Index

A B C D E F G H I M N O P S W
All Classes All Packages

A

add(String, StoreSupplier<TimeSeries>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap

Adds an entry to the map.

add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap

addToStore(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

Adds the main stack and other stacks to the store.

addToStore(NamedProviderStore<TimeSeries>, Logger) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

addToStore(NamedProviderStore<T>, Logger) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap

Copies all the existing entries into a NamedProviderStore.

addToStore(NamedProviderStore<T>, Logger) - Method in class org.anchoranalysis.mpp.io.input.OperationMap

addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.mpp.io.input.MultiInput

addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.mpp.io.input.MultiInput

B

BackgroundCreator - Class in org.anchoranalysis.mpp.io.output

Utility class for creating background DisplayStacks.

C

close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput

close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

Closes resources and cleans up.

copyTo(SharedObjects, Logger) - Method in interface org.anchoranalysis.mpp.io.input.ExportSharedObjects

Adds any exported shared objects to the target container.

copyTo(SharedObjects, Logger) - Method in class org.anchoranalysis.mpp.io.input.MultiInput

create(Optional<? extends ExportSharedObjects>, InitializationContext, Optional<Define>) - Static method in class org.anchoranalysis.mpp.io.input.MarksInitializationFactory

Creates a new MarksInitialization instance.

createBackground(NamedProviderStore<Stack>, String, StackDisplayer) - Static method in class org.anchoranalysis.mpp.io.output.BackgroundCreator

Creates a background DisplayStack from a named stack in a collection.

createFromExisting(InitializationContext, Optional<Define>, Optional<SharedObjects>, Optional<Dictionary>) - Static method in class org.anchoranalysis.mpp.io.input.MarksInitializationFactory

Creates a new MarksInitialization instance from existing shared objects and dictionary.

D

DEFAULT_IMAGE_INPUT_NAME - Static variable in class org.anchoranalysis.mpp.io.input.MultiInput

The default name for the input image stack.

dictionary() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the map of Dictionarys.

E

EnergyStackWriter - Class in org.anchoranalysis.mpp.io.output

Writes an energy-stack to the file-system.

EnergyStackWriter(EnergyStack, Outputter) - Constructor for class org.anchoranalysis.mpp.io.output.EnergyStackWriter

ExportSharedObjects - Interface in org.anchoranalysis.mpp.io.input

An interface for exporting shared objects to a target container.

F

filePath() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the map of Paths.

G

get(String) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap

Retrieves an entry from the map.

get(String) - Method in class org.anchoranalysis.mpp.io.input.OperationMap

get(String) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

getAppendDictionary() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of dictionaries to append.

getAppendFilePath() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of file paths to append.

getAppendHistogram() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of histograms to append.

getAppendMarks() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks to append.

getAppendMarksFromAnnotation() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks from annotations (both accepted and rejected) to append.

getAppendMarksFromAnnotationAcceptedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks from annotations (accepted only) to append.

getAppendMarksFromAnnotationRejectedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks from annotations (rejected only) to append.

getAppendObjects() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of object-collections to append to the MultiInput.

getAppendStack() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of additional stacks to append.

getInput() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

The input manager for the main stack.

getInputName() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

The name of the input to be used in the MultiInput.

getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the name of the main input object.

getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

Gets the name of the main object.

getMap() - Method in class org.anchoranalysis.mpp.io.input.OperationMap

Retrieves the internal map storing the operations.

H

histogram() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the map of Histograms.

I

identifier() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

inputName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

Gets the input name.

inputs(InputManagerParameters) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

M

marks() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the map of MarkCollections.

MarksInitializationFactory - Class in org.anchoranalysis.mpp.io.input

Factory for creating MarksInitialization instances.

MultiInput - Class in org.anchoranalysis.mpp.io.input

An input to an experiment that combines a particular Stack with other types of entities.

MultiInput(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput

Creates a new MultiInput with a specified name for the main input object.

MultiInput(ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput

Creates a new MultiInput with a default name for the main input object.

MultiInputManager - Class in org.anchoranalysis.mpp.io.bean.input

Manages input for MultiInput objects, combining various input sources.

MultiInputManager() - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

MultiInputManager(String, InputManager<? extends ProvidesStackInput>) - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

Creates a new MultiInputManager with specified input name and input manager.

MultiInputSubMap<T> - Interface in org.anchoranalysis.mpp.io.input

A sub-item of a MultiInput that manages a map of objects.

N

numberFrames() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

numFrames() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

Gets the number of frames.

O

objects() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the map of ObjectCollections.

OperationMap<T> - Class in org.anchoranalysis.mpp.io.input

Stores objects as operations in a map, implementing the MultiInputSubMap interface.

OperationMap() - Constructor for class org.anchoranalysis.mpp.io.input.OperationMap

org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input

Beans for reading data structures related to marked point processes from the file system.

org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input

Non-beans for reading data structures related to marked point processes from the file system.

org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output

Non-beans for writing data structures related to marked point processes from the file system.

OUTPUT_ENERGY_STACK_DIRECTORY - Static variable in class org.anchoranalysis.mpp.io.output.EnergyStackWriter

The output name for the directory containing energy stack channels.

P

pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap

Gets the path for binding.

S

setAppendDictionary(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of dictionaries to append.

setAppendFilePath(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of file paths to append.

setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of histograms to append.

setAppendMarks(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks to append.

setAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks from annotations (both accepted and rejected) to append.

setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks from annotations (accepted only) to append.

setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of marks from annotations (rejected only) to append.

setAppendObjects(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of object-collections to append to the MultiInput.

setAppendStack(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

List of additional stacks to append.

setInput(InputManager<? extends ProvidesStackInput>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

The input manager for the main stack.

setInputName(String) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager

The name of the input to be used in the MultiInput.

stack() - Method in class org.anchoranalysis.mpp.io.input.MultiInput

Gets the map of TimeSeries (stacks).

StackWithMap - Class in org.anchoranalysis.mpp.io.input

Combines a Stack with a map of other stacks.

StackWithMap(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.StackWithMap

W

writeEnergyStack() - Method in class org.anchoranalysis.mpp.io.output.EnergyStackWriter

Writes the energy stack to output.

A B C D E F G H I M N O P S W
All Classes All Packages