Index (anchor-feature 1.0.0 API)

A B C D E F G H I K M N O P Q R S T W
All Classes and Interfaces|All Packages|Serialized Form

A

add(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Adds a feature-name.
add(String, int) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex: Adds a new featureName and index
add(String, Feature<T>) - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Adds a named-feature to the store.
add(Feature<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Adds a feature to the current list.
add(ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVectorList: Add a ResultsVector to the list in the final position.
addAll(FeatureList<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Add all the features in other to the current list.
addFromList(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Add features from a feature-list.
addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Add features from a NamedProvider of feature-lists.
addTypedValuesTo(Collection<TypedValue>, int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Adds TypedValue representations of the results to a Collection.
append(Optional<FeatureList<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Appends the features one or more (optional) feature-lists to the existing list.
asList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Exposes the underlying list of features in this data-structure.
asList() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Exposes the underlying list of names.
AssignFeatureNameUtilities - Class in org.anchoranalysis.feature.name: Utilities for assigning a name to a feature.
assignTo(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.Feature: Copies fields in this (base) class to target.
assignWithPrefix(Feature<? extends FeatureInput>, String, String) - Static method in class org.anchoranalysis.feature.name.AssignFeatureNameUtilities: Assigns a new custom-name to a feature, by combining an existing-name with a prefix.
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStack: Derive a Stack representation containing the identical channels to the current instance.
asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Derive a Stack representation containing the identical channels to the current instance.

B

beforeCalc(FeatureInitialization) - Method in class org.anchoranalysis.feature.bean.Feature: Dummy method, that children can optionally override.
bothNameAndParameters() - Static method in class org.anchoranalysis.feature.store.NamedFeatureStoreFactory: The custom-names of the features are derived from both their name and their parameters.
bySymbol() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.

