- calc_sigma(double[], int, int) - Static method in class de.mpg.biochem.mars.kcp.KCP
-
- calcR2(RandomAccess<T>, int, Gaussian2D) - Static method in class de.mpg.biochem.mars.image.MarsImageUtils
-
This method calculates the R-squared for the 2D gaussian provided within
the radius specified for the image given as a RandomAccess.
- calcRegionDifference(Molecule, String, String, MarsRegion, MarsRegion, String) - Static method in class de.mpg.biochem.mars.molecule.commands.RegionDifferenceCalculatorCommand
-
- calculate(double) - Method in class de.mpg.biochem.mars.util.ForceCalculator
-
- calculate(double) - Method in class de.mpg.biochem.mars.util.MotionBlurForceCalculator
-
- calculateDrift(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, String, String, String, boolean, String, String) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- calculateDrift(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, String, String, String, boolean, String, String, LogService) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- calculateDrift(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, String, String, String, boolean, String, String, boolean, int, LogService) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- calculateForceAndLength(double) - Static method in class de.mpg.biochem.mars.util.MarsMath
-
- calculateForceAndLength(double, double, double, double) - Static method in class de.mpg.biochem.mars.util.MarsMath
-
- calcVariance(Molecule, String, String) - Static method in class de.mpg.biochem.mars.molecule.commands.VarianceCalculatorCommand
-
- cancel() - Method in class de.mpg.biochem.mars.image.commands.DNAFinderCommand
-
- cancel() - Method in class de.mpg.biochem.mars.image.commands.PeakFinderCommand
-
- cancel() - Method in class de.mpg.biochem.mars.image.commands.PeakTrackerCommand
-
- cancel() - Method in class de.mpg.biochem.mars.object.commands.ObjectTrackerCommand
-
- cancel() - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- cancel() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- cancelBtn - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- cancelCallback - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- catchConsumerException(MarsUtil.ThrowingConsumer<T, E>, Class<E>) - Static method in class de.mpg.biochem.mars.util.MarsUtil
-
- channels() - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- channelSet - Variable in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
- characteristics() - Method in class de.mpg.biochem.mars.table.MarsTableRowCollector
-
- checkOMEMetadataForDt(MarsMetadata) - Static method in class de.mpg.biochem.mars.metadata.MarsOMEUtils
-
- children() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSwingTreeNode
-
- childrenList() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveTreeNode
-
- chiSq - Variable in class de.mpg.biochem.mars.util.LevenbergMarquardt
-
- chiSquared - Variable in class de.mpg.biochem.mars.util.MarsFunctionFitter
-
- CIRCULARITY - Static variable in class de.mpg.biochem.mars.image.Peak
-
- circularity() - Method in class de.mpg.biochem.mars.image.PeakShape
-
- clear() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
- clear() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveProperties
-
Clear contents of all global sets and records counts.
- clearParameterList() - Method in class de.mpg.biochem.mars.util.LogBuilder
-
- clearRecent() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- clearRecent() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveOpenDialog
-
- clearRecent() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.MoleculeArchiveSaveDialog
-
- clearRecentBtn - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- clone() - Method in class de.mpg.biochem.mars.table.MarsTable
-
Create a copy of the MarsTable.
- close() - Method in interface de.mpg.biochem.mars.io.MoleculeArchiveStorage
-
Default implementation of AutoCloseable.close() for all
implementations that do not hold any closable resources.
- close() - Method in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- CollectionDate - Variable in class de.mpg.biochem.mars.metadata.OLDMarsMetadata
-
- colocalize(List<Roi>, double, int, int) - Method in class de.mpg.biochem.mars.roi.commands.TransformROIsCommand
-
- columnCount() - Method in class de.mpg.biochem.mars.table.MarsTableRow
-
- columnNames() - Method in class de.mpg.biochem.mars.table.MarsTableRow
-
- combiner() - Method in class de.mpg.biochem.mars.table.MarsTableRowCollector
-
- comp - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- components(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess
-
- compose(String...) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess
-
- containerPath - Variable in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3Source
-
- containerPathText - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- containerPathUpdateCallback - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- containerTree - Variable in class de.mpg.biochem.mars.swingUI.MoleculeArchiveSelector.AbstractMoleculeArchiveDialog
-
- contains(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Used to check if there is a molecule record with the UID given.
