcms.io.xml.mzData.CvLookupType

Sets the value of the fullName property.

setGap(int) - Method in class maltcms.ui.charts.CombinedDomainXYChart

setGenerator(String) - Method in class maltcms.io.xml.bindings.alignment.Alignment

Sets the value of the generator property.

setGenerator(String) - Method in class maltcms.io.xml.bindings.annotation.AnnotationsType

Sets the value of the generator property.

setHeadless(boolean) - Method in class maltcms.ui.charts.PlotRunner

setHigherScoreBetter(boolean) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Sets the value of the higherScoreBetter property.

setHigherScoreBetter(boolean) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the higherScoreBetter property.

setHigherScoreBetter(boolean) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the higherScoreBetter property.

setID(int) - Method in class maltcms.datastructures.cluster.ACluster

setID(int) - Method in interface maltcms.datastructures.cluster.ICluster

setID(long) - Method in class maltcms.datastructures.ms.Experiment1D

setID(String) - Method in interface maltcms.datastructures.ms.IMetabolite

setID(String) - Method in class maltcms.datastructures.ms.Metabolite

setId(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Sets the value of the id property.

setId(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Sets the value of the id property.

setId(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Sets the value of the id property.

setId(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Sets the value of the id property.

setId(int) - Method in class maltcms.io.xml.mzData.SpectrumType

Sets the value of the id property.

setId(int) - Method in class maltcms.io.xml.mzData.SupDataBinaryType

Sets the value of the id property.

setId(int) - Method in class maltcms.io.xml.mzData.SupDataType

Sets the value of the id property.

setIdentificationRunRef(Object) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the identificationRunRef property.

setIdentificationRunRef(Object) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the identificationRunRef property.

setIgnoreNegativeInfinity(boolean) - Method in class maltcms.commands.scanners.ArrayStatsScanner

setIgnorePositiveInfinity(boolean) - Method in class maltcms.commands.scanners.ArrayStatsScanner

setImages(BufferedImage, BufferedImage, BufferedImage) - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

setImgheight(int) - Method in class maltcms.ui.charts.PlotRunner

setImgwidth(int) - Method in class maltcms.ui.charts.PlotRunner

setIndex(int) - Method in class maltcms.datastructures.peak.Peak2D

Setter.

setIndexed(boolean) - Method in class maltcms.io.xml.mzData.SupDataType

Sets the value of the indexed property.

setIndexedVars(List<String>) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

setIndexedVars(List<String>) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

setIndexedVars(List<String>) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

setIndexVar(String) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

setIndexVar(String) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

setIndexVar(String) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

setInputFiles(TupleND<IFileFragment>) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setInputFiles(TupleND<IFileFragment>) - Method in interface maltcms.commands.fragments.cluster.IClusteringAlgorithm

setInstitution(String) - Method in class maltcms.io.xml.mzData.PersonType

Sets the value of the institution property.

setInstrument(InstrumentDescriptionType) - Method in class maltcms.io.xml.mzData.MzData.Description

Sets the value of the instrument property.

setInstrumentName(String) - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Sets the value of the instrumentName property.

setInt(Index, int) - Method in class maltcms.datastructures.array.Sparse

setIntenArrayBinary(PeakListBinaryType) - Method in class maltcms.io.xml.mzData.SpectrumType

Sets the value of the intenArrayBinary property.

setIntensity(double) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Sets the value of the intensity property.

setIntensityValuesVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setIntensityValuesVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setInterppath(List<Tuple2DI>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setIonSelection(ParamType) - Method in class maltcms.io.xml.mzData.PrecursorType

Sets the value of the ionSelection property.

setIsAlignmentReference(boolean) - Method in class maltcms.io.xml.bindings.alignment.MappedPointsType

Sets the value of the isAlignmentReference property.

setIsCompleteMap(boolean) - Method in class maltcms.io.xml.bindings.alignment.Alignment

Sets the value of the isCompleteMap property.

setIsMinimizing(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setJfc(JFreeChart) - Method in class maltcms.ui.charts.JFreeChartViewer.ChartSerializeAction

setJmb(JMenuBar) - Method in class maltcms.ui.charts.JFreeChartViewer

setJtp(JTabbedPane) - Method in class maltcms.ui.charts.JFreeChartViewer

setKostenfunktion(double[][]) - Method in class smueller.alignment.Alignment

setL(int) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setLabelString(String) - Method in class maltcms.datastructures.cluster.ACluster

setLabelString(String) - Method in interface maltcms.datastructures.cluster.ICluster

setLastIndex(int) - Method in class maltcms.datastructures.caches.AScanLineCache

Setter.

setLastIndex(int) - Method in interface maltcms.datastructures.caches.IScanLine

Setter.

setLastIndex(int) - Method in class maltcms.datastructures.caches.ScanLineCache

Setter.

setLastIndex(int) - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Setter.

setLastIndex(int) - Method in class maltcms.datastructures.caches.SparseScanLineCache

Setter.

setLChild(BinaryCluster) - Method in class maltcms.datastructures.cluster.BinaryCluster

setLDF(PairwiseFeatureSequenceSimilarity) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setLeftHandSideId(String) - Method in class maltcms.commands.distances.dtwng.DTW

setLeftHandSideId(String) - Method in interface maltcms.commands.distances.dtwng.IAlignment

setLength(int) - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Sets the value of the length property.

setLength(int) - Method in class maltcms.io.xml.mzData.SupDataType

Sets the value of the length property.

setLocation(List<String>) - Method in class maltcms.commands.fragments.io.CSVAnchorReader

setLog(boolean) - Method in class maltcms.commands.filters.array.NormalizationFilter

setLong(Index, long) - Method in class maltcms.datastructures.array.Sparse

setLowerBound(double) - Method in class maltcms.ui.charts.GradientPaintScale

setLowThreshold(double) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setMassRangeMax(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setMassRangeMax(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setMassRangeMin(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setMassRangeMin(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setMassSpectrum(ArrayDouble.D1, ArrayInt.D1) - Method in interface maltcms.datastructures.ms.IMetabolite

setMassSpectrum(ArrayDouble.D1, ArrayInt.D1) - Method in class maltcms.datastructures.ms.Metabolite

setMassType(MassType) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the massType property.

setMassValuesVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setMassValuesVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setMatchWeight(double) - Method in interface maltcms.commands.distances.IDtwSimilarityFunction

setMaxAnnotations(int) - Method in class maltcms.ui.charts.MassSpectrumPlot

Setter.

setMaxBBHErrors(int) - Method in class maltcms.datastructures.peak.Clique

setMaxBBHErrors(int) - Method in class maltcms.experimental.bipace.datastructures.api.Clique

setMaxFirstDelta(int) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

setMaxIntensity(double) - Method in interface maltcms.datastructures.ms.IMetabolite

setMaxIntensity(double) - Method in class maltcms.datastructures.ms.Metabolite

setMaxMass(double) - Method in interface maltcms.datastructures.ms.IMetabolite

setMaxMass(double) - Method in class maltcms.datastructures.ms.Metabolite

setMaxSecondDelta(int) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

setMeanFirstScanIndex(int) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

setMeanSecondScanIndex(int) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

setMerged(boolean) - Method in class maltcms.datastructures.peak.PeakArea2D

setMetaboliteView(MetaboliteView) - Method in class maltcms.db.ui.MetaboliteViewModel

setMetadata(String, String) - Method in class maltcms.datastructures.ms.Experiment1D

setMetadata(String, String) - Method in interface maltcms.datastructures.ms.IExperiment

setMethodOfCombination(String) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Sets the value of the methodOfCombination property.

setMethodOnTargetType(Method) - Method in interface maltcms.db.predicates.IMatchPredicate

setMethodOnTargetType(Method) - Method in class maltcms.db.predicates.MatchPredicate

setMethodOnTargetType(Method) - Method in class maltcms.db.predicates.metabolite.MetabolitePredicate

setMinArrayComp(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setMinDist(double) - Method in class maltcms.commands.fragments2d.peakfinding.PeakSeparator

setMinimize(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setMinimize(boolean) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setMinimizeDist(boolean) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setMinimizing(boolean) - Method in class maltcms.commands.distances.DtwRecurrence

setMinimizing(boolean) - Method in interface maltcms.commands.distances.IRecurrence

setMinimizingArrayCompVariableName(String) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setMinIntensity(double) - Method in interface maltcms.datastructures.ms.IMetabolite

setMinIntensity(double) - Method in class maltcms.datastructures.ms.Metabolite

setMinMass(double) - Method in interface maltcms.datastructures.ms.IMetabolite

setMinMass(double) - Method in class maltcms.datastructures.ms.Metabolite

setMinScansBetweenAnchors(int) - Method in class maltcms.datastructures.alignment.DefaultPairSet

setMissedCleavages(Long) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the missedCleavages property.