C

CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache: Creates a FeatureCalculationCache that accepts a particular input type.
calculate(Feature<S>, CalculationPart<S, T>, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a feature in a child-cache using a new input created from a CalculationPart.
calculate(Feature<S>, S, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a feature in a child-cache.
calculate(Feature<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates the result of a feature using this input.
calculate(Feature<T>, FeatureCalculationInput<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculator: Calculate the result of feature with a particular input.
calculate(FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates the results of several features using this input.
calculate(FeatureList<T>, FeatureCalculationInput<T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculator: Calculates results for a list of features with a particular input, throwing an exception if a calculation fails.
calculate(ChildCacheName, S, Function<CalculationPartResolver<S>, ResolvedPart<U, S>>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild: Calculates a CalculationPart in a child-cache.
calculate(ResolvedPart<S, T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates a resolved Feature-calculation.
calculate(FeatureCalculationInput<FeatureInputResults>) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature: Calculates a value for some input.
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Constant
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Reference
calculate(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Sum
calculate(CalculationPart<S, T>) - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Calculates a feature-calculation after resolving it against the main cache.
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.Count
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults: Calculates the feature-result given a FeatureInputResults.
calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic
calculate(T) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculate the results of the features with a particular input.
calculate(T) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
calculate(T) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingle: Calculate the results of the feature with a particular input.
calculate(T) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleChangeInput
calculate(T) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleFromMulti
calculate(T, ErrorReporter, boolean) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculates the results for an input, either calling FeatureCalculatorMulti.calculate(T) or FeatureCalculatorMulti.calculateSuppressErrors(T, org.anchoranalysis.core.log.error.ErrorReporter) depending on a flag.
calculate(T, FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculates the results of a subset of the features with a particular input.
calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
calculateCheckInitialized(FeatureCalculationInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature: Calculates the result of a feature and throws an exception if the feature has not been initialized.
calculateFeatureByIdentifier(String, FeatureCalculationInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator: Searches for a feature that matches a particular identifier.
CalculateForChild<T> - Interface in org.anchoranalysis.feature.calculate.cache: Performs calculations using child-caches instead of the main cache
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: Calculates the results for an input recording the error to an ErrorReporter if anything goes wrong, but throwing no exception.
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingle: Calculates the result for an input recording the error to an ErrorReporter if anything goes wrong, but throwing no exception.
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleChangeInput
calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleFromMulti
CalculationPart<S,T> - Class in org.anchoranalysis.feature.calculate.part: A sub-part of the calculation of a feature, that can be cached, and reused by other features.
CalculationPart() - Constructor for class org.anchoranalysis.feature.calculate.part.CalculationPart
CalculationPartMap<S,T,U,E> - Class in org.anchoranalysis.feature.calculate.part: Similar to a CalculationPart but stores several evaluation results, differentiated by a key.
CalculationPartMap(int) - Constructor for class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Creates for a particular cache-size.
CalculationPartResolver<T> - Interface in org.anchoranalysis.feature.calculate.part: Searches a cache to reuses a CalculationPart if it already exists.
calculator() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: A means of calculating feature values using this cache.
canEqual(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
castAs() - Method in class org.anchoranalysis.feature.bean.Feature: Casts the feature to having a different input-type.
childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Gets/creates a child-cache for a given name.
ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache: A unique identifier for a child-cache's name commposed potentially of two elements.
ChildCacheName(Class<?>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses only the class as an identifier.
ChildCacheName(Class<?>, int) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses only the class combines with an integer part-name.
ChildCacheName(Class<?>, String) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName: Uses both the class and a part-name as an identifier.
clear() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Removes all of the elements from this list.
Constant<T> - Class in org.anchoranalysis.feature.bean.operator: A constant value that is entirely invariant to the feature-input.
Constant() - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
Constant(double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant: Constructor with a particular value.
Constant(String, double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant: Constructor with a particular value and a custom-name.
contains(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Whether a particular feature is contained in this instance.
copyChangeDictionary(Dictionary) - Method in class org.anchoranalysis.feature.energy.EnergyStack: Makes a copy of the EnergyStack but assigns a new Dictionary.
copyFrom(int, int, ResultsVector, int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Copies a contiguous subset of results from another vector.
Count - Class in org.anchoranalysis.feature.bean.results: The sum of the results from a particular feature.
Count() - Constructor for class org.anchoranalysis.feature.bean.results.Count
create(Class<? extends FeatureInput>) - Method in interface org.anchoranalysis.feature.calculate.cache.CacheCreator: Creates a FeatureCalculationCache that accepts a particular input type.
create(SharedObjects) - Static method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Creates with shared-objects, and otherwise empty initialization.
create(Logger, Path) - Static method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Creates a log and a model-directory, and otherwise empty initialization.
createListChildFeatures() - Method in class org.anchoranalysis.feature.bean.Feature: Returns a list of Features that exist as bean-properties of this feature, either directly or in lists.
createMapToIndex() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Creates a map from the feature-names to their indices in the list.
createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.store.NamedFeatureStoreFactory: Create a NamedFeatureStore from a list of beans.

D

Define<T> - Class in org.anchoranalysis.feature.bean.list: Specifies a list of features directly without assigning any custom-naming.
Define() - Constructor for class org.anchoranalysis.feature.bean.list.Define
Define(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.Define: Creates a new Define instance.
Define(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.Define: Create from a single Feature.
DefinedNamed<T> - Class in org.anchoranalysis.feature.bean.list: Specifies features via a list of names and associated with features.
DefinedNamed() - Constructor for class org.anchoranalysis.feature.bean.list.DefinedNamed
DefineSingle<T> - Class in org.anchoranalysis.feature.bean.list: Specifies a single feature directly without assigning any custom-naming.
DefineSingle() - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle
DefineSingle(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle: Creates a new DefineSingle instance.
deriveNames() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Derives the names of the features.
describeBean() - Method in class org.anchoranalysis.feature.bean.Feature
describeBean() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
describeParameters() - Method in class org.anchoranalysis.feature.bean.Feature: A human-readable description of the parameterization of the bean.
describeParameters() - Method in class org.anchoranalysis.feature.bean.operator.Constant
descriptionForList(String) - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: Derive a string description of all the items of the list concatenated together.
descriptionLong() - Method in class org.anchoranalysis.feature.bean.Feature: A long human-readable description of the feature and some or all of its parameterization.
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Constant
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Reference
descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Sum
determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Finds a common input-type for two classes, throwing an exception if the two types aren't compatible.
determineInputType(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Finds a common input-type for classes in the list, throwing an exception if any two types aren't compatible.
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The image-dimensions associated with the energy-stack.
dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: The dimensions of all channels in the stack.
dimensions() - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions: The dimensions of the associated image.
dimensions() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
dimensionsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The image-dimensions associated with the energy-stack, if it exists.
dimensionsRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The image-dimensions associated with the energy-stack, or an exception if no energy-stack exists.
dropKey() - Method in exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Removes any feature-name from the exception.
duplicate() - Method in class org.anchoranalysis.feature.shared.SharedFeatures: A deep copy of the current instance.
duplicate() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Deep-copies the store, including duplicating each feature.
duplicateChangeName(String) - Method in class org.anchoranalysis.feature.bean.Feature: Duplicates the feature as per AnchorBean.duplicateBean() but sets a particular custom-name.
duplicateShallow() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: A shallow-copy of the current initialization.
duplicateShallow() - Method in class org.anchoranalysis.feature.name.FeatureNameList: Shallow copy of the current instance.

