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

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

Convenience method to retrieve a metadata stream.

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

Convenience method to retrieve a multithreaded Molecule stream.

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

Convenience method to retrieve a multithreaded Molecule stream.

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

Convenience method to retrieve a multithreaded Molecule stream.

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

parent(String) - Method in class de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess

parent - Variable in class de.mpg.biochem.mars.molecule.AbstractMarsRecord

Reference to MoleculeArchive containing the record.

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

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

passThroughUnknownArrays(JsonParser) - Static method in class de.mpg.biochem.mars.util.MarsUtil

Used to bypass unknown Json arrays with JacksonJson streaming interface.

passThroughUnknownObjects(JsonParser) - Static method in class de.mpg.biochem.mars.util.MarsUtil

Used to bypass unknown Json objects with JacksonJson streaming interface.

Peak - Class in de.mpg.biochem.mars.image

Stores information about detected 2D intensity peaks.

Peak(JsonParser) - Constructor for class de.mpg.biochem.mars.image.Peak

Peak(double[]) - Constructor for class de.mpg.biochem.mars.image.Peak

Peak(double, double, double, double, double, int) - Constructor for class de.mpg.biochem.mars.image.Peak

Peak(double, double, int) - Constructor for class de.mpg.biochem.mars.image.Peak

Peak(String, double, double) - Constructor for class de.mpg.biochem.mars.image.Peak

Peak(double, double) - Constructor for class de.mpg.biochem.mars.image.Peak

Peak(Peak) - Constructor for class de.mpg.biochem.mars.image.Peak

PeakFinderCommand - Class in de.mpg.biochem.mars.image.commands

PeakFinderCommand() - Constructor for class de.mpg.biochem.mars.image.commands.PeakFinderCommand

PeakFitter<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> - Class in de.mpg.biochem.mars.image

The PeakFitter determines the subpixel location of peaks with a symmetric gaussian function that include a baseline parameter.

PeakFitter() - Constructor for class de.mpg.biochem.mars.image.PeakFitter

PeakFitter(boolean[]) - Constructor for class de.mpg.biochem.mars.image.PeakFitter

PeakFitter(boolean[], double) - Constructor for class de.mpg.biochem.mars.image.PeakFitter

PeakLink - Class in de.mpg.biochem.mars.image

PeakLinks are used to link peaks over time during peak tracking.

PeakLink(Peak, Peak, double, int, int) - Constructor for class de.mpg.biochem.mars.image.PeakLink

PeakLink(long, long, double, int, int) - Constructor for class de.mpg.biochem.mars.image.PeakLink

PeakPixel - Class in de.mpg.biochem.mars.image

PeakPixel(double, double, double) - Constructor for class de.mpg.biochem.mars.image.PeakPixel

PeakShape - Class in de.mpg.biochem.mars.image

Stores shape information for objects as 2D polygons.

PeakShape(double[], double[]) - Constructor for class de.mpg.biochem.mars.image.PeakShape

PeakShape(JsonParser) - Constructor for class de.mpg.biochem.mars.image.PeakShape

PeakTracker - Class in de.mpg.biochem.mars.image

PeakTracker tracks the relative position of peaks over time based on peak feature differences, minimum distance change, and minimum total track length.

PeakTracker(double, double, double, int, int, boolean, LogService, double) - Constructor for class de.mpg.biochem.mars.image.PeakTracker

PeakTracker(double[], boolean[], int, int, boolean, boolean, LogService, double) - Constructor for class de.mpg.biochem.mars.image.PeakTracker

PeakTrackerCommand - Class in de.mpg.biochem.mars.image.commands

PeakTrackerCommand() - Constructor for class de.mpg.biochem.mars.image.commands.PeakTrackerCommand

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

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

pixelValue - Variable in class de.mpg.biochem.mars.image.PeakPixel

planes() - Method in class de.mpg.biochem.mars.metadata.MarsOMEImage

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

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

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

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

precision - Variable in class de.mpg.biochem.mars.util.LevenbergMarquardt

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

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

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

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

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

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

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

Called when the DNAFinderCommand.preview parameter value changes.

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

Called when the PeakFinderCommand.preview parameter value changes.

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

Called when the PeakTrackerCommand.preview parameter value changes.

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

Called when the ObjectTrackerCommand.preview parameter value changes.

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

Called when the TransformROIsCommand.preview parameter value changes.

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

process(Module) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchivePostprocessor

process(Module) - Method in class de.mpg.biochem.mars.molecule.MoleculeArchivePreprocessor

process(Module) - Method in class de.mpg.biochem.mars.swingUI.MarsLegacyInputHarvester

process(Module) - Method in class de.mpg.biochem.mars.table.MarsTablePostprocessor

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

Get the MoleculeArchiveProperties which contain general information about the archive.

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

Get the MoleculeArchiveProperties which contain general information about the archive.

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

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

Adds a molecule to the archive.

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

Adds a molecule to the archive.

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

Add or update the MarsBdvSource with the name provided.

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

Add or update the MarsBdvSource with the name provided.

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

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

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

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

Add additional comments or reports as documents.

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

Add additional comments or reports as documents.

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

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

Adds a metadata record to the archive.

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

Adds a MarsMetadata record to the archive.

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

Add or update a MarsPosition.

putPosition(MarsPosition) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule

Add or update a MarsPosition.

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

Add or update a MarsPosition.

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

Add or update a MarsRegion.

putRegion(MarsRegion) - Method in class de.mpg.biochem.mars.molecule.AbstractMolecule

Add or update a MarsRegion.

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

Add or update a MarsRegion.

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

Add or update a segments table (MarsTable) generated using the x column and y column names.

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

Add or update a segments table (MarsTable) generated using the x column, y column and region names.

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

Add or update a segments table (MarsTable) generated using the x column and y column names.

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

Add or update a segments table (MarsTable) generated using the x column, y column and region names.

putShape(int, PeakShape) - Method in class de.mpg.biochem.mars.object.MartianObject

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