- s3 - Variable in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3Source
-
- sample(Peak, ImgPlus<T>) - Method in class de.mpg.biochem.mars.image.PeakShape
-
- sample(double, double, RandomAccessibleInterval<T>, double, double) - Method in class de.mpg.biochem.mars.image.PeakShape
-
- save() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Saves the MoleculeArchive to the file from which it was opened.
- save() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Saves the MoleculeArchive to the file from which it was opened.
- save(MoleculeArchive, String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveIOPlugin
-
- save(MoleculeArchive, Location) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveIOPlugin
-
- save(MarsTable, String) - Method in class de.mpg.biochem.mars.table.MarsTableIOPlugin
-
- save(MarsTable, Location) - Method in class de.mpg.biochem.mars.table.MarsTableIOPlugin
-
- saveAs(File) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Saves MoleculeArchive to the given file destination.
- saveAs(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Saves MoleculeArchive to the given file destination.
- saveAs(File) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Saves MoleculeArchive to the given file destination in smile format.
- saveAs(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Saves MoleculeArchive to the given file destination in smile format.
- saveAs(File) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Saves the table to the file path in smile encoded json format.
- saveAsCSV(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Saves the table to the string file path specified in csv format.
- saveAsJson(File) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
- saveAsJson(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
- saveAsJson(File) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Saves MoleculeArchive to the given file destination in json format.
- saveAsJson(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Saves MoleculeArchive to the given file destination in json format.
- saveAsJSON(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Saves the table to the file path specified in json format.
- saveAsJsonVirtualStore(File) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format with .json file extension.
- saveAsJsonVirtualStore(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format with .json file extension.
- saveAsJsonVirtualStore(String, int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format with .json file extension.
- saveAsJsonVirtualStore(File, int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format with .json file extension.
- saveAsJsonVirtualStore(File) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format and with .json file extensions.
- saveAsJsonVirtualStore(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format and with .json file extensions.
- saveAsJsonVirtualStore(String, int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format and with .json file extensions.
- saveAsJsonVirtualStore(File, int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
json format with .json file extension.
- saveAsVirtualStore(File) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsVirtualStore(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsVirtualStore(String, int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsVirtualStore(File, int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsVirtualStore(File) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside.
- saveAsVirtualStore(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsVirtualStore(String, int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsVirtualStore(File, int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Creates the directory given and a virtual store inside with all files in
smile format with .sml file extension.
- saveAsYAMT(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Saves the table to the file path specified in yamt format.
- saveMetadataToSource(MoleculeArchiveSource, I, JsonFactory) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Saves a MarsMetadata record as a json file.
- saveMoleculeToSource(MoleculeArchiveSource, M, JsonFactory) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Saves a molecule record as a json file.
- scale(double) - Method in class de.mpg.biochem.mars.image.PeakShape
-
- SCHEMA - Static variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
- ScijavaTableConversionCommand - Class in de.mpg.biochem.mars.table.commands
-
- ScijavaTableConversionCommand() - Constructor for class de.mpg.biochem.mars.table.commands.ScijavaTableConversionCommand
-
- SegmentDistributionBuilder - Class in de.mpg.biochem.mars.kcp
-
- SegmentDistributionBuilder(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, ArrayList<String>, String, String, double, double, int, LogService, StatusService) - Constructor for class de.mpg.biochem.mars.kcp.SegmentDistributionBuilder
-
- sem(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Calculates the standard error of the mean for the column given.
- sem(String, String, double, double) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Calculates the standard error of the mean for the meanColumn within the
range given for a rowSelectionColumn (inclusive of bounds).