E

empty() - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates an empty list of features
EnergyStack - Class in org.anchoranalysis.feature.energy: A EnergyStackWithoutParameters with associated parameters in a Dictionary.
EnergyStack(EnergyStackWithoutParameters) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a EnergyStackWithoutParameters without any additional parameters.
EnergyStack(EnergyStackWithoutParameters, Dictionary) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Creates a new EnergyStack instance.
EnergyStack(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a single Channel.
EnergyStack(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create a new stack of Dimensions with zero-voxel values, without any additional parameters.
EnergyStack(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a EnergyStack without any additional parameters.
EnergyStack(Stack, Dictionary) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack: Create from a Stack with associated parameters in a Dictionary.
EnergyStackWithoutParameters - Class in org.anchoranalysis.feature.energy: A stack of channels used as context to calculate features (or calculating energy more broadly).
EnergyStackWithoutParameters(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Create a energy-stack comprised of a single channel
EnergyStackWithoutParameters(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Create a energy-stack with no channels - but with associated dimensions.
EnergyStackWithoutParameters(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Create a energy-stack comprised of all channels from a stack
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart
equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap
equals(Object) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart
equals(Object) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap
equals(Object) - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputResults
equals(Object) - Method in class org.anchoranalysis.feature.results.ResultsVector
equals(Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector: Does the instance have exactly these values?
equalsPrecision(double, Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector: Like ResultsVector.equals(Object) but includes a tolerance for checking equality of the doubles.
execute(T) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart: This performs the actual calculation when needed.
execute(T, U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Calculates a result for a particular input and key.
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The width and height and depth of all Channels in the stack.
extent() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: The width and height and depth of all Channels in the stack.
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack: Extract a particular z-slice from the EnergyStack as a new stack.
extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Extract a particular z-slice from the EnergyStackWithoutParameters as a new stack.