setModel(FeatureType.Model) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Sets the value of the model property.

setMsLevel(int) - Method in class maltcms.io.xml.mzData.PrecursorType

Sets the value of the msLevel property.

setMsLevel(int) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

Sets the value of the msLevel property.

setMW(int) - Method in interface maltcms.datastructures.ms.IMetabolite

setMw(double) - Method in interface maltcms.datastructures.ms.IMetabolite

setMW(int) - Method in class maltcms.datastructures.ms.Metabolite

setMw(double) - Method in class maltcms.datastructures.ms.Metabolite

setMZ(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the mz property.

setMZ(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the mz property.

setMzArrayBinary(PeakListBinaryType) - Method in class maltcms.io.xml.mzData.SpectrumType

Sets the value of the mzArrayBinary property.

setMzRangeStart(Float) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

Sets the value of the mzRangeStart property.

setMzRangeStop(Float) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

Sets the value of the mzRangeStop property.

setMzVariableName(String) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setName(Peak2D) - Method in interface maltcms.commands.fragments2d.peakfinding.output.IPeakIdentification

Tries to identify the peak an set his name.

setName(Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakIdentification

Tries to identify the peak an set his name.

setName(ICluster, ICluster) - Method in class maltcms.datastructures.cluster.ACluster

setName(String) - Method in class maltcms.datastructures.cluster.ACluster

setName(String) - Method in interface maltcms.datastructures.cluster.ICluster

setName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setName(String) - Method in interface maltcms.datastructures.ms.IAnchor

setName(String) - Method in interface maltcms.datastructures.ms.ITreatmentGroup

setName(String) - Method in class maltcms.datastructures.ms.Metabolite

setName(String) - Method in class maltcms.datastructures.ms.RetentionInfo

setName(String) - Method in class maltcms.datastructures.ms.TreatmentGroup1D

setName(String) - Method in class maltcms.datastructures.ms.TreatmentGroup2D

setName(String) - Method in class maltcms.io.xml.bindings.alignment.PointType.Dimension

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.annotation.AnnotationType

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.annotation.AttributeType

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.ProcessingAction

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.Software

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.FixedModification

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters.VariableModification

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model.Param

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.UserParam

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.mzData.CvParamType

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.mzData.PersonType

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.mzData.SoftwareType

Sets the value of the name property.

setName(String) - Method in class maltcms.io.xml.mzData.UserParamType

Sets the value of the name property.

setName(String) - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Creator

setNameOfFile(String) - Method in class maltcms.io.xml.mzData.SourceFileType

Sets the value of the nameOfFile property.

setNames(String[]) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setNames(ArrayChar.D2) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setNames(List<Tuple2D<Double, IMetabolite>>) - Method in class maltcms.datastructures.peak.Peak2D

Setter.

setNavigateToResults(boolean) - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

setNodes(List<double[]>) - Method in class maltcms.commands.distances.dtwng.NodeBuilder

setNormalization(String) - Method in class maltcms.commands.filters.array.NormalizationFilter

setNormalize(boolean) - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

Setter.

setNormalize(boolean) - Method in interface maltcms.commands.fragments2d.warp.visualization.IVisualization

Setter.

setNormalizeByMapLength(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setNormalizeGlobal(boolean) - Method in class maltcms.commands.filters.array.NormalizationFilter

setNr(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull

Sets the value of the nr property.

setNumberOfMaps(BigInteger) - Method in class maltcms.io.xml.bindings.alignment.Alignment

Sets the value of the numberOfMaps property.

setNumberOfScansQuery(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setNumberOfScansReference(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setNumPartitions(int) - Method in class maltcms.datastructures.array.PartitionedArray

setOffset(Integer) - Method in class maltcms.io.xml.mzData.SupDataType

Sets the value of the offset property.

setOptimizationFunction(IOptimizationFunction) - Method in class maltcms.commands.distances.dtwng.DTW

setOptimizationFunction(IOptimizationFunction) - Method in interface maltcms.commands.distances.dtwng.IAlignment

setOverallquality(Double) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Sets the value of the overallquality property.

setPairwise(boolean) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setPairwiseDistance(PairwiseFeatureSimilarity) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setPairwiseDistanceMatrixVariableName(String) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setPairwiseDistanceNamesVariableName(String) - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

setPairwiseDistances(IArrayD2Double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setPairwiseDistances(ArrayDouble.D2) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setPairwiseFeatureSimilarity(PairwiseFeatureSimilarity) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

setPairwiseFeatureVectorOperation(TwoFeatureVectorOperation) - Method in class maltcms.commands.distances.dtwng.DTW

setPairwiseFeatureVectorOperation(TwoFeatureVectorOperation) - Method in interface maltcms.commands.distances.dtwng.IPairwiseFeatureVectorSequenceOperation

setPairwiseWithFirst(boolean) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setParent(Component) - Method in class maltcms.ui.charts.JFreeChartViewer.FileOpenAction

setPath(List<Tuple2DI>) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setPathToFile(String) - Method in class maltcms.io.xml.mzData.SourceFileType

Sets the value of the pathToFile property.

setPeakArea(PeakArea2D) - Method in class maltcms.datastructures.peak.Peak2D

Setter.

setPeakMassTolerance(float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the peakMassTolerance property.

setPipelines(List<Callable<T>>) - Method in class net.sf.maltcms.evaluation.spi.tasks.execution.APipeline

setPipelineWizard(PipelineWizard) - Method in class maltcms.ui.wizard.PipelineWizard.CreateConfigurationAction

setPipelineWizard(PipelineWizard) - Method in class maltcms.ui.wizard.PipelineWizard.EditConfigurationAction

setPlainVars(List<String>) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

setPlainVars(List<String>) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

setPlainVars(List<String>) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

setPlot(Plot) - Method in class maltcms.ui.charts.PlotRunner

setPointMap(PointMapType) - Method in class maltcms.io.xml.bindings.alignment.MappedPointsType

Sets the value of the pointMap property.

setPointNumber(BigInteger) - Method in class maltcms.io.xml.bindings.alignment.PointMapType

Sets the value of the pointNumber property.

setPrecision(String) - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Sets the value of the precision property.

setPrecursorList(SpectrumDescType.PrecursorList) - Method in class maltcms.io.xml.mzData.SpectrumDescType

Sets the value of the precursorList property.

setPrecursorPeakTolerance(float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the precursorPeakTolerance property.

setPredecessors(byte[][]) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setPredicate(Predicate<T>) - Method in class maltcms.db.QueryDB

Allows to set the predicate used for matching by this QueryDB object.

setProcessingMethod(ParamType) - Method in class maltcms.io.xml.mzData.DataProcessingType

Sets the value of the processingMethod property.

setProteinIdentification(FeatureMap.IdentificationRun.ProteinIdentification) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Sets the value of the proteinIdentification property.

setPwd(PairwiseFeatureSimilarity) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setPwDistAlignmentsVarName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setPwDistMatrixVariableName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setPwDistVariableName(String) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setQuery(IFileFragment) - Method in class smueller.alignment.Alignment

setQuerysize(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setRamp(int[][]) - Method in class maltcms.ui.charts.GradientPaintScale

setRChild(BinaryCluster) - Method in class maltcms.datastructures.cluster.BinaryCluster

setRecurrence(DtwRecurrence) - Method in interface maltcms.commands.distances.dtw.IDynamicTimeWarp

setRef(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setRef(IFileFragment) - Method in class smueller.alignment.Alignment

setRefsize(int) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setResource(ResourceType) - Method in class maltcms.io.xml.bindings.alignment.MappedPointsType

Sets the value of the resource property.

setResource(ResourceType) - Method in class maltcms.io.xml.bindings.annotation.MaltcmsAnnotation

Sets the value of the resource property.

