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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