F

Feature<T> - Class in org.anchoranalysis.feature.bean: Base class for a measurement that calculates a result (double) given input parameters.
Feature() - Constructor for class org.anchoranalysis.feature.bean.Feature: Creates with the default initializer.
Feature(BeanInitializer<FeatureInitialization>) - Constructor for class org.anchoranalysis.feature.bean.Feature: Creates with a custom initializer.
FeatureBinary<T> - Class in org.anchoranalysis.feature.bean.operator: A base class for a Feature that is a binary-function of the results from two other features.
FeatureBinary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureBinary
FeatureCalculationCache<T> - Interface in org.anchoranalysis.feature.calculate.cache: A context in which to calculate features while caching certain duplicated internal calculations among the features.
FeatureCalculationException - Exception Class in org.anchoranalysis.feature.calculate: When the calculation of a feature cannot complete successfully.
FeatureCalculationException(String) - Constructor for exception class org.anchoranalysis.feature.calculate.FeatureCalculationException: Creates with a message only.
FeatureCalculationException(String, Throwable) - Constructor for exception class org.anchoranalysis.feature.calculate.FeatureCalculationException: Creates with both a message and a cause.
FeatureCalculationException(Throwable) - Constructor for exception class org.anchoranalysis.feature.calculate.FeatureCalculationException: Creates with a cause only.
FeatureCalculationInput<T> - Interface in org.anchoranalysis.feature.calculate: Gives a FeatureInput the necessary context for feature-calculation, including associating it with a cache.
FeatureCalculator<T> - Interface in org.anchoranalysis.feature.calculate: Calculates FeatureCalculationInput when passed a particular Feature and corresponding FeatureCalculationInput.
FeatureCalculatorMulti<T> - Interface in org.anchoranalysis.feature.calculate.bound: Like a FeatureCalculator but is permanently associated with one or more Features.
FeatureCalculatorMultiChangeInput<T> - Class in org.anchoranalysis.feature.calculate.bound: A FeatureCalculatorMulti but changes the input before calculation.
FeatureCalculatorMultiChangeInput(FeatureCalculatorMulti<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput: Creates a new FeatureCalculatorMultiChangeInput instance.
FeatureCalculatorSingle<T> - Interface in org.anchoranalysis.feature.calculate.bound: Like a FeatureCalculator but is permanently associated with a single Feature.
FeatureCalculatorSingleChangeInput<T> - Class in org.anchoranalysis.feature.calculate.bound: A FeatureCalculatorSingle but changes the input before calculation.
FeatureCalculatorSingleChangeInput(FeatureCalculatorSingle<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleChangeInput: Creates a new FeatureCalculatorSingleChangeInput instance.
FeatureCalculatorSingleFromMulti<T> - Class in org.anchoranalysis.feature.calculate.bound: Exposes a FeatureCalculatorMulti as a FeatureCalculatorSingle.
FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorSingleFromMulti: Creates from a FeatureCalculatorMulti.
FeatureFromList<T> - Class in org.anchoranalysis.feature.bean.operator: A base class for a Feature that is a function of the results from a list of other features.
FeatureFromList() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureFromList
FeatureFromList(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureFromList: Create from a list of features.
FeatureGeneric<T> - Class in org.anchoranalysis.feature.bean.operator: Base class for features that broadly accept any type of feature-input.
FeatureGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureGeneric
FeatureInitialization - Class in org.anchoranalysis.feature.initialization: Parameters used to initialize a Feature before any calculation occurs.
FeatureInitialization() - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create without any dictionary, energy-stack or shared-objects.
FeatureInitialization(Optional<Dictionary>, Optional<EnergyStackWithoutParameters>, Optional<SharedObjects>) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Creates a new FeatureInitialization instance.
FeatureInitialization(SharedObjects) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create only with shared-objects.
FeatureInitialization(Dictionary) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create only with a dictionary.
FeatureInitialization(EnergyStack) - Constructor for class org.anchoranalysis.feature.initialization.FeatureInitialization: Create only with an energy-stack.
FeatureInput - Interface in org.anchoranalysis.feature.input: A single input used for feature-calculation to produce a result.
FeatureInputDictionary - Interface in org.anchoranalysis.feature.input: A FeatureInputWithResolution that has an optional associated Dictionary.
FeatureInputDimensions - Class in org.anchoranalysis.feature.input: A FeatureInput that exposes the Dimensions of an image or scene.
FeatureInputDimensions() - Constructor for class org.anchoranalysis.feature.input.FeatureInputDimensions
FeatureInputEnergy - Class in org.anchoranalysis.feature.input: A FeatureInputDimensions that has an optional EnergyStack associated with it.
FeatureInputEnergy() - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy: Creates without an associated energy-stack.
FeatureInputEnergy(Optional<EnergyStack>) - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
FeatureInputNull - Class in org.anchoranalysis.feature.input: A FeatureInput with no associated parameterization.
FeatureInputResults - Class in org.anchoranalysis.feature.input: A FeatureInput with the stored results from a prior feature-calculation.
FeatureInputResults(ResultsVectorList, FeatureNameMapToIndex) - Constructor for class org.anchoranalysis.feature.input.FeatureInputResults: Creates a new FeatureInputResults instance.
FeatureInputType - Class in org.anchoranalysis.feature.input: Performs checks and aggregations on feature-input types are compatible with others