setResult(double) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setRetentionIndex(double) - Method in interface maltcms.datastructures.ms.IRetentionInfo

setRetentionIndex(double) - Method in class maltcms.datastructures.ms.Metabolite

setRetentionIndex(double) - Method in class maltcms.datastructures.ms.RetentionInfo

setRetentionIndex2D(double) - Method in interface maltcms.datastructures.ms.IRetentionInfo2D

setRetentionIndex2D(double) - Method in class maltcms.datastructures.ms.Metabolite2D

setRetentionTime(double) - Method in interface maltcms.datastructures.ms.IRetentionInfo

setRetentionTime(double) - Method in class maltcms.datastructures.ms.Metabolite

setRetentionTime(double) - Method in class maltcms.datastructures.ms.RetentionInfo

setRetentionTime2D(double) - Method in interface maltcms.datastructures.ms.IRetentionInfo2D

setRetentionTime2D(double) - Method in class maltcms.datastructures.ms.Metabolite2D

setRetentionTimeUnit(String) - Method in interface maltcms.datastructures.ms.IRetentionInfo

setRetentionTimeUnit(String) - Method in class maltcms.datastructures.ms.Metabolite

setRetentionTimeUnit(String) - Method in class maltcms.datastructures.ms.RetentionInfo

setRetentionTimeUnit2D(String) - Method in interface maltcms.datastructures.ms.IRetentionInfo2D

setRetentionTimeUnit2D(String) - Method in class maltcms.datastructures.ms.Metabolite2D

setRightHandSideId(String) - Method in class maltcms.commands.distances.dtwng.DTW

setRightHandSideId(String) - Method in interface maltcms.commands.distances.dtwng.IAlignment

setRowLength(ArrayInt.D1) - Method in class maltcms.datastructures.array.PartitionedArray

setRowOffset(ArrayInt.D1) - Method in class maltcms.datastructures.array.PartitionedArray

setRT(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the rt property.

setRT(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the rt property.

setRunGui(boolean) - Method in class net.sf.maltcms.apps.Maltcms

setSampleDescription(DescriptionType) - Method in class maltcms.io.xml.mzData.AdminType

Sets the value of the sampleDescription property.

setSampleName(String) - Method in class maltcms.io.xml.mzData.AdminType

Sets the value of the sampleName property.

setSampleSize(int) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setSaveCDM(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setSaveGraphics(boolean) - Method in class maltcms.ui.charts.PlotRunner

setSavePWDM(boolean) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setScalarSimilarities(IScalarSimilarity...) - Method in interface maltcms.math.functions.IScalarArraySimilarity

setScale(double) - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

setScanAcquisitionTimeVariableName(String) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setScanAcquisitionTimeVariableName(String) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setScanAcquisitionTimeVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setScanAcquisitionTimeVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setScanIndex(int) - Method in interface maltcms.datastructures.ms.IAnchor

setScanIndex(int) - Method in class maltcms.datastructures.ms.Metabolite

setScanIndex(int) - Method in class maltcms.datastructures.ms.RetentionInfo

setScanIndex(int) - Method in class maltcms.datastructures.peak.Peak2D

Setter.

setScanIndexVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setScanIndexVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setScore(float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Sets the value of the score property.

setScore(float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Sets the value of the score property.

setScore(float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Sets the value of the score property.

setScoreType(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Sets the value of the scoreType property.

setScoreType(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the scoreType property.

setScoreType(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the scoreType property.

setSearchEngine(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Sets the value of the searchEngine property.

setSearchEngineVersion(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Sets the value of the searchEngineVersion property.

setSearchParameters(FeatureMap.IdentificationRun.SearchParameters) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun

Sets the value of the searchParameters property.

setSecondColumnScanAcquisitionTime(double) - Method in interface maltcms.datastructures.ms.IScan2D

setSecondColumnScanAcquisitionTime(double) - Method in class maltcms.datastructures.ms.Scan2D

setSecondColumnScanIndex(int) - Method in interface maltcms.datastructures.ms.IScan2D

setSecondColumnScanIndex(int) - Method in class maltcms.datastructures.ms.Scan2D

setSecondRetTime(double) - Method in class maltcms.datastructures.peak.Peak2D

Setter.

setSeedPoint(Point) - Method in class maltcms.datastructures.peak.PeakArea2D

setSeq1(String) - Method in class smueller.alignment.Alignment

setSeq2(String) - Method in class smueller.alignment.Alignment

setSequence(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification.ProteinHit

Sets the value of the sequence property.

setSequence(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification.PeptideHit

Sets the value of the sequence property.

setSequence(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification.PeptideHit

Sets the value of the sequence property.

setSerializeJFreeChart(boolean) - Method in class maltcms.ui.charts.PlotRunner

setShortName(String) - Method in interface maltcms.datastructures.ms.IMetabolite

setShortName(String) - Method in class maltcms.datastructures.ms.Metabolite

setSignificanceThreshold(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.ProteinIdentification

Sets the value of the significanceThreshold property.

setSignificanceThreshold(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the significanceThreshold property.

setSignificanceThreshold(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the significanceThreshold property.

setSize(int) - Method in class maltcms.datastructures.cluster.ACluster

setSize(int) - Method in interface maltcms.datastructures.cluster.ICluster

setSizeOverride(boolean) - Method in class maltcms.ui.charts.PlotRunner

setSkip(String) - Method in class maltcms.io.csv.CSVReader

setSkipCommentLines(boolean) - Method in class maltcms.io.csv.CSVReader

setSoftware(FeatureMap.DataProcessing.Software) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing

Sets the value of the software property.

setSoftware(DataProcessingType.Software) - Method in class maltcms.io.xml.mzData.DataProcessingType

Sets the value of the software property.

setSortedjavarray1(double[]) - Method in class smueller.datastructure.SortedJavArrays

setSortedjavarray2(double[]) - Method in class smueller.datastructure.SortedJavArrays

setSource(ParamType) - Method in class maltcms.io.xml.mzData.InstrumentDescriptionType

Sets the value of the source property.

setSourceFile(SourceFileType) - Method in class maltcms.io.xml.mzData.AdminType

Sets the value of the sourceFile property.

setSourceFilesVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setSourceFilesVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setSP(String) - Method in interface maltcms.datastructures.ms.IMetabolite

setSP(String) - Method in class maltcms.datastructures.ms.Metabolite

setSpectrumDesc(SpectrumDescType) - Method in class maltcms.io.xml.mzData.SpectrumType

Sets the value of the spectrumDesc property.

setSpectrumInstrument(SpectrumSettingsType.SpectrumInstrument) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType

Sets the value of the spectrumInstrument property.

setSpectrumList(MzData.SpectrumList) - Method in class maltcms.io.xml.mzData.MzData

Sets the value of the spectrumList property.

setSpectrumRef(int) - Method in class maltcms.io.xml.mzData.PrecursorType

Sets the value of the spectrumRef property.

setSpectrumReference(Long) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.UnassignedPeptideIdentification

Sets the value of the spectrumReference property.

setSpectrumReference(Long) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.PeptideIdentification

Sets the value of the spectrumReference property.

setSpectrumSettings(SpectrumSettingsType) - Method in class maltcms.io.xml.mzData.SpectrumDescType

Sets the value of the spectrumSettings property.

setSpectrumType(String) - Method in class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

Sets the value of the spectrumType property.

setStats(StatsMap) - Method in class maltcms.datastructures.ms.Experiment1D

setStatsMap(StatsMap) - Method in interface maltcms.commands.distances.PairwiseFeatureSequenceSimilarity

setStatus(JLabel) - Method in class maltcms.ui.charts.JFreeChartViewer

setStdArray(ArrayDouble.D1) - Method in class maltcms.math.functions.similarities.ArrayDotMap

Setter.

setStop(boolean) - Method in class maltcms.ui.charts.PlotRunner

setSubordinate(FeatureType.Subordinate) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType

Sets the value of the subordinate property.

setSubstractStartTime(boolean) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setSubstractStartTime(boolean) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setSupDataArrayRef(int) - Method in class maltcms.io.xml.mzData.SupDescType

Sets the value of the supDataArrayRef property.

setSupDataDesc(DescriptionType) - Method in class maltcms.io.xml.mzData.SupDescType

Sets the value of the supDataDesc property.

setTableColumnVisible(String, boolean) - Method in class maltcms.db.ui.MetaboliteViewModel

setTarget(IFileFragment) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setTargetContainer(JFrame) - Method in class maltcms.ui.charts.PlotRunner

setTargetType(Class<T>) - Method in interface maltcms.db.predicates.IMatchPredicate

setTargetType(Class<T>) - Method in class maltcms.db.predicates.MatchPredicate

setTargetType(Class<IMetabolite>) - Method in class maltcms.db.predicates.metabolite.MetabolitePredicate

setTaxonomy(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.IdentificationRun.SearchParameters