- set(WidgetModel) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveWidget
-
- set(WidgetModel) - Method in class de.mpg.biochem.mars.table.MarsTableWidget
-
- setAcquisitionDate(Timestamp) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setAddPosition(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setAddSegmentsTable(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setAddToMe(ImagePlus) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setAddToRoiManager(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setAddToRoiManager(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setAffineTransform2D(double, double, double, double, double, double) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setAnalyzeRegion(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setAnalyzeRegion(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setApplyInverseTransformation(boolean) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.molecule.commands.AddTimeCommand
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setArchive(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>) - Method in class de.mpg.biochem.mars.molecule.commands.VarianceCalculatorCommand
-
- setArchive1(SingleMoleculeArchive) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setArchive1Name(String) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setArchive2(SingleMoleculeArchive) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setArchive2Name(String) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setArchive3(SingleMoleculeArchive) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setArchive3Name(String) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setAscending(boolean) - Method in class de.mpg.biochem.mars.table.commands.MarsTableSorterCommand
-
- setBackgroundImage(ImagePlus) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setBackgroundRegion(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setBackgroundTag(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setBackwardLink(Peak) - Method in class de.mpg.biochem.mars.image.Peak
-
- setBackwardLinkID(long) - Method in class de.mpg.biochem.mars.image.Peak
-
- setBinning(Binning) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setC(int) - Method in class de.mpg.biochem.mars.image.Peak
-
- setC(NonNegativeInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setCalculateBackgroundSigma(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setCalculateDrift(boolean) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setCancelCallback(Consumer<Void>) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- setChannel(int) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setChannel(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setChannel(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setChannel(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setChannel(int) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setChannel(MarsOMEChannel, int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setChannel(int) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Set the channel for this molecule.
- setChannel(int) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setChannel(int) - Method in interface de.mpg.biochem.mars.molecule.Molecule
-
Set the channel for this molecule record.
- setChannel(int) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setChannel(int) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setChannelIndex(int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setChannelSet(Set<Integer>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the set of molecule channels in use.
- setChannelSet(Set<Integer>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the set of molecule channels in use.
- setColocalize(boolean) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setColocalizeSearchRadius(int) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setColor(String) - Method in class de.mpg.biochem.mars.util.MarsPosition
-
Set the hex color string.
- setColor(String) - Method in class de.mpg.biochem.mars.util.MarsRegion
-
Set the hex color string.
- setColorName(String) - Method in class de.mpg.biochem.mars.image.Peak
-
- setColumn(String) - Method in class de.mpg.biochem.mars.molecule.commands.VarianceCalculatorCommand
-
- setColumn(String) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setColumn(String) - Method in class de.mpg.biochem.mars.table.commands.MarsTableSorterCommand
-
- setColumn(String) - Method in class de.mpg.biochem.mars.util.MarsPosition
-
Set the name of the column the position value refers to.
- setColumn(String) - Method in class de.mpg.biochem.mars.util.MarsRegion
-
Set the name of the column the start and end values refer to.
- setColumnSet(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the unique set of column names in use in molecule DataTables.
- setColumnSet(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the unique set of column names in use in molecule Tables.
- setComments(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Sets the global comments.
- setComments(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Overwrite archive comments with new set of comments.
- setComments(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Sets the global comments.
- setComments(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Overwrite archive comments with new set of comments.
- setConfidenceLevel(double) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setContainerPathUpdateCallback(Consumer<String>) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- setContent(String) - Method in class de.mpg.biochem.mars.util.MarsDocument
-
- setCorrectDrift(boolean) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setCorrectDrift(boolean) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.GradientCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setDataset(Dataset) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setDeltaT(Time) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setDescription(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setDetectorManufacturer(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setDetectorModel(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setDetectorSerialNumber(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setDetectorSettingsID(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setDetectorType(DetectorType) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setDimensionOrder(DimensionOrder) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setDirection(String) - Method in class de.mpg.biochem.mars.image.commands.GradientCommand
-
- setDirectory(String) - Method in class de.mpg.biochem.mars.molecule.commands.MergeCommand
-
- setDirectory(File) - Method in class de.mpg.biochem.mars.molecule.commands.MergeCommand
-
- setDirectory(String) - Method in class de.mpg.biochem.mars.molecule.commands.MergeVirtualStoresCommand
-
- setDirectory(File) - Method in class de.mpg.biochem.mars.molecule.commands.MergeVirtualStoresCommand
-
- setDNALength(int) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setDNASearchRadius(double) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setDogFilterRadius(double) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setDogFilterRadius(double) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setDogFilterRadius(double) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setDogFilterRadius(double) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setDogFilterRadius(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setElectronicOffset(double) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setEnd(double) - Method in class de.mpg.biochem.mars.util.MarsRegion
-
Set the upper bound of the region.