FeatureInputWithResolution - Interface in org.anchoranalysis.feature.input: A FeatureInput that exposes the Resolution of an image or scene.
FeatureList<T> - Class in org.anchoranalysis.feature.bean.list: A list of features with the same input-type.
FeatureList() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates with an empty list.
FeatureList(int) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates with an empty list of particular capacity.
FeatureList(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Wraps an existing list.
FeatureList(Stream<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates from a stream of Features.
FeatureList(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList: Creates with a single Feature.
FeatureListFactory - Class in org.anchoranalysis.feature.bean.list: Factory for creating FeatureList in different ways.
FeatureListProvider<T> - Class in org.anchoranalysis.feature.bean.list: Provides a list of Features with identical input-type.
FeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureListProvider
FeatureNameList - Class in org.anchoranalysis.feature.name: A list of Strings representing feature names.
FeatureNameList() - Constructor for class org.anchoranalysis.feature.name.FeatureNameList: Create with no names (an empty list).
FeatureNameList(List<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
FeatureNameList(Stream<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList: Create from a stream of names.
FeatureNameMapToIndex - Class in org.anchoranalysis.feature.name: A map of feature-names (strings) to indexes (int).
FeatureNameMapToIndex() - Constructor for class org.anchoranalysis.feature.name.FeatureNameMapToIndex
featureNames() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: The names of all Features in the store, in identical order to the store.
FeatureProvider<T> - Class in org.anchoranalysis.feature.bean.provider: Provides a single Feature.
FeatureProvider() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProvider
FeatureProviderBean<B,P> - Class in org.anchoranalysis.feature.bean.provider: Base class for FeatureRelatedBeans that implement Provider to provide an object of type S.
FeatureProviderBean() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderBean
FeatureProviderDefine<T> - Class in org.anchoranalysis.feature.bean.provider: Defines a single Feature to provide via a bean property.
FeatureProviderDefine() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
FeatureProviderDefine(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine: Creates a new FeatureProviderDefine instance.
FeatureProviderReference - Class in org.anchoranalysis.feature.bean.provider: Provides an existing Feature identified by its name and optionally a feature-list in which is resides.
FeatureProviderReference() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
FeatureRelatedBean<T> - Class in org.anchoranalysis.feature.bean: Beans-related to Features, and which require initialization with FeatureRelatedInitialization.
FeatureRelatedBean() - Constructor for class org.anchoranalysis.feature.bean.FeatureRelatedBean: Create with default initializers.
FeatureRelatedInitialization - Class in org.anchoranalysis.feature.initialization: Parameters for initializing a FeatureRelatedBean.
FeatureResults - Class in org.anchoranalysis.feature.bean.results: Features that process ResultsVectorList.
FeatureResults() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResults
FeatureResultsStatistic - Class in org.anchoranalysis.feature.bean.results: Base class for an instance of FeatureResults that calculating a statistic across all results in the ResultsVectorList for a particular feature-value.
FeatureResultsStatistic() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic
features() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: All Features in the store, in identical order.
FeatureSymbolCalculator<T> - Interface in org.anchoranalysis.feature.calculate.cache: Resolves and calculates a feature by a symbol.
FeatureUnary<T,S> - Class in org.anchoranalysis.feature.bean.operator: A feature that contains another feature as a bean-parameter.
FeatureUnary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
FeatureUnary(Feature<S>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
FeatureUnaryGeneric<T> - Class in org.anchoranalysis.feature.bean.operator: A FeatureUnary that accepts any FeatureInput irrespective of type.
FeatureUnaryGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
FeatureUnaryGeneric(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric: Create with a specific feature, that provides the input to the unary function.
filterAndMap(Predicate<Feature<T>>, CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Filters inputs and then performs a FeatureList.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.feature.bean.Feature<T>, org.anchoranalysis.feature.bean.Feature<S>, E>).
flatMapFromOptional(Iterable<S>, CheckedFunction<S, Optional<FeatureList<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by flat-mapping an iterable to an optional feature
forChild() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Performs calculations not on the main cache, but on a child cache.
forEach(Consumer<Feature<T>>) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Iterates over each feature in the instance.
from(Feature<T>...) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list for one or more features
fromIterable(Iterable<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from an iterable
fromProvider(Provider<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list for a single-feature created from a provider
fromProviders(Collection<FeatureProvider<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from a collection of feature-providers
fromStream(Stream<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a list of features from a stream