- contains(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Used to check if there is a molecule record with the UID given.
- contains(String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService
-
- contains(MoleculeArchive) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService
-
- contains(String) - Method in class de.mpg.biochem.mars.table.MarsTableService
-
- containsMetadata(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Used to check if there is a MarsMetadata record with the UID given.
- containsMetadata(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Used to check if there is a metadata record with the UID given.
- containsMetadataUID(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
-
- containsMetadataUID(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex
-
- containsMoleculeUID(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
-
- containsMoleculeUID(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchiveIndex
-
- correctDrift(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, String, String, String, String) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- correctDrift(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, String, String, String, String, LogService) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- correctDrift(MoleculeArchive<Molecule, MarsMetadata, MoleculeArchiveProperties<Molecule, MarsMetadata>, MoleculeArchiveIndex<Molecule, MarsMetadata>>, String, String, String, String, boolean, int, LogService) - Static method in class de.mpg.biochem.mars.molecule.ArchiveUtils
-
- correctFrame(int, int) - Method in class de.mpg.biochem.mars.image.commands.BeamProfileCorrectionCommand
-
- createArchive(String) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService
-
- createArchive(String, File) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService
-
- createArchive(String, MoleculeArchiveSource) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchiveService
-
- createColumn(String) - Method in class de.mpg.biochem.mars.table.MarsTable
-
- createDirectories(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess
-
- createIndex() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create empty MoleculeArchiveIndex.
- createIndex(JsonParser) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create MoleculeArchiveIndex using JsonParser stream.
- createIndex() - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
- createIndex(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
- createIndex() - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createIndex(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createIndex() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create empty MoleculeArchiveIndex.
- createIndex(JsonParser) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create empty MoleculeArchiveIndex using the JsonParser stream given.
- createIndex() - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
- createIndex(JsonParser) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
- createIndex() - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createIndex(JsonParser) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createInputPanel() - Method in class de.mpg.biochem.mars.swingUI.MarsLegacyInputHarvester
-
- createIOMaps() - Method in class de.mpg.biochem.mars.image.Peak
-
- createIOMaps() - Method in class de.mpg.biochem.mars.image.PeakShape
-
- createIOMaps() - Method in class de.mpg.biochem.mars.metadata.AbstractMarsMetadata
-
- createIOMaps() - Method in class de.mpg.biochem.mars.metadata.MarsBdvSource
-
- createIOMaps() - Method in class de.mpg.biochem.mars.metadata.MarsOMEChannel
-
- createIOMaps() - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage
-
- createIOMaps() - Method in class de.mpg.biochem.mars.metadata.MarsOMEPlane
-
- createIOMaps() - Method in class de.mpg.biochem.mars.metadata.OLDMarsMetadata
-
- createIOMaps() - Method in class de.mpg.biochem.mars.molecule.AbstractJsonConvertibleRecord
-
Must be implemented in subclasses to define how fields, objects, arrays
should be saved based on the Jackson streaming API.
- createIOMaps() - Method in class de.mpg.biochem.mars.molecule.AbstractMarsRecord
-
- createIOMaps() - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule
-
- createIOMaps() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
- createIOMaps() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveIndex
-
- createIOMaps() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchiveProperties
-
- createIOMaps() - Method in class de.mpg.biochem.mars.object.MartianObject
-
- createIOMaps() - Method in class de.mpg.biochem.mars.util.DefaultJsonConverter
-
- createIOMaps() - Method in class de.mpg.biochem.mars.util.MarsDocument
-
- createIOMaps() - Method in class de.mpg.biochem.mars.util.MarsPosition
-
- createIOMaps() - Method in class de.mpg.biochem.mars.util.MarsRegion
-
- createMetadata(JsonParser) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create MarsMetadata record using JsonParser stream.
- createMetadata(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create empty MarsMetadata record with the metaUID specified.
- createMetadata(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create MarsOMEMetadata record using JsonParser stream.
- createMetadata(String) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create empty DefaultMarsImageMetadata record with the metaUID specified.
- createMetadata(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
Create MarsOMEMetadata record using JsonParser stream.
- createMetadata(String) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createMetadata(JsonParser) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create MarsMetadata record using JsonParser stream.
- createMetadata(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create empty MarsMetadata record with the metaUID specified.
- createMetadata(JsonParser) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create MarsOMEMetadata record using JsonParser stream.
- createMetadata(String) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create empty MarsOMEMetadata record with the metaUID specified.
- createMetadata(JsonParser) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
Create MarsOMEMetadata record using JsonParser stream.
- createMetadata(String) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createMolecule() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create empty Molecule record.
- createMolecule(JsonParser) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create Molecule record using the JsonParser stream given.
- createMolecule(String) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create empty Molecule record with the UID specified.
- createMolecule(String, MarsTable) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create Molecule record using the UID and
MarsTable specified.
- createMolecule() - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create empty DefaultMolecule record.
- createMolecule(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create DefaultMolecule record using the JsonParser stream given.
- createMolecule(String) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create empty DefaultMolecule record with the UID specified.
- createMolecule(String, MarsTable) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create DefaultMolecule record using the UID and
MarsTable
specified.
- createMolecule() - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createMolecule(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createMolecule(String) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createMolecule(String, MarsTable) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createMolecule() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create empty Molecule record.
- createMolecule(JsonParser) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create Molecule record using the JsonParser stream given.
- createMolecule(String) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create empty Molecule record with the UID specified.
- createMolecule(String, MarsTable) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create Molecule record using the UID and
MarsTable specified.
- createMolecule() - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create empty SingleMolecule record.
- createMolecule(JsonParser) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create SingleMolecule record using the JsonParser stream given.
- createMolecule(String) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create empty SingleMolecule record with the UID specified.
- createMolecule(String, MarsTable) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create SingleMolecule record using the UID and
MarsTable specified.
- createMolecule() - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createMolecule(JsonParser) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createMolecule(String) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createMolecule(String, MarsTable) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createOMEXMLMetadata(OMEXMLService, Dataset) - Static method in class de.mpg.biochem.mars.metadata.MarsOMEUtils
-
- createPeak(double[], double[]) - Static method in class de.mpg.biochem.mars.image.PeakShape
-
- createProperties() - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create empty MoleculeArchiveProperties record.
- createProperties(JsonParser) - Method in class de.mpg.biochem.mars.molecule.AbstractMoleculeArchive
-
Create MoleculeArchiveProperties record using JsonParser stream.
- createProperties() - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create empty DefaultMoleculeArchiveProperties record.
- createProperties(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DefaultMoleculeArchive
-
Create DefaultMoleculeArchiveProperties record using JsonParser stream.
- createProperties() - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createProperties(JsonParser) - Method in class de.mpg.biochem.mars.molecule.DnaMoleculeArchive
-
- createProperties() - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create empty MoleculeArchiveProperties record.
- createProperties(JsonParser) - Method in interface de.mpg.biochem.mars.molecule.MoleculeArchive
-
Create MoleculeArchiveProperties record using JsonParser stream.
- createProperties() - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create empty SingleMoleculeArchiveProperties record.
- createProperties(JsonParser) - Method in class de.mpg.biochem.mars.molecule.SingleMoleculeArchive
-
Create SingleMoleculeArchiveProperties record using JsonParser stream.
- createProperties() - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createProperties(JsonParser) - Method in class de.mpg.biochem.mars.object.ObjectArchive
-
- createTable(ResultsTable) - Method in class de.mpg.biochem.mars.table.MarsTableService
-