Sets the value of the taxonomy property.

setTimeUnit(String) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setTimeUnit(String) - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

setTitle(String) - Method in class maltcms.ui.charts.AChart

setTitle(String) - Method in class maltcms.ui.charts.AlignmentMapChart

setTitle(String) - Method in class maltcms.ui.charts.BHeatMapChart

setTitle(String) - Method in class maltcms.ui.charts.CombinedDomainXYChart

setTitle(String) - Method in class maltcms.ui.charts.HeatMapChart

setTitle(String) - Method in class maltcms.ui.charts.MassSpectrumPlot

setTitle(String) - Method in class maltcms.ui.charts.PlotRunner

setTitle(String) - Method in class maltcms.ui.charts.SpiderWebChart

setTitle(String) - Method in class maltcms.ui.charts.XYChart

setTitle(String) - Method in class maltcms.ui.charts.XYZChart

setTotalIntensityVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

setTotalIntensityVarName(String) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

setTraceMatrix(byte[][]) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setType(String) - Method in class maltcms.io.xml.bindings.alignment.Alignment

Sets the value of the type property.

setType(String) - Method in class maltcms.io.xml.bindings.annotation.AnnotationsType

Sets the value of the type property.

setType(String) - Method in class maltcms.io.xml.bindings.annotation.AnnotationType

Sets the value of the type property.

setType(UserParamType) - Method in class maltcms.io.xml.bindings.openms.featurexml.UserParam

Sets the value of the type property.

setUnit(String) - Method in class maltcms.io.xml.bindings.alignment.PointType.Dimension

Sets the value of the unit property.

setUnit(String) - Method in class maltcms.io.xml.bindings.annotation.AttributeType

Sets the value of the unit property.

setUpperBound(double) - Method in class maltcms.ui.charts.GradientPaintScale

setupUI() - Method in class net.sf.maltcms.apps.MetaboliteBrowser

setUri(String) - Method in class maltcms.io.xml.bindings.alignment.ResourceType

Sets the value of the uri property.

setUri(String) - Method in class maltcms.io.xml.bindings.annotation.ResourceType

Sets the value of the uri property.

setValue(String) - Method in class maltcms.io.xml.bindings.alignment.PointType.Dimension

Sets the value of the value property.

setValue(String) - Method in class maltcms.io.xml.bindings.annotation.AttributeType

Sets the value of the value property.

setValue(Object) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Convexhull.Hullpoint.Hposition

Sets the value of the value property.

setValue(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Model.Param

Sets the value of the value property.

setValue(Object) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Position

Sets the value of the value property.

setValue(Object) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureType.Quality

Sets the value of the value property.

setValue(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.UserParam

Sets the value of the value property.

setValue(String) - Method in class maltcms.io.xml.mzData.CvParamType

Sets the value of the value property.

setValue(byte[]) - Method in class maltcms.io.xml.mzData.PeakListBinaryType.Data

Sets the value of the value property.

setValue(String) - Method in class maltcms.io.xml.mzData.UserParamType

Sets the value of the value property.

setVariableFragments(IVariableFragment...) - Method in class maltcms.commands.scanners.ArrayStatsScanner

setVariableName(String) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setVariance(double) - Method in class maltcms.commands.filters.array.wavelet.MexicanHatWaveletFilter

setVersion(String) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap.DataProcessing.Software

Sets the value of the version property.

setVersion(Float) - Method in class maltcms.io.xml.bindings.openms.featurexml.FeatureMap

Sets the value of the version property.

setVersion(String) - Method in class maltcms.io.xml.mzData.CvLookupType

Sets the value of the version property.

setVersion(String) - Method in class maltcms.io.xml.mzData.MzData

Sets the value of the version property.

setVersion(String) - Method in class maltcms.io.xml.mzData.SoftwareType

Sets the value of the version property.

setWarpFrom(Image) - Method in class maltcms.datastructures.warp.WarpMap2D

setWarpTo(Image) - Method in class maltcms.datastructures.warp.WarpMap2D

setWeight(String, double) - Method in interface maltcms.commands.distances.dtwng.IOptimizationFunction

setWeight(String, double) - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

setWorkflow(IWorkflow) - Method in class maltcms.datastructures.fragments.PairwiseAlignment

setWorkflow(IWorkflow) - Method in class maltcms.datastructures.fragments.PairwiseDistances

setWorkflow(IWorkflow) - Method in class maltcms.io.misc.StatsWriter

setWorkflow(IWorkflow) - Method in class maltcms.statistics.LogDeltaEvaluation

setWorkflow(IWorkflow) - Method in class maltcms.statistics.OneWayPeakAnova

setXAxisLabel(String) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

setYaxis_max(double) - Method in class maltcms.ui.charts.AChart

setYaxis_min(double) - Method in class maltcms.ui.charts.AChart

setYAxisLabel(String) - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

shareLayout(PartitionedArray) - Static method in class maltcms.datastructures.array.PartitionedArray

SHORTNAME - Variable in class maltcms.db.ui.MetaboliteViewModel

shouldBeMemberOf(IClique<T>, T) - Method in interface maltcms.datastructures.cluster.ICliqueMemberCriterion

shouldBeMemberOf(IClique<Peak1D>, Peak1D) - Method in class maltcms.datastructures.cluster.Peak1DBidiBestHitsCriterion

shouldBeSeparated(List<PeakArea2D>, IScalarArraySimilarity, IScanLine, List<ArrayDouble.D1>, boolean) - Method in class maltcms.commands.fragments2d.peakfinding.PeakSeparator

showCumScoreMatrix() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

showPwScoreMatrix() - Method in class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

showStat() - Method in class maltcms.datastructures.caches.AScanLineCache

Will view some statistical information about the cache usage.

showStat() - Method in interface maltcms.datastructures.caches.IScanLine

Will show some information about the usage.

showStat() - Method in class maltcms.datastructures.caches.ScanLineCache

Will view some statistical information about the cache usage.

showStat() - Method in class maltcms.datastructures.caches.ScanLineCacheOld

Will view some statistical information about the cache usage.

showStat() - Method in class maltcms.datastructures.caches.SparseScanLineCache

Will view some statistical information about the cache usage.

shutdown() - Method in class maltcms.db.connection.DB4oServer

sim(Peak2D, Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

sim(Peak2D, Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BiPaceBidirectionalBestHit

sim(Peak2D, Peak2D) - Method in class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

sim(Peak2D, Peak2D) - Method in interface maltcms.commands.fragments2d.peakfinding.bbh.IBidirectionalBestHit

SimilarityTools - Class in maltcms.math.functions.similarities

SimilarityTools() - Constructor for class maltcms.math.functions.similarities.SimilarityTools

SimplePeakPicking - Class in maltcms.commands.fragments2d.peakfinding.picking

SimplePeakPicking() - Constructor for class maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking

SingleLinkageAlgorithm - Class in maltcms.commands.fragments.cluster

Implements SingleLinkage clustering.

SingleLinkageAlgorithm() - Constructor for class maltcms.commands.fragments.cluster.SingleLinkageAlgorithm

size() - Method in class maltcms.datastructures.cluster.Clique

size() - Method in interface maltcms.datastructures.cluster.IClique

size() - Method in class maltcms.datastructures.peak.FiFoQueue

size() - Method in class maltcms.datastructures.peak.PeakArea2D

Getter.

size() - Method in class maltcms.datastructures.quadTree.QuadTree

size() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

size() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

size() - Method in class net.sf.maltcms.evaluation.spi.BeansXmlGenerator

smueller - package smueller

smueller.alignment - package smueller.alignment

smueller.datastructure - package smueller.datastructure

smueller.tools - package smueller.tools

SoftwareType - Class in maltcms.io.xml.mzData

Software information (the software that produced the peak list).

SoftwareType() - Constructor for class maltcms.io.xml.mzData.SoftwareType

sort(List<Rank<Ridge>>) - Method in class maltcms.datastructures.rank.RankSorter

sort(Array, Array) - Method in class smueller.datastructure.SortedJavArrays

SortedJavArrays - Class in smueller.datastructure

SortedJavArrays() - Constructor for class smueller.datastructure.SortedJavArrays

sortToOrder(List<String>, List<Rank<Ridge>>) - Method in class maltcms.datastructures.rank.RankSorter

SourceFileType - Class in maltcms.io.xml.mzData

Description of the source file, including location and type.

SourceFileType() - Constructor for class maltcms.io.xml.mzData.SourceFileType

SP - Variable in class maltcms.db.ui.MetaboliteViewModel

Sparse - Class in maltcms.datastructures.array

Sparse array implementation, mimicking a ucar.ma2.ArrayDouble.D1.

Sparse(Array, Array, int, int, int, double) - Constructor for class maltcms.datastructures.array.Sparse

Sparse(int, int, int) - Constructor for class maltcms.datastructures.array.Sparse

SparseArray - Class in maltcms.datastructures.array

SparseArray(int, int) - Constructor for class maltcms.datastructures.array.SparseArray

SparseScanLineCache - Class in maltcms.datastructures.caches

This class is a dataholder for mass spectra.

SparseTools - Class in maltcms.tools

Deprecated. You can use the usual array operations on Sparse array instances.

SparseTools() - Constructor for class maltcms.tools.SparseTools

Deprecated.

SpectrumDescType - Class in maltcms.io.xml.mzData

Description of the process of performing an acquisition Java class for spectrumDescType complex type.

SpectrumDescType() - Constructor for class maltcms.io.xml.mzData.SpectrumDescType

SpectrumDescType.PrecursorList - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

SpectrumDescType.PrecursorList() - Constructor for class maltcms.io.xml.mzData.SpectrumDescType.PrecursorList

SpectrumSettingsType - Class in maltcms.io.xml.mzData

Description of the parameters for the mass spectrometer for a given acquisition (or list of) Java class for spectrumSettingsType complex type.

SpectrumSettingsType() - Constructor for class maltcms.io.xml.mzData.SpectrumSettingsType

SpectrumSettingsType.AcqSpecification - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

SpectrumSettingsType.AcqSpecification() - Constructor for class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification

SpectrumSettingsType.AcqSpecification.Acquisition - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

SpectrumSettingsType.AcqSpecification.Acquisition() - Constructor for class maltcms.io.xml.mzData.SpectrumSettingsType.AcqSpecification.Acquisition

SpectrumSettingsType.SpectrumInstrument - Class in maltcms.io.xml.mzData

Java class for anonymous complex type.

SpectrumSettingsType.SpectrumInstrument() - Constructor for class maltcms.io.xml.mzData.SpectrumSettingsType.SpectrumInstrument

SpectrumType - Class in maltcms.io.xml.mzData

The structure tha captures the generation of a peak list (including the underlying acquisitions) Java class for spectrumType complex type.

SpectrumType() - Constructor for class maltcms.io.xml.mzData.SpectrumType

SpiderWebChart - Class in maltcms.ui.charts

Chart displaying a plot of different variables organized as a spider's web.

SpiderWebChart(String, CategoryDataset) - Constructor for class maltcms.ui.charts.SpiderWebChart

SpiderWebChart(String, String[], String[], double[][]) - Constructor for class maltcms.ui.charts.SpiderWebChart

split(String, String) - Method in class maltcms.io.csv.CSVReader

sq(Array) - Static method in class maltcms.tools.ArrayTools

sqrt(Array) - Static method in class maltcms.tools.ArrayTools2

Concrete implementation of a filter with a square root.

sqrt(List<Array>) - Static method in class maltcms.tools.ArrayTools2

Concrete implementation of a filter with a square root.

SqrtFilter - Class in maltcms.commands.filters.array

Will take the square root of all elements.

SqrtFilter() - Constructor for class maltcms.commands.filters.array.SqrtFilter

Default constructor.

standardDeviation(Array, double) - Method in class smueller.tools.Standardizer

Standardizer - Class in smueller.tools

Standardizer() - Constructor for class smueller.tools.Standardizer

startSeparationFor(List<PeakArea2D>, IScanLine, List<ArrayDouble.D1>, Tuple2D<ArrayDouble.D1, ArrayDouble.D1>) - Method in class maltcms.commands.fragments2d.peakfinding.PeakSeparator

StatsWriter - Class in maltcms.io.misc

Writes StatsMap objects to CSV Files.

StatsWriter() - Constructor for class maltcms.io.misc.StatsWriter

strToDoubArray(String) - Static method in class smueller.datastructure.ReBuild

structureWrite(IFileFragment, ArrayList<IVariableFragment>) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

structureWrite(IFileFragment, ArrayList<IVariableFragment>) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

submitFilter(String) - Method in class maltcms.db.ui.FilterButtonActionListener

Submit filter method for the extra Search Preferences Frame

sum(Array, Array) - Static method in class maltcms.tools.ArrayTools

Calculates A + B elementwise.

SupDataBinaryType - Class in maltcms.io.xml.mzData

Extension of binary data group for supplemental data Java class for supDataBinaryType complex type.

SupDataBinaryType() - Constructor for class maltcms.io.xml.mzData.SupDataBinaryType

SupDataType - Class in maltcms.io.xml.mzData

Data type for additional data vectors (beyond m/z and intensity).

SupDataType() - Constructor for class maltcms.io.xml.mzData.SupDataType

SupDescType - Class in maltcms.io.xml.mzData

Description of a supplemental data array Java class for supDescType complex type.

SupDescType() - Constructor for class maltcms.io.xml.mzData.SupDescType

supportedFormats() - Method in class maltcms.io.andims.NetcdfDataSource

supportedFormats() - Method in class maltcms.io.csv.FsaTxtDataSource

supportedFormats() - Method in class maltcms.io.xml.mzData.MZDataDataSource

supportedFormats() - Method in class maltcms.io.xml.mzML.MZMLDataSource

supportedFormats() - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

supportedFormats() - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

supportedFormats() - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

swapPath(ArrayList<Tuple2DI>) - Static method in class maltcms.tools.PathTools

Inverts pairs of matching indices.

SymbolConvert - Class in smueller.tools

SymbolConvert() - Constructor for class smueller.tools.SymbolConvert

symbolic(Array, double[]) - Static method in class smueller.tools.SymbolConvert

SymbolicRepresentationAlignment - Class in smueller

SymbolicRepresentationAlignment() - Constructor for class smueller.SymbolicRepresentationAlignment

T

TabbedPanel - Class in maltcms.ui

Visual class displaying the proposed partitioning of an array with a given set of anchors.

TabbedPanel(PartitionedArray, AnchorPairSet) - Constructor for class maltcms.ui.TabbedPanel

tableChanged(TableModelEvent) - Method in class maltcms.db.ui.MetaboliteView

tableChanged(TableModelEvent) - Method in class maltcms.ui.wizard.AnchorDefinitionPane

Task - Class in net.sf.maltcms.evaluation.spi.tasks

Task(List<String>, File, List<IPostProcessor>, File) - Constructor for class net.sf.maltcms.evaluation.spi.tasks.Task

terminate() - Method in class maltcms.db.QueryCallable

TestCallable - Class in maltcms.mpaxs

TestCallable() - Constructor for class maltcms.mpaxs.TestCallable

TestConfigurableCallable - Class in maltcms.mpaxs

TestConfigurableCallable() - Constructor for class maltcms.mpaxs.TestConfigurableCallable

TestRunnable - Class in maltcms.mpaxs

TestRunnable() - Constructor for class maltcms.mpaxs.TestRunnable

ThreePredecessorsOptimization - Class in maltcms.commands.distances.dtwng

ThreePredecessorsOptimization() - Constructor for class maltcms.commands.distances.dtwng.ThreePredecessorsOptimization

ThreePredecessorsOptimization.State - Enum in maltcms.commands.distances.dtwng

TicAreaNormalizer - Class in maltcms.datastructures.peak.normalization

TicAreaNormalizer() - Constructor for class maltcms.datastructures.peak.normalization.TicAreaNormalizer

TicDtwWorkerFactory - Class in maltcms.commands.fragments.cluster.pairwiseDistanceCalculator

TicDtwWorkerFactory() - Constructor for class maltcms.commands.fragments.cluster.pairwiseDistanceCalculator.TicDtwWorkerFactory

TICDynamicTimeWarp - Class in maltcms.commands.distances.dtw

Dynamic Time Warp on univariate Time Series, e.g. the total ion current (TIC).

TICDynamicTimeWarp() - Constructor for class maltcms.commands.distances.dtw.TICDynamicTimeWarp

TICHeatmapCoplot - Class in maltcms.commands.fragments.visualization

TICHeatmapCoplot() - Constructor for class maltcms.commands.fragments.visualization.TICHeatmapCoplot

TICPeakFinder - Class in maltcms.commands.fragments.peakfinding

Find Peaks based on TIC, estimates a local baseline and, based on a given signal-to-noise ratio, decides whether a maximum is a peak candidate or not.