G

get() - Method in class org.anchoranalysis.feature.bean.list.Define
get() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
get() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
get() - Method in class org.anchoranalysis.feature.bean.list.PrependName
get() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
get() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
get() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: The underlying feature-input.
get(int) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Returns the element at the specified position in this list.
get(int) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Gets a name corresponding to a particular position.
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVector: The result of a feature-calculation stored at a particular index.
get(int) - Method in class org.anchoranalysis.feature.results.ResultsVectorList: Gets a ResultsVector at a particular position i nthe list.
get(int) - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Gets a feature at a particular position.
get(String) - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: Gets a feature corresponding to a particular name.
getCache() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: Get the associated FeatureCalculationCache.
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack: Returns the channel at a particular position in the stack.
getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: Returns the channel at a particular position in the stack.
getCustomName() - Method in class org.anchoranalysis.feature.bean.Feature: An optional additional name that be associated with the feature (defaults to an empty string).
getDictionary() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: A dictionary of key-value pairs.
getDictionary() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: The associated initialization for a DictionaryBean.
getDictionaryOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputDictionary: The associated dictionary, if it exists.
getDictionaryOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getDictionaryRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputDictionary: The associated dictionary, or an exception if it doesn't exist.
getEnergyStack() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: An energy-stack, which may form an input to the feature for calculation.
getEnergyStackOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The associated energy-stack.
getEnergyStackRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: The associated energy-stack or throws an exception if it isn't present.
getError(int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Gets an error state at a particular position.
getException(String) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Gets a feature by name, throwing an exception if it doesn't exist.
getFeature() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine: The feature to provide.
getFeatureLists() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Gets the underlying NamedProviderStore that provides shared-features.
getFeatureNameIndex() - Method in class org.anchoranalysis.feature.input.FeatureInputResults: A mapping from the name of the feature that produced a result, to its index position in results.
getFilePaths() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: A named-set of file-paths.
getFriendlyName() - Method in class org.anchoranalysis.feature.bean.Feature: A user-friendly human-readable name for the Feature.
getId() - Method in class org.anchoranalysis.feature.bean.operator.Reference: The identifier that uniquely determines the other feature to reference.
getId() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the feature to reference.
getId() - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic: The name of the feature, whose results will provide the statistic.
getItem() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle: The sole feature that forms the list.
getItem() - Method in class org.anchoranalysis.feature.bean.list.PrependName: Provides the features and names before any prepending.
getItem() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
getItem1() - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the first value for the binary-function.
getItem2() - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the second value for the binary-function.
getList() - Method in class org.anchoranalysis.feature.bean.list.Define: The list that specifies features.
getList() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed: A list of FeatureListProviders with an associated name.
getList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: The list of features.
getList() - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: The features whose results will be somehow combined, to form the result of this class.
getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The number of channels in the stack.
getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParameters: The number of channels in the stack.
getOptional(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatures
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from a previous execution.
getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from a previous execution.
getOrNull(U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Gets an existing result for the current input from the cache.
getParameters() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The associated parameters.
getPrefix() - Method in class org.anchoranalysis.feature.bean.list.PrependName: The string to prepend to the custom-name of each feature.
getQuantile() - Method in class org.anchoranalysis.feature.bean.results.Quantile: The quantile.
getReferences() - Method in class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider: The names of other feature-lists, whose features may be referenced by this feature.
getReferencesList() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the list in which the feature referenced by id resides.
getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
getResolutionOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution: The resolution of the associated image, if it is available.
getResolutionRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution: The resolution of the associated image, or an exception if it is not available.
getResult(int) - Method in class org.anchoranalysis.feature.results.ResultsVector: Gets a result value at a particular position.
getResults() - Method in class org.anchoranalysis.feature.input.FeatureInputResults: The results of a prior feature-calculation, corresponding to a list of features.
getSharedFeatures() - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Shared features available for reference during calculation.
getSharedObjects() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: Shared-objects, which can be referenced by the feature to influence calculation.
getUnitConverterOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Converts voxelized measurements to/from physical units.
getValue() - Method in class org.anchoranalysis.feature.bean.operator.Constant: The constant value.