- setExcludedTimePointsList(String) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setExcludedTimePointsList(String) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setExposureTime(Time) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setField(String, double) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setFields(Map<String, Double>) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setFile(File) - Method in class de.mpg.biochem.mars.table.MarsTable
-
- setFilename(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setFilter(double, double) - Method in class de.mpg.biochem.mars.kcp.SegmentDistributionBuilder
-
- setFilterByMedianIntensity(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setFilterByMedianIntensity(boolean) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setFilterByVariance(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setFilterByVariance(boolean) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setFilterColocalizingRois(boolean) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setFilterOriginalRois(boolean) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setFilterTable(MarsTable) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setFindNegativePeaks(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setFindNegativePeaks(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setFit(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setFit(boolean) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setFitPeaks(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setFitRadius(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setFitRadius(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setFitRadius(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setFitRadius(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setFitSecondOrder(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setFitSecondOrder(boolean) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setFitSteps(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setFitSteps(boolean) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setForwardLink(Peak) - Method in class de.mpg.biochem.mars.image.Peak
-
- setForwardLinkID(long) - Method in class de.mpg.biochem.mars.image.Peak
-
- setFrom(double) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setGain(Double) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setGaussianSigma(double) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setGaussianSigma(double) - Method in class de.mpg.biochem.mars.image.commands.GradientCommand
-
- setGaussianSigma(double) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setGenerateDNACountTable(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setGenerateDNATable(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setGeneratePeakCountTable(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setGeneratePeakTable(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setGlobalSigma(double) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setGridProcess(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setGroupColumn(String) - Method in class de.mpg.biochem.mars.table.commands.MarsTableSorterCommand
-
- setHorizontalGridRegions(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setID(long) - Method in class de.mpg.biochem.mars.image.Peak
-
- setID(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setID(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setIFD(NonNegativeInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setImage(ImagePlus) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setImage(MarsOMEImage, int) - Method in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
-
- setImage(MarsOMEImage, int) - Method in interface de.mpg.biochem.mars.metadata.MarsMetadata
-
- setImage(MarsOMEImage) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setImage(MarsOMEImage, int) - Method in class de.mpg.biochem.mars.metadata.OLDMarsMetadata
-
- setImage(int) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Set the image index for this molecule.
- setImage(int) - Method in interface de.mpg.biochem.mars.molecule.Molecule
-
Set the image position for this molecule record.
- setImageID(int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setImageID(int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setImagePlus(ImagePlus) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setImagePlus(ImagePlus) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setIncludeTags(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setIncludeTags(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setInnerRadius(int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setInnerRadius(int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setInputX(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setInputY(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setIntegrate(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setIntegrate(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setIntegrationChannel(int, String) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
Method used to set the channels that will be integrated in a script.
- setIntegrationChannel(String, String) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
Method used to set the channels that will be integrated in a script.
- setIntegrationInnerRadius(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setIntegrationInnerRadius(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setIntegrationOuterRadius(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setIntegrationOuterRadius(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setIntensity(double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setInterpolationFactor(double) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setJsonField(String, MarsUtil.ThrowingConsumer<JsonGenerator, IOException>, MarsUtil.ThrowingConsumer<JsonParser, IOException>) - Method in class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord
-
- setJsonField(String, MarsUtil.ThrowingConsumer<JsonGenerator, IOException>, MarsUtil.ThrowingConsumer<JsonParser, IOException>) - Method in interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord
-
- setJsonField(String, MarsUtil.ThrowingConsumer<JsonGenerator, IOException>, MarsUtil.ThrowingConsumer<JsonParser, IOException>) - Method in class de.mpg.biochem.mars.table.MarsTable
-
- setKeepOriginals(boolean) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setLeaf(boolean) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
-
- setLocalOtsuRadius(int) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setM00(double) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setM00(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setM01(double) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setM01(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setM02(double) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setM02(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setM10(double) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setM10(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setM11(double) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setM11(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setM12(double) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setM12(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setMax(double) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setMaxDifferenceT(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMaxDifferenceT(int) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMaxDifferenceX(double) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMaxDifferenceX(double) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMaxDifferenceY(double) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMaxDifferenceY(double) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMeanBackground(double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setMedianBackground(double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setMedianIntensity(int) - Method in class de.mpg.biochem.mars.image.DNASegment
-
- setMedianIntensityLowerBound(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setMedianIntensityLowerBound(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setMessage(String) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- setMetadataUID(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Set the UID of the
MarsMetadata record associated with this
molecule.
- setMetadataUID(String) - Method in interface de.mpg.biochem.mars.molecule.Molecule
-
Set the UID of the
MarsMetadata record associated with this
molecule.
- setMetadataUIDSource(String) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
Determines whether the metadata UID is taken directly from the
image metadata or randomly generated.
- setMetadataUIDSource(String) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setMetadataUIDSource(String) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMetadataUIDSource(String) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMicroscope(String) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setMicroscope(String) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setMicroscope(String) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMicroscope(String) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMicroscopeName(String) - Method in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
-
Set the name of the microscope used for data collection.
- setMicroscopeName(String) - Method in interface de.mpg.biochem.mars.metadata.MarsMetadata
-
Set the name of the microscope used for data collection.
- setMicroscopeName(String) - Method in class de.mpg.biochem.mars.metadata.OLDMarsMetadata
-
- setMin(double) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setMinimumArea(double) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMinimumDistance(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setMinimumDistance(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setMinimumDistance(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMinimumDistance(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setMinimumDistance(int) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMinimumRsquared(double) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setMinimumRsquared(double) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMinimumTrackLength(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setMinimumTrackLength(int) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setMode(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setMoleculeIdColumn(String) - Method in class de.mpg.biochem.mars.molecule.commands.BuildArchiveFromTableCommand
-
- setN5(boolean) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setN5Dataset(String) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setName(String) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setName(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setName(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setName(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Set the name of the archive.
- setName(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Set the name of the archive.
- setName(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Sets the name of the table.
- setName(String) - Method in class de.mpg.biochem.mars.util.MarsDocument
-
Set position name.
- setName(String) - Method in class de.mpg.biochem.mars.util.MarsPosition
-
Set position name.
- setName(String) - Method in class de.mpg.biochem.mars.util.MarsRegion
-
Set the region name.
- setNotes(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
-
Sets the notes for this record.
- setNotes(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
-
Sets the notes for this record.
- setNSTD(double) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setNumberOfMetadatas(int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Set the number of MarsMetadata records in the archive.
- setNumberOfMetadatas(int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Set the number of MarsMetadata records in the archive.
- setNumberOfMolecules(int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Set the number of molecule in the archive.
- setNumberOfMolecules(int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Set the number of molecule in the archive.
- setOpacity(double) - Method in class de.mpg.biochem.mars.util.MarsRegion
-
Set the opacity of the region.
- setOptimalDNALength(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setOptimalDNALength(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setOuterRadius(int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setOuterRadius(int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setOutputX(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setOutputY(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setParameter(String, double) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
-
Add or update a parameter value.
- setParameter(String, String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
-
Add or update a parameter value.
- setParameter(String, boolean) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
-
Add or update a parameter value.
- setParameter(String, double) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Add or update a parameter value.
- setParameter(String, String) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Add or update a parameter value.
- setParameter(String, boolean) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Add or update a parameter value.
- setParameter(String, double) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
-
Add or update a parameter value.
- setParameter(String, String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
-
Add or update a parameter value.
- setParameter(String, boolean) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
-
Add or update a parameter value.
- setParameterName(String) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setParameterName(String) - Method in class de.mpg.biochem.mars.molecule.commands.VarianceCalculatorCommand
-
- setParameterSet(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the set of parameter names in use.
- setParameterSet(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the set of molecule parameter names in use.
- setParent(MoleculeArchive<? extends Molecule, ? extends MarsMetadata, ? extends MoleculeArchiveProperties<?, ?>, ? extends MoleculeArchiveIndex<?, ?>>) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
-
- setParent(MoleculeArchive<? extends Molecule, ? extends MarsMetadata, ? extends MoleculeArchiveProperties<?, ?>, ? extends MoleculeArchiveIndex<?, ?>>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Set the parent MoleculeArchive that these MoleculeArchiveProperties belong
to.
- setParent(MoleculeArchive<? extends Molecule, ? extends MarsMetadata, ? extends MoleculeArchiveProperties<?, ?>, ? extends MoleculeArchiveIndex<?, ?>>) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord
-
- setParent(MoleculeArchive<? extends Molecule, ? extends MarsMetadata, ? extends MoleculeArchiveProperties<?, ?>, ? extends MoleculeArchiveIndex<?, ?>>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
- setParent(MutableTreeNode) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
-
- setPath(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3Source
-
- setPath(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveFSSource
-
- setPath(String) - Method in interface de.mpg.biochem.mars.io.MoleculeArchiveSource
-
- setPath(String) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setPixelID(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setPixelLength(double) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setPixelLength(double) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setPixelsPhysicalSizeX(Length) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setPixelsPhysicalSizeY(Length) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setPixelsPhysicalSizeZ(Length) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setPixelUnits(String) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setPixelUnits(String) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setPlane(MarsOMEPlane, int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setPlane(MarsOMEPlane, int, int, int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setPlaneIndex(int) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setPosition(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setPosition(double) - Method in class de.mpg.biochem.mars.util.MarsPosition
-
Set the position value in units of column.
- setPositionSet(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the set of molecule position names in use.
- setPositionSet(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the set of molecule position names in use.
- setPosX(float) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setPosY(float) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setPosZ(float) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setPrecision(int) - Method in class de.mpg.biochem.mars.table.MarsTable
-
- setProcessAllFrames(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setProcessAllFrames(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setProgress(double) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveWindow
-
This is used to report the progress for a long-running task working on the
archive when it is locked.
- setProperty(String, Double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setProperty(String, String) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setRegion(String) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setRegion(String) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setRegion(String) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setRegion(String) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setRegion(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setRegion(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setRegion(String) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setRegionBoundaries(String, int, int, int, int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setRegionInterval(String, Interval) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setRegionName(String) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setRegionOne(String) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setRegionSet(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the set of molecule region names in use.
- setRegionSet(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the set of molecule region names in use.
- setRegionSource(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setRegionSource(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setRegionSource(String) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setRegionTwo(String) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setRegionType(String) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setRoiManager(RoiManager) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setRoiManager(RoiManager) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setRoiManager(RoiManager) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setROIs(Roi[]) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setRois(Roi[]) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setRois(Roi[]) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setRois(Roi[]) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setRoiType(String) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
This method specifies the type of Roi to add to the RoiManager.
- setRootName(String) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeCellRenderer
-
- setRsquared(double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setSegmentsTableNames(Set<List<String>>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the unique set of segment table names found in molecule records.
- setSegmentsTableNames(Set<List<String>>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the unique set of segment table names found in molecule records.
- setSelection(String) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setShape(PeakShape) - Method in class de.mpg.biochem.mars.image.Peak
-
- setShowWarnings(boolean) - Method in class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord
-
- setShowWarnings(boolean) - Method in interface de.mpg.biochem.mars.molecule.JsonConvertibleRecord
-
- setShowWarnings(boolean) - Method in class de.mpg.biochem.mars.table.MarsTable
-
- setSingleChannel(boolean) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setSingleTimePoint(int) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setSingleTimePointMode(boolean) - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- setSizeC(PositiveInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setSizeT(PositiveInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setSizeX(PositiveInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setSizeY(PositiveInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setSizeZ(PositiveInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setSource(String) - Method in class de.mpg.biochem.mars.molecule.commands.AddTimeCommand
-
- setSourceDirectory(String) - Method in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
-
Set the Source Directory where the images are stored.
- setSourceDirectory(String) - Method in interface de.mpg.biochem.mars.metadata.MarsMetadata
-
Set the Source Directory where the images are stored.
- setSourceDirectory(String) - Method in class de.mpg.biochem.mars.metadata.OLDMarsMetadata
-
- setSquaredDistance(double) - Method in class de.mpg.biochem.mars.image.PeakLink
-
- setStart(double) - Method in class de.mpg.biochem.mars.util.MarsRegion
-
Set the lower bound of the region.
- setStringField(String, String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setStringFields(Map<String, String>) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setStroke(double) - Method in class de.mpg.biochem.mars.util.MarsPosition
-
Set the stroke value (line thickness).
- setT(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setT(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setT(int) - Method in class de.mpg.biochem.mars.image.Peak
-
- setT(int) - Method in class de.mpg.biochem.mars.image.PeakLink
-
- setT(NonNegativeInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setT(int) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setTable(MarsTable) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
Set the
MarsTable holding the primary data for this record.
- setTable(MarsTable) - Method in class de.mpg.biochem.mars.molecule.commands.BuildArchiveFromTableCommand
-
- setTable(MarsTable) - Method in interface de.mpg.biochem.mars.molecule.Molecule
-
Set the
MarsTable holding the primary data for this molecule
record.
- setTable(MarsTable) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setTable(MarsTable) - Method in class de.mpg.biochem.mars.table.commands.MarsTableSorterCommand
-
- setTags(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setTags(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setTagSet(Set<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
Redefine the set of molecule tags in use.
- setTagSet(Set<String>) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Redefine the set of molecule tags in use.
- setTDifference(int) - Method in class de.mpg.biochem.mars.image.PeakLink
-
- setTemperature(Temperature) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.GradientCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setThreads(int) - Method in class de.mpg.biochem.mars.molecule.commands.MergeVirtualStoresCommand
-
- setThreads(int) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setThreshold(double) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setThreshold(double) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setThreshold(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setThreshold(double) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setThreshold(double) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setTimeIncrement(double) - Method in class de.mpg.biochem.mars.molecule.commands.AddTimeCommand
-
- setTimeIncrementInSeconds(double) - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- setTo(double) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setTrackUID(String) - Method in class de.mpg.biochem.mars.image.Peak
-
- setTransformFromRegion(String) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setTransformMe(ImagePlus) - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand
-
- setTransformToRegion(String) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setTreeRenderer(TreeCellRenderer) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- setType(String) - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand
-
- setUseAreaFilter(boolean) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setUseDogFiler(boolean) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setUseDogFiler(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setUseDogFiler(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setUseDogFiler(boolean) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setUseDogFilter(boolean) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- setUseIncompleteTraces(boolean) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- setUseLocalOstu(boolean) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setUserObject(Object) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
-
- setUUID(String) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setValid(boolean) - Method in class de.mpg.biochem.mars.image.Peak
-
- setValue(int, int, double) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Set the double value for a pair of column and row indices.
- setValue(int, int, String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Set the String value for a pair of column and row indices.
- setValue(String, int, double) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Set the double value for the column heading and row index specified.
- setValue(String, int, String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Set the String value for the column heading and row index specified.
- setValue(int, double) - Method in class de.mpg.biochem.mars.table.MarsTableRow
-
- setValue(String, double) - Method in class de.mpg.biochem.mars.table.MarsTableRow
-
- setValue(int, String) - Method in class de.mpg.biochem.mars.table.MarsTableRow
-
- setValue(String, String) - Method in class de.mpg.biochem.mars.table.MarsTableRow
-
- setValues(double[]) - Method in class de.mpg.biochem.mars.image.Peak
-
- setVariance(double) - Method in class de.mpg.biochem.mars.image.DNASegment
-
- setVarianceUpperBound(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setVarianceUpperBound(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setVerbose(boolean) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand
-
- setVerbose(boolean) - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand
-
- setVerbose(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- setVerboseOutput(boolean) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setVerboseOutput(boolean) - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- setVerticalGridRegions(int) - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- setVoltage(ElectricPotential) - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- setWindow(MoleculeArchiveWindow) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Set the window containing this archive.
- setWindow(MoleculeArchiveWindow) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Set the window containing this archive.
- setWindow(MarsTableWindow) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Sets a reference to the window holding the table.
- setX(double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setX1(double) - Method in class de.mpg.biochem.mars.image.DNASegment
-
- setX2(double) - Method in class de.mpg.biochem.mars.image.DNASegment
-
- setXColumn(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setXColumn(String) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setXColumn(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setXColumn(String) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setXColumn(String) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setXDNAEndSearchRadius(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setXDNAEndSearchRadius(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setXDrift(double) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setY(double) - Method in class de.mpg.biochem.mars.image.Peak
-
- setY1(double) - Method in class de.mpg.biochem.mars.image.DNASegment
-
- setY2(double) - Method in class de.mpg.biochem.mars.image.DNASegment
-
- setYColumn(String) - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand
-
- setYColumn(String) - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- setYColumn(String) - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- setYColumn(String) - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand
-
- setYColumn(String) - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- setYDNAEndSearchRadius(int) - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- setYDNAEndSearchRadius(int) - Method in class de.mpg.biochem.mars.image.DNAFinder
-
- setYDrift(double) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setZ(NonNegativeInteger) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setZDrift(double) - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- setZeroPoint(String) - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand
-
- showConversionWarning - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeCellRenderer
-
- SIGMA - Static variable in class de.mpg.biochem.mars.image.Peak
-
- sigma - Variable in class de.mpg.biochem.mars.util.Gaussian2D
-
- sigma_a - Variable in class de.mpg.biochem.mars.kcp.KCPSegment
-
- SIGMA_A - Static variable in class de.mpg.biochem.mars.kcp.KCPSegment
-
- sigma_b - Variable in class de.mpg.biochem.mars.kcp.KCPSegment
-
- SIGMA_B - Static variable in class de.mpg.biochem.mars.kcp.KCPSegment
-
- SigmaCalculatorCommand - Class in de.mpg.biochem.mars.kcp.commands
-
- SigmaCalculatorCommand() - Constructor for class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand
-
- SingleChangePointFinder - Class in de.mpg.biochem.mars.kcp.commands
-
- SingleChangePointFinder() - Constructor for class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder
-
- SingleMolecule - Class in de.mpg.biochem.mars.molecule
-
SingleMolecule records act as the storage location for an array of molecule
properties.
- SingleMolecule() - Constructor for class de.mpg.biochem.mars.molecule.SingleMolecule
-
Constructor for creating an empty Molecule record.
- SingleMolecule(JsonParser) - Constructor for class de.mpg.biochem.mars.molecule.SingleMolecule
-
Constructor for loading a Molecule record from a file.
- SingleMolecule(String) - Constructor for class de.mpg.biochem.mars.molecule.SingleMolecule
-
Constructor for creating an empty Molecule record with the specified UID.
- SingleMolecule(String, MarsTable) - Constructor for class de.mpg.biochem.mars.molecule.SingleMolecule
-
Constructor for creating a new Molecule record with the specified UID and
the
MarsTable given as the DataTable.
- SingleMoleculeArchive - Class in de.mpg.biochem.mars.molecule
-
- SingleMoleculeArchive(String) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Creates an empty SingleMoleculeArchive with the given name.
- SingleMoleculeArchive(File) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Constructor for loading a SingleMoleculeArchive.
- SingleMoleculeArchive(URI) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Constructor for loading a MoleculeArchive.
- SingleMoleculeArchive(MoleculeArchiveSource) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Constructor for loading a MoleculeArchive from a MoleculeArchiveSource.
- SingleMoleculeArchive(String, File) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Constructor for loading a SingleMoleculeArchive.
- SingleMoleculeArchive(String, MarsTable) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Constructor for building a Molecule Archive from a MarsTable.
- SingleMoleculeArchive(String, MarsTable, String) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Constructor for building a molecule archive from a MarsTable.
- SingleMoleculeArchiveIndex - Class in de.mpg.biochem.mars.molecule
-
- SingleMoleculeArchiveIndex() - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchiveIndex
-
- SingleMoleculeArchiveIndex(JsonParser) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchiveIndex
-
- SingleMoleculeArchiveProperties - Class in de.mpg.biochem.mars.molecule
-
- SingleMoleculeArchiveProperties() - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchiveProperties
-
- SingleMoleculeArchiveProperties(JsonParser) - Constructor for class de.mpg.biochem.mars.molecule.SingleMoleculeArchiveProperties
-
- smileEncoding - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Encoding.
- solve(double[][], double[], double[], int, double[], boolean[], double[], double) - Method in class de.mpg.biochem.mars.util.LevenbergMarquardt
-
- solve(double[], boolean[], double[][], double[], double[], double, double[]) - Method in class de.mpg.biochem.mars.util.MarsFunctionFitter
-
- sort(String...) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Sort the table in ascending order on one or more columns.
- sort(boolean, String...) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Sort the table on one or more columns either in ascending or descending
order.
- source - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
The archive IO Source.
- source - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- sourceDirectory - Variable in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
-
- SourceDirectory - Variable in class de.mpg.biochem.mars.metadata.OLDMarsMetadata
-
- std(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Calculates the standard deviation of the column.
- std(String, String, double, double) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Calculates the standard deviation of the values for the stdColumn within
the range given for a rowSelectionColumn (inclusive of bounds).
- storeFileExtensionFixer(File) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- storeFileExtensionFixer(String) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- structureEquals(MoleculeArchiveTreeNode) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode
-
- sum(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Calculates the sum of the values for the column given.
- sum(String, String, double, double) - Method in class de.mpg.biochem.mars.table.MarsTable
-
Calculates the sum of the values for the sumColumn within the range given
for a rowSelectionColumn (inclusive of bounds).
- supplier() - Method in class de.mpg.biochem.mars.table.MarsTableRowCollector
-
- supports(WidgetModel) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveWidget
-
- supports(WidgetModel) - Method in class de.mpg.biochem.mars.table.MarsTableWidget
-
- supportsOpen(String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveIOPlugin
-
- supportsOpen(Location) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveIOPlugin
-
- supportsOpen(String) - Method in class de.mpg.biochem.mars.table.MarsTableIOPlugin
-
- supportsOpen(Location) - Method in class de.mpg.biochem.mars.table.MarsTableIOPlugin
-
- supportsSave(String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveIOPlugin
-
- supportsSave(Location) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveIOPlugin
-
- supportsSave(String) - Method in class de.mpg.biochem.mars.table.MarsTableIOPlugin
-
- supportsSave(Location) - Method in class de.mpg.biochem.mars.table.MarsTableIOPlugin
-