TICPeakFinder() - Constructor for class maltcms.commands.fragments.peakfinding.TICPeakFinder

TICPeakListImporter - Class in maltcms.commands.fragments.io

TICPeakListImporter() - Constructor for class maltcms.commands.fragments.io.TICPeakListImporter

TICWarpInput - Class in maltcms.datastructures.warp

Specialization for TICs.

TICWarpInput(IFileFragment, IWorkflow) - Constructor for class maltcms.datastructures.warp.TICWarpInput

TiledArray - Class in maltcms.datastructures.array

TiledArray(int, int, int, int, double) - Constructor for class maltcms.datastructures.array.TiledArray

tilt(List<Array>) - Static method in class maltcms.tools.ArrayTools

Creates a new Array containing all values of elements in al along every dimension.

tiltD1(List<ArrayDouble.D1>) - Static method in class maltcms.tools.ArrayTools

Creates a new Array containing all values of elements in al along every dimension.

TN - Static variable in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

toArray() - Method in class maltcms.datastructures.peak.FiFoQueue

toArray(T[]) - Method in class maltcms.datastructures.peak.FiFoQueue

toArrays() - Method in class maltcms.datastructures.array.Sparse

toArrays(TreeMap<Double, Integer>) - Static method in class maltcms.tools.ArrayTools

toArrays(List<Tuple2DI>) - Static method in class maltcms.tools.PathTools

Constructs array representation from List of pairs of indices.

toCRS(List<Array>) - Static method in class maltcms.tools.ArrayTools

toDoubleArray(float[]) - Static method in class maltcms.tools.ImageTools

toFloatArray(double[]) - Static method in class maltcms.tools.ImageTools

toGraphML(IClusteringAlgorithm) - Static method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

toNewick() - Method in class maltcms.datastructures.cluster.BinaryCluster

toNewick() - Method in interface maltcms.datastructures.cluster.ICluster

TopHatFilter - Class in maltcms.commands.filters.array

TopHatFilter() - Constructor for class maltcms.commands.filters.array.TopHatFilter

toPointList(List<Tuple2DI>) - Static method in class maltcms.tools.PathTools

Converts a tuple 2D list into a point list.

toString() - Method in class maltcms.commands.ArrayStatsMap

toString(ThreePredecessorsOptimization.State) - Static method in enum maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State

toString() - Method in class maltcms.commands.fragments.alignment.CenterStarAlignment

toString() - Method in class maltcms.commands.fragments.alignment.PeakCliqueAlignment

toString() - Method in class maltcms.commands.fragments.alignment.ProgressiveTreeAlignment

toString() - Method in class maltcms.commands.fragments.cluster.ClusteringAlgorithm

toString() - Method in class maltcms.commands.fragments.io.ANDIChromImporter

toString() - Method in class maltcms.commands.fragments.io.ANDIMSExporter

toString() - Method in class maltcms.commands.fragments.io.CSVAnchorReader

toString() - Method in class maltcms.commands.fragments.io.MSPExporter

toString() - Method in class maltcms.commands.fragments.io.ObiWarplmataExporter

toString() - Method in class maltcms.commands.fragments.io.TICPeakListImporter

toString() - Method in class maltcms.commands.fragments.io.VariableDataExporter

toString() - Method in class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtEicPeakFinderCallable

toString() - Method in class maltcms.commands.fragments.peakfinding.cwtEicPeakFinder.CwtTicPeakFinderCallable

toString() - Method in class maltcms.commands.fragments.peakfinding.EICPeakFinder

toString() - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

toString() - Method in class maltcms.commands.fragments.preprocessing.DefaultVarLoader

toString() - Method in class maltcms.commands.fragments.preprocessing.DenseArrayProducer

toString() - Method in class maltcms.commands.fragments.preprocessing.MassFilter

toString() - Method in class maltcms.commands.fragments.visualization.Array1DVisualizer

toString() - Method in class maltcms.commands.fragments.visualization.ChromatogramVisualizer

toString() - Method in class maltcms.commands.fragments.visualization.EICHeatmapCoplot

toString() - Method in class maltcms.commands.fragments.visualization.MZIDistributionVisualizer

toString() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentMatrixVisualizer

toString() - Method in class maltcms.commands.fragments.visualization.PairwiseAlignmentVisualizer

toString() - Method in class maltcms.commands.fragments.visualization.ScoreDistributionVisualizer

toString() - Method in class maltcms.commands.fragments.visualization.TICHeatmapCoplot

toString() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated.

toString() - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

toString() - Method in class maltcms.commands.fragments.warp.PathWarp

toString() - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

toString() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.BidirectionalBestHit

toString() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.FastBidirectionalBestHit

toString() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.MissingPeak2D

toString() - Method in class maltcms.commands.fragments2d.peakfinding.bbh.Peak2DClique

toString() - Method in class maltcms.commands.fragments2d.peakfinding.CwtPeakFinder

toString() - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakExporter

toString() - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakIdentification

toString() - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakIntegration

toString() - Method in class maltcms.commands.fragments2d.peakfinding.output.PeakNormalization

toString() - Method in class maltcms.commands.fragments2d.peakfinding.picking.MaxSortPeakPicking

toString() - Method in class maltcms.commands.fragments2d.peakfinding.picking.SimplePeakPicking

toString() - Method in class maltcms.commands.fragments2d.peakfinding.SeededRegionGrowing

toString() - Method in class maltcms.commands.fragments2d.peakfinding.srg.OneByOneRegionGrowing

toString() - Method in class maltcms.commands.fragments2d.preprocessing.Data2DNormalizer

toString() - Method in class maltcms.commands.fragments2d.preprocessing.Default2DVarLoader

toString() - Method in class maltcms.commands.fragments2d.preprocessing.GCGCToGCMSConverter

toString() - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarProducer

toString() - Method in class maltcms.commands.fragments2d.preprocessing.MeanVarVis

toString() - Method in class maltcms.commands.fragments2d.preprocessing.ModulationExtractor

toString() - Method in class maltcms.commands.fragments2d.testing.Alignment2D

toString() - Method in class maltcms.commands.fragments2d.visualization.Chromatogram2DVisualizer

toString() - Method in class maltcms.commands.fragments2d.visualization.DeltaMasses

toString() - Method in class maltcms.commands.fragments2d.visualization.GradientVisualizer

toString() - Method in class maltcms.commands.fragments2d.visualization.MassSpectrumVisualization

toString() - Method in class maltcms.commands.fragments2d.warp.CreateHorizontalTicVector

toString() - Method in class maltcms.commands.fragments2d.warp.DTW2DPeakAreaVisualizer

toString() - Method in class maltcms.commands.fragments2d.warp.DTW2DTicVisualizer

toString() - Method in class maltcms.commands.fragments2d.warp.ScanlineFilterTicWarp

toString() - Method in class maltcms.commands.fragments2d.warp.ScanlineHorizontalTicWarp

toString() - Method in class maltcms.commands.fragments2d.warp.ScanlineMaxMSWarp

toString() - Method in class maltcms.commands.fragments2d.warp.ScanlineMeanMSWarp

toString() - Method in class maltcms.commands.fragments2d.warp.ScanlineTicWarp

toString() - Method in class maltcms.commands.fragments2d.warp.visualization.Default2DTWVisualizer

toString() - Method in class maltcms.commands.fragments2d.warp.visualization.Ident2DTWVisualizer

toString() - Method in interface maltcms.datastructures.array.IArrayD2Byte

toString() - Method in interface maltcms.datastructures.array.IArrayD2Double

toString() - Method in class maltcms.datastructures.array.PartitionedArray

toString() - Method in class maltcms.datastructures.caches.RingBuffer

toString() - Method in class maltcms.datastructures.cluster.BinaryCluster

toString() - Method in class maltcms.datastructures.cluster.Clique

toString() - Method in interface maltcms.datastructures.cluster.ICluster

toString() - Method in class maltcms.datastructures.ms.Experiment1D

toString() - Method in class maltcms.datastructures.ms.Metabolite

toString() - Method in class maltcms.datastructures.ms.Metabolite2D

toString() - Method in class maltcms.datastructures.ms.RetentionInfo

toString() - Method in class maltcms.datastructures.peak.Clique

toString() - Method in class maltcms.datastructures.peak.Peak

toString() - Method in class maltcms.datastructures.peak.PeakArea2D

toString() - Method in class maltcms.datastructures.quadTree.QuadTreeNode

toString() - Method in class maltcms.datastructures.rank.Rank

toString() - Method in class maltcms.datastructures.ridge.Ridge

toString() - Method in class maltcms.experimental.bipace.datastructures.api.Clique

toString() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2D

toString() - Method in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumn

toString() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

toString() - Method in class net.sf.maltcms.evaluation.api.Category

toString() - Method in class net.sf.maltcms.evaluation.api.classification.Category

toString() - Method in class net.sf.maltcms.evaluation.api.classification.Entity

toString() - Method in class net.sf.maltcms.evaluation.api.classification.EntityGroup

toString() - Method in class net.sf.maltcms.evaluation.api.Entity

toString() - Method in class net.sf.maltcms.evaluation.api.EntityGroup

toString() - Method in class net.sf.maltcms.evaluation.api.EntityGroupClassificationResult

toString() - Method in class net.sf.maltcms.evaluation.api.PeakRTFeatureVector

toString() - Method in class net.sf.maltcms.evaluation.api.PerformanceMetrics

toString() - Method in class net.sf.maltcms.evaluation.spi.classification.EntityGroupClassificationResult

toString() - Method in class net.sf.maltcms.evaluation.spi.classification.PeakRTFeatureVector

toString() - Method in class net.sf.maltcms.evaluation.spi.classification.PerformanceMetrics

toString() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Chromatogram

toString() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Creator

toString() - Method in class net.sf.maltcms.evaluation.spi.xcalibur.Peak

toString(Cell[]) - Static method in class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

toTupleList(List<Point>) - Static method in class maltcms.tools.PathTools

Converts a point list into a tuple 2D list.

TP - Static variable in class net.sf.maltcms.evaluation.api.alignment.AlignmentColumnComparator

traceback(int[][]) - Method in class maltcms.experimental.operations.EditDistance

Returns a String encoding an optimal edit sequence, recovered from the edit matrix d.

traceback(Point[][]) - Method in class maltcms.experimental.operations.MSPeaklistAlignment

traceback(byte[][], IFileFragment, IFileFragment) - Method in class maltcms.tools.PathTools

Calculates a trace based on the byte[][] argument.

translatePointToImageCoord(Point2D, Rectangle2D) - Method in class maltcms.ui.charts.XYBPlot

Translates a given screen point from a mouse event to the coredponding image coordinates.

translatePointToImageCoords(double, double) - Method in class maltcms.ui.charts.XYBPlot

Maps a point from axis coordinates to image coordinates.

transpose(List<Array>) - Static method in class maltcms.tools.ArrayTools2

Transpose a list of arrays.

TreatmentGroup1D - Class in maltcms.datastructures.ms

TreatmentGroup1D() - Constructor for class maltcms.datastructures.ms.TreatmentGroup1D

TreatmentGroup2D - Class in maltcms.datastructures.ms

TreatmentGroup2D() - Constructor for class maltcms.datastructures.ms.TreatmentGroup2D

TwoFeatureVectorOperation - Class in maltcms.commands.distances.dtwng

TwoFeatureVectorOperation() - Constructor for class maltcms.commands.distances.dtwng.TwoFeatureVectorOperation

U

uncaughtException(Thread, Throwable) - Method in class maltcms.runtime.LocalHostLauncher

Deprecated.

uncaughtException(Thread, Throwable) - Method in class net.sf.maltcms.apps.Maltcms

unique(List<T>) - Static method in class maltcms.tools.MaltcmsTools

Creates a copy of l, then sorts the list and returns a condensed version of the list, with only one instance of every Object remaining.

unlog(Array) - Static method in class smueller.datastructure.ReBuild

unscale(Array, double, double) - Static method in class smueller.datastructure.ReBuild

update(IClique<T>, T) - Method in interface maltcms.datastructures.cluster.ICliqueUpdater

update(IMetabolite) - Method in interface maltcms.datastructures.ms.IMetabolite

update(IMetabolite) - Method in class maltcms.datastructures.ms.Metabolite

update(IMetabolite) - Method in class maltcms.datastructures.ms.Metabolite2D

update() - Method in class maltcms.experimental.bipace.datastructures.api.CliqueStatistics

update() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak1DCliqueStatistics

update() - Method in class maltcms.experimental.bipace.datastructures.spi.Peak2DCliqueStatistics

updateBackground() - Method in class maltcms.ui.charts.XYBPlot

This method will update the background image on the chart.

UPGMAAlgorithm - Class in maltcms.commands.fragments.cluster

Implements UPGMA Algorithm by ?

UPGMAAlgorithm() - Constructor for class maltcms.commands.fragments.cluster.UPGMAAlgorithm

UPGMAAlgorithm(double[][], String[]) - Constructor for class maltcms.commands.fragments.cluster.UPGMAAlgorithm

UPGMAAlgorithm(double[][], TupleND<IFileFragment>, PairwiseFeatureSequenceSimilarity) - Constructor for class maltcms.commands.fragments.cluster.UPGMAAlgorithm

UserParam - Class in maltcms.io.xml.bindings.openms.featurexml

Type-Name-Value type for annotations Java class for userParam complex type.

UserParam() - Constructor for class maltcms.io.xml.bindings.openms.featurexml.UserParam

UserParamType - Enum in maltcms.io.xml.bindings.openms.featurexml

Java class for UserParamType.

UserParamType - Class in maltcms.io.xml.mzData

Uncontrolled user parameters (vocabulary).

UserParamType() - Constructor for class maltcms.io.xml.mzData.UserParamType

V

value() - Method in enum maltcms.io.xml.bindings.openms.featurexml.DigestionEnzyme

value() - Method in enum maltcms.io.xml.bindings.openms.featurexml.MassType

value() - Method in enum maltcms.io.xml.bindings.openms.featurexml.UserParamType

valueChanged(ListSelectionEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

valueOf(String) - Static method in enum maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.datastructures.peak.PeakIntegration

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.datastructures.peak.PeakType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.datastructures.quadTree.Quad

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.io.xml.bindings.openms.featurexml.DigestionEnzyme

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.io.xml.bindings.openms.featurexml.MassType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.io.xml.bindings.openms.featurexml.UserParamType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum maltcms.tools.PathTools.Direction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.maltcms.evaluation.spi.xcalibur.RTUnit

Returns the enum constant of this type with the specified name.

values() - Static method in enum maltcms.commands.distances.dtwng.ThreePredecessorsOptimization.State

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.datastructures.peak.PeakIntegration

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.datastructures.peak.PeakType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.datastructures.quadTree.Quad

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.io.xml.bindings.openms.featurexml.DigestionEnzyme

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.io.xml.bindings.openms.featurexml.MassType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.io.xml.bindings.openms.featurexml.UserParamType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum maltcms.tools.PathTools.Direction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Method in class net.sf.maltcms.evaluation.api.alignment.MultipleAlignment

values() - Static method in enum net.sf.maltcms.evaluation.spi.xcalibur.RTUnit

Returns an array containing the constants of this enum type, in the order they are declared.

VariableDataExporter - Class in maltcms.commands.fragments.io

Writes 1D-variables to csv files, one entry per row.

VariableDataExporter() - Constructor for class maltcms.commands.fragments.io.VariableDataExporter

VariableSelectionPanel - Class in maltcms.ui.charts

VariableSelectionPanel() - Constructor for class maltcms.ui.charts.VariableSelectionPanel

Creates new form VariableSelectionPanel

VBetaFamilyComparison - Class in maltcms.commands.fragments.spectratyping

VBetaFamilyComparison() - Constructor for class maltcms.commands.fragments.spectratyping.VBetaFamilyComparison

vector(int) - Static method in class maltcms.tools.ArrayTools

vergleiche(int, int) - Method in class smueller.alignment.Alignment

visit(LinkedList<Tuple2D<Point2D, T>>) - Method in class maltcms.datastructures.quadTree.QuadTreeNodeDepthFirstVisitor

visit(LinkedList<Tuple2D<Point2D, T>>) - Method in interface maltcms.datastructures.quadTree.QuadTreeNodeVisitor

Visualization2D - Class in maltcms.commands.fragments2d.testing

Visualization2D() - Constructor for class maltcms.commands.fragments2d.testing.Visualization2D

VisualizationPane - Class in maltcms.ui.wizard

VisualizationPane() - Constructor for class maltcms.ui.wizard.VisualizationPane

Creates new form VisualizationPane

visualize(IFileFragment, Array, Array, double[], ArrayInt.D1, double, PolynomialSplineFunction) - Method in class maltcms.commands.fragments.peakfinding.TICPeakFinder

visualizePeakSimilarities(HashMap<String, List<Peak>>, int, String, IWorkflow) - Method in class maltcms.commands.fragments.alignment.peakCliqueAlignment.PeakSimilarityVisualizer

visualizePeakSimilarities(HashMap<String, List<Peak>>, int, String) - Method in class maltcms.experimental.bipace.peakCliqueAlignment.PeakSimilarityVisualizer

W

warp(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, boolean, IWorkflow) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated. Warps by projecting data from originalFile to ref, given the alignment path. toLHS determines, whether the alignment reference ref is on the left hand side of the alignment path, or on the right hand side.

warp(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, boolean, IWorkflow) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

Warps by projecting data from originalFile to ref, given the alignment path. toLHS determines, whether the alignment reference ref is on the left hand side of the alignment path, or on the right hand side.

warp(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, boolean, IWorkflow) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

Warps by projecting data from originalFile to ref, given the alignment path. toLHS determines, whether the alignment reference ref is on the left hand side of the alignment path, or on the right hand side.

warp1D(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, List<String>, boolean) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated. Warp non-indexed arrays, which are for example scan_acquisisition_time, tic etc.

warp1D(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, List<String>, boolean) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

Warp non-indexed arrays, which are for example scan_acquisisition_time, tic etc.

warp1D(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, List<String>, boolean) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

Warp non-indexed arrays, which are for example scan_acquisisition_time, tic etc.

warp2D(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, List<String>, boolean) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated. Warp indexed arrays, which are lists of 1D arrays, so pseudo 2D.

warp2D(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, List<String>, boolean) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

Warp indexed arrays, which are lists of 1D arrays, so pseudo 2D.

warp2D(IFileFragment, IFileFragment, IFileFragment, List<Tuple2DI>, List<String>, boolean) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

Warp indexed arrays, which are lists of 1D arrays, so pseudo 2D.

warpAnchors(IFileFragment, IFileFragment, List<Tuple2DI>, boolean) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp

Deprecated. Warp anchors according to pairwise scan mapping in path, reads anchors from processedFile and stores them in warped file.

warpAnchors(IFileFragment, IFileFragment, List<Tuple2DI>, boolean) - Method in class maltcms.commands.fragments.warp.ChromatogramWarp2

Warp anchors according to pairwise scan mapping in path, reads anchors from processedFile and stores them in warped file.

warpAnchors(IFileFragment, IFileFragment, List<Tuple2DI>, boolean) - Method in class maltcms.commands.fragments.warp.RTGroupCorrectionWarp

Warp anchors according to pairwise scan mapping in path, reads anchors from processedFile and stores them in warped file.

WarpMap2D - Class in maltcms.datastructures.warp

WarpMap2D() - Constructor for class maltcms.datastructures.warp.WarpMap2D

windowActivated(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

windowClosed(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

windowClosing(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

windowDeactivated(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

windowDeiconified(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

windowIconified(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

windowOpened(WindowEvent) - Method in class maltcms.db.ui.MetaboliteListSelectionListener

WorkerFactory - Class in maltcms.commands.fragments.alignment.peakCliqueAlignment

WorkerFactory() - Constructor for class maltcms.commands.fragments.alignment.peakCliqueAlignment.WorkerFactory

write(IFileFragment) - Method in class maltcms.io.andims.NetcdfDataSource

write(IFileFragment) - Method in class maltcms.io.csv.FsaTxtDataSource

write(IFileFragment) - Method in class maltcms.io.misc.StatsWriter

write(StatsMap...) - Method in class maltcms.io.misc.StatsWriter

write(IFileFragment) - Method in class maltcms.io.xml.mzData.MZDataDataSource

write(IFileFragment) - Method in class maltcms.io.xml.mzML.MZMLDataSource

write(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLDataSource

write(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLSaxDataSource

write(IFileFragment) - Method in class maltcms.io.xml.mzXML.MZXMLStaxDataSource

writeAlignmentPath(String, String, List<Tuple2DI>, IArrayD2Double, String, String, String, String) - Method in class maltcms.io.csv.CSVWriter

writeArray(String, String, Array) - Method in class maltcms.io.csv.CSVWriter

writeArray2D(String, String, ArrayDouble.D2) - Method in class maltcms.io.csv.CSVWriter

writeArray2DwithLabels(String, String, ArrayDouble.D2, ArrayChar.D2, Class<?>, WorkflowSlot, Date, IFileFragment...) - Method in class maltcms.io.csv.CSVWriter

writeArrayListOfArrays(String, String, List<Array>) - Method in class maltcms.io.csv.CSVWriter

writeArrayListsOfArrays(String, String, List<Array>, List<Array>) - Method in class maltcms.io.csv.CSVWriter

writeExternal(ObjectOutput) - Method in class maltcms.datastructures.ms.Experiment1D

writefile(String, String, Vector<OptimalAlignmentVector>, double[][], String, double[][], String, int, Alignment, int, int, IWorkflow) - Method in class smueller.datastructure.AlignmentOutput

writeImage(JFreeChart, File, int, int) - Static method in class maltcms.tools.ImageTools

writeLine(PrintWriter, List<String>) - Method in class maltcms.io.csv.CSVWriter

writeOneFilePerArray(String, String, List<Array>) - Method in class maltcms.io.csv.CSVWriter

writePNG(JFreeChart, FileOutputStream, int, int) - Static method in class maltcms.tools.ImageTools

writeStatsMap(IFileFragment, StatsMap) - Method in class maltcms.io.csv.CSVWriter

writeStatsMap(String, String, StatsMap) - Method in class maltcms.io.csv.CSVWriter

writeStatsMaps(String, String, StatsMap...) - Method in class maltcms.io.csv.CSVWriter

writeSVG(JFreeChart, FileOutputStream, int, int) - Static method in class maltcms.tools.ImageTools

writeTableByCols(String, String, List<List<String>>, WorkflowSlot) - Method in class maltcms.io.csv.CSVWriter

writeTableByRows(String, String, List<List<String>>, WorkflowSlot) - Method in class maltcms.io.csv.CSVWriter

X

XLSIOProvider - Class in net.sf.maltcms.evaluation.spi.xcalibur

Based on ExcelTools by Alexander Bunkowski.

XLSIOProvider() - Constructor for class net.sf.maltcms.evaluation.spi.xcalibur.XLSIOProvider

XmlAlignmentWriter - Class in maltcms.experimental.bipace.peakCliqueAlignment.io

XmlAlignmentWriter() - Constructor for class maltcms.experimental.bipace.peakCliqueAlignment.io.XmlAlignmentWriter

XYBPlot - Class in maltcms.ui.charts

This class extends the XYPlot to a Plot with a zoomable background image.

XYBPlot(String, NumberAxis, NumberAxis) - Constructor for class maltcms.ui.charts.XYBPlot

Default constructor.

XYBPlot(String, String, String) - Constructor for class maltcms.ui.charts.XYBPlot

Default constructor.

XYChart - Class in maltcms.ui.charts

Chart to display one Variable's data, or additionally combined with domain values.

XYChart(String, String[], Array[], Array[], Array, Array, String[], String, String) - Constructor for class maltcms.ui.charts.XYChart

XYChart(String, String[], Array[], Array[], String, String, boolean) - Constructor for class maltcms.ui.charts.XYChart

XYChart(String, String[], Array[], Array[], String, String) - Constructor for class maltcms.ui.charts.XYChart

XYChart(String, String[], Array[], String, String) - Constructor for class maltcms.ui.charts.XYChart

XYZChart - Class in maltcms.ui.charts

Heatmap like chart, using to variable's values as indices for a third variable's value.

XYZChart(String, String, String, String, Array, ArrayList<Array>, ArrayList<Array>) - Constructor for class maltcms.ui.charts.XYZChart

Z

ZipResourceExtractor - Class in maltcms.io

ZipResourceExtractor() - Constructor for class maltcms.io.ZipResourceExtractor

zoomDomainAxes(double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

zoomDomainAxes(double, PlotRenderingInfo, Point2D, boolean) - Method in class maltcms.ui.charts.XYBPlot

zoomDomainAxes(double, double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

zoomRangeAxes(double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

zoomRangeAxes(double, PlotRenderingInfo, Point2D, boolean) - Method in class maltcms.ui.charts.XYBPlot

zoomRangeAxes(double, double, PlotRenderingInfo, Point2D) - Method in class maltcms.ui.charts.XYBPlot

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