H

hasCachedResult() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart: Has the calculation already been executed, with a cached result existing?
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart
hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap
hashCode() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart
hashCode() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap
hashCode() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputDimensions
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputNull
hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
hashCode() - Method in class org.anchoranalysis.feature.results.ResultsVector
hasKey(U) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Does a result exist for the current input, and a particular key?
hasOneSlice() - Method in class org.anchoranalysis.feature.energy.EnergyStack: Does exactly one z-slice exist in the energy stack?

I

indexOf(String) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex: The index for a particular featureName
initialize(FeatureInitialization, Logger) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Initializes the cache.
initializeRecursive(FeatureInitialization, Logger) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Initializes all features in the list, and recursively any features they contain.
initializeRecursive(FeatureInitialization, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Initialize all features in this instance, recursively also initializating any child-features.
inputType() - Method in class org.anchoranalysis.feature.bean.Feature: The class corresponding to feature input-type.
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureGeneric
inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
inputType() - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
insertBeginning(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Inserts a new feature-name at the beginning of the list.
insertBeginning(String[]) - Method in class org.anchoranalysis.feature.name.FeatureNameList: Inserts new feature-names at the beginning of the list.
instance() - Static method in class org.anchoranalysis.feature.input.FeatureInputNull: A singleton instance.
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Invalidates existing caches so the next calculation occurs freshly.
invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.ResettableCalculation: Resets the cached-calculation, so the next call to doOperationWithParameters() is guaranteed to calculation the operation, and store the value in the cache.
invalidate() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPart
invalidate() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Invalidates the cache, removing any items already stored.
invalidateExcept(Set<ChildCacheName>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureCalculationCache: Invalidates existing caches so the next calculations occur freshly - except some particular child-caches who are not invalidated.
isAsPercentage() - Method in class org.anchoranalysis.feature.bean.results.Quantile: If true, the quantile is interpreted as a percentage rather than a decimal.
isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Can these parameters be used with a particular feature?
isEmpty() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Returns true if this list contains no elements.
isEmpty() - Method in class org.anchoranalysis.feature.results.ResultsVectorList: Returns true if the list contains no elements.
isIgnoreNaN() - Method in class org.anchoranalysis.feature.bean.operator.Sum: If true, we ignore any NaN values.
iterator() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
iterator() - Method in class org.anchoranalysis.feature.name.FeatureNameList
iterator() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
iterator() - Method in class org.anchoranalysis.feature.shared.SharedFeatures
iterator() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore

K

keys() - Method in class org.anchoranalysis.feature.shared.SharedFeatures

M

map(CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list where each feature is the result of applying a map-function to an existing feature.
mapFrom(Iterable<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping an Iterable to Feature
mapFromFiltered(Iterable<S>, Predicate<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by filtering an iterable and then mapping it to a feature
mapFromRange(int, int, IntFunction<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to a feature
mapFromRangeOptional(int, int, Class<? extends Exception>, CheckedIntFunction<Optional<Feature<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Creates a new feature-list by mapping integers (from a range) each to an optional feature
Maximum - Class in org.anchoranalysis.feature.bean.results: The maximum of the results from a particular feature.
Maximum() - Constructor for class org.anchoranalysis.feature.bean.results.Maximum
Mean - Class in org.anchoranalysis.feature.bean.results: The mean of the results from a particular feature.
Mean() - Constructor for class org.anchoranalysis.feature.bean.results.Mean
Minimum - Class in org.anchoranalysis.feature.bean.results: The minimum of the results from a particular feature.
Minimum() - Constructor for class org.anchoranalysis.feature.bean.results.Minimum

