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

R

R2 - Static variable in class de.mpg.biochem.mars.image.Peak

radius() - Method in class de.mpg.biochem.mars.image.PeakShape

readJsonObject(JsonParser, JsonConvertibleRecord, String...) - Static method in class de.mpg.biochem.mars.util.MarsUtil

rebuildIndexes() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

Rebuild all indexes by inspecting the contents of store directories.

rebuildIndexes(int) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

Rebuild all indexes by inspecting the contents of store directories.

rebuildIndexes() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive

Rebuild all indexes by inspecting the contents of store directories.

rebuildIndexes(int) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive

Rebuild all indexes by inspecting the contents of store directories.

recentList - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog

recentURLs - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog

recordLocks - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

Map from molecule UID to ReentrantLock to ensure thread blocking when accessing molecule files in virtual mode.

RegionDifferenceCalculatorCommand - Class in de.mpg.biochem.mars.molecule.commands

RegionDifferenceCalculatorCommand() - Constructor for class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand

regionSet - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties

remove(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

Removes the molecule record with the given UID.

remove(M) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

Removes the molecule record provided.

remove(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive

Removes the molecule record with the given UID.

remove(M) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive

Removes the molecule record provided.

remove(int) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode

remove(MutableTreeNode) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode

remove(MoleculeArchiveTreeNode) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode

removeAllBdvSources() - Method in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata

Remove all MarsBdvSources.

removeAllBdvSources() - Method in interface de.mpg.biochem.mars.metadata.MarsMetadata

Remove all MarsBdvSources.

removeAllBdvSources() - Method in class de.mpg.biochem.mars.metadata.OLDMarsMetadata

Remove all MarsBdvSources.

removeAllChildren() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode

removeAllDocuments() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties

removeAllDocuments() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties

Remove all documents.

removeAllMedia() - Method in class de.mpg.biochem.mars.util.MarsDocument

removeAllParameters() - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove all parameter values from the record.

removeAllParameters() - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove all parameter values from the record.

removeAllPositions() - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove all positions from the record.

removeAllPositions() - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove all MarsPositions from the record.

removeAllRegions() - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove all regions from the record.

removeAllRegions() - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove all MarsRegions from the record.

removeAllTags() - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove all tags from the record.

removeAllTags() - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove all tags from the record.

removeArchive(String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService

removeArchive(MoleculeArchive) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService

removeBdvSource(String) - Method in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata

Remove the MarsBdvSource with the name provided.

removeBdvSource(String) - Method in interface de.mpg.biochem.mars.metadata.MarsMetadata

Remove the MarsBdvSource with the name provided.

removeBdvSource(String) - Method in class de.mpg.biochem.mars.metadata.OLDMarsMetadata

removeDocument(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties

removeDocument(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties

Remove document.

removeFromParent() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode

removeLeadingSlash(String) - Static method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess

When absolute paths are passed (e.g.

removeLeadingSlash(String) - Static method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode

Removes the leading slash from a given path and returns the corrected path.

removeMedia(String) - Method in class de.mpg.biochem.mars.util.MarsDocument

removeMetadata(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3Source

removeMetadata(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveFSSource

removeMetadata(String) - Method in interface de.mpg.biochem.mars.io.MoleculeArchiveSource

removeMetadata(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

The metadata record with the UID given is removed from the archive.

removeMetadata(I) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive

The Metadata record given is removed from the archive.

removeMetadata(I) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex

removeMetadata(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex

removeMetadata(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive

The metadata record with the UID given is removed from the archive.

removeMetadata(I) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive

The metadata record given is removed from the archive.

removeMetadata(I) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex

removeMetadata(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex

removeMolecule(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3Source

removeMolecule(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveFSSource

removeMolecule(String) - Method in interface de.mpg.biochem.mars.io.MoleculeArchiveSource

removeMolecule(Molecule) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex

removeMolecule(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex

removeMolecule(M) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex

removeMolecule(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex

removeNearestNeighbors(List<Peak>, int) - Static method in class de.mpg.biochem.mars.image.MarsImageUtils

This method removes peaks from the provided list that are closer than the minimum distance given.

removeParameter(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove parameter.

removeParameter(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove parameter.

removePosition(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove a MarsPosition from the record using the name.

removePosition(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove a MarsPosition from the record using the name.

removeRegion(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove a MarsRegion from the record using the name.

removeRegion(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove a MarsRegion from the record using the name.

removeSegmentsTable(List<String>) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule

Remove the Segments table (MarsTable) generated using x column, y column and region names provided.

removeSegmentsTable(String, String) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule

Remove the Segments table (MarsTable) generated using xColumn and yColumn.

removeSegmentsTable(String, String, String) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule

Remove the segments table (MarsTable) generated using x column, y column, and region names provided.

removeSegmentsTable(List<String>) - Method in interface de.mpg.biochem.mars.molecule.Molecule

Remove the segments table (MarsTable) generated using x column, y column, and region names provided as a list.

removeSegmentsTable(String, String) - Method in interface de.mpg.biochem.mars.molecule.Molecule

Remove the segments table (MarsTable) generated using xColumn and y Column.

removeSegmentsTable(String, String, String) - Method in interface de.mpg.biochem.mars.molecule.Molecule

Remove the segments table (MarsTable) generated using x column, y column, and region names provided.

removeShape(int) - Method in class de.mpg.biochem.mars.object.MartianObject

removeTable(String) - Method in class de.mpg.biochem.mars.table.MarsTableService

removeTable(MarsTable) - Method in class de.mpg.biochem.mars.table.MarsTableService

removeTag(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Remove a string tag from the record.

removeTag(String) - Method in interface de.mpg.biochem.mars.molecule.MarsRecord

Remove a string tag from the record.

rename(String, String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService

rename(String, String) - Method in class de.mpg.biochem.mars.table.MarsTableService

reset() - Method in class de.mpg.biochem.mars.image.Peak

reset(double, double, int) - Method in class de.mpg.biochem.mars.image.Peak

reset(Peak, Peak, double, int, int) - Method in class de.mpg.biochem.mars.image.PeakLink

reset(long, long, double, int, int) - Method in class de.mpg.biochem.mars.image.PeakLink

rootName - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeCellRenderer

rootNode - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog

round(double, int) - Static method in class de.mpg.biochem.mars.util.MarsMath

roundArray(double[], int) - Static method in class de.mpg.biochem.mars.util.MarsMath

ROVER_FILE_EXTENSION - Static variable in interface de.mpg.biochem.mars.io.MoleculeArchiveSource

rows() - Method in class de.mpg.biochem.mars.table.MarsTable

Returns a stream of MarsTableRow.

run() - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand

run() - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand

run() - Method in class de.mpg.biochem.mars.image.commands.GradientCommand

run() - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorCommand

run() - Method in class de.mpg.biochem.mars.image.commands.MoleculeIntegratorMultiViewCommand

run() - Method in class de.mpg.biochem.mars.image.commands.OverlayChannelsCommand

run() - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand

run() - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand

run() - Method in class de.mpg.biochem.mars.kcp.commands.KCPCommand

run() - Method in class de.mpg.biochem.mars.kcp.commands.SigmaCalculatorCommand

run() - Method in class de.mpg.biochem.mars.kcp.commands.SingleChangePointFinder

run() - Method in class de.mpg.biochem.mars.molecule.commands.AddTimeCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.BuildArchiveFromTableCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.BuildDnaArchiveCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.DriftCorrectorCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.ImportCloudArchiveCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.ImportMoleculeArchiveCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.ImportVirtualStoreCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.MergeCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.MergeVirtualStoresCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand

run() - Method in class de.mpg.biochem.mars.molecule.commands.VarianceCalculatorCommand

run() - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand

run() - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand

run(Consumer<MoleculeArchiveSelection>) - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog

run() - Method in class de.mpg.biochem.mars.table.commands.IJ1ResultsTableConversionCommand

run() - Method in class de.mpg.biochem.mars.table.commands.MarsTableFilterCommand

run() - Method in class de.mpg.biochem.mars.table.commands.MarsTableImporterCommand

run() - Method in class de.mpg.biochem.mars.table.commands.MarsTableSorterCommand

run() - Method in class de.mpg.biochem.mars.table.commands.ScijavaTableConversionCommand

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