N

NamedFeatureCalculateException - Exception Class in org.anchoranalysis.feature.calculate: An exception that occurs when a feature fails to successfully calculate.
NamedFeatureCalculateException(Exception) - Constructor for exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a calculation error that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String) - Constructor for exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a general failure message that doesn't pertain to any particular feature.
NamedFeatureCalculateException(String, String) - Constructor for exception class org.anchoranalysis.feature.calculate.NamedFeatureCalculateException: Creates with a failure message associated with a particular feature.
NamedFeatureStore<T> - Class in org.anchoranalysis.feature.store: Stores Features, each with an associated name, with list-like access and map-like access.
NamedFeatureStore() - Constructor for class org.anchoranalysis.feature.store.NamedFeatureStore
NamedFeatureStoreFactory - Class in org.anchoranalysis.feature.store: Creates a NamedFeatureStore.
numberItemsCurrentlyStored() - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Number of items currently stored in cache.

O

onInitialization(FeatureInitialization) - Method in class org.anchoranalysis.feature.bean.Feature: Called after initialization.
onInitialization(FeatureRelatedInitialization) - Method in class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider
org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean: Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list: A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator: Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider: Provider of a single feature.
org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results: Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate: Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.bound - package org.anchoranalysis.feature.calculate.bound: Interfaces like FeatureCalculator but bound to particular features.
org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache: Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.calculate.cache.part - package org.anchoranalysis.feature.calculate.cache.part: Equivalent classes to org.anchoranalysis.feature.calculate.part after having been resolved against a cache.
org.anchoranalysis.feature.calculate.part - package org.anchoranalysis.feature.calculate.part: A sub-part of the calculation of a feature, that can be cached, and reused by other features.
org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy: A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.initialization - package org.anchoranalysis.feature.initialization: Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input: Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name: Data objects for the names of features.
org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results: Results from one or more feature calculations.
org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared: Features shared for referencing among calculations.
org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store: A collection of named-Features.

P

parametersOnly() - Static method in class org.anchoranalysis.feature.store.NamedFeatureStoreFactory: The custom-names of the features are derived only from their parameters, but not their name.
populate(List<NamedBean<FeatureListProvider<FeatureInput>>>, Logger) - Method in class org.anchoranalysis.feature.initialization.FeatureRelatedInitialization: Adds features into the shared-feature storage from a list of named-beans.
prefer(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Prefer to keep descriptor whose input-class is a sub-class rather than a super-class.
prefer(Feature<?>, Feature<?>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType: Like FeatureInputType.prefer(Class, Class) but accepts features directly as input.
PrependName - Class in org.anchoranalysis.feature.bean.list: Prepends a string to the custom-name of each feature in a list.
PrependName() - Constructor for class org.anchoranalysis.feature.bean.list.PrependName
put(U, S) - Method in class org.anchoranalysis.feature.calculate.part.CalculationPartMap: Assigns a evaluation result to the cache for a particular key.

Q

Quantile - Class in org.anchoranalysis.feature.bean.results: A quantile of the results from a particular feature.
Quantile() - Constructor for class org.anchoranalysis.feature.bean.results.Quantile

R

Reference<T> - Class in org.anchoranalysis.feature.bean.operator: Uses another feature to calculate the value.
Reference() - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
Reference(String) - Constructor for class org.anchoranalysis.feature.bean.operator.Reference: Create with a specific identifier.
ReferencingFeatureListProvider<T> - Class in org.anchoranalysis.feature.bean.list: A base class for implementations of FeatureListProvider that may reference features created elsewhere.
ReferencingFeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider
registerBeanFactories() - Static method in class org.anchoranalysis.feature.bean.RegisterFeatureBeanFactories: Registers all custom feature-related beans.
RegisterFeatureBeanFactories - Class in org.anchoranalysis.feature.bean: Similar to RegisterBeanFactories but registers additional feature-related bean-factories.
removeIfExists(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Remove all features, if they currently exist, from features.
ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache: A calculation that be invalidated (resetted), removing any existing cached value.
resolution() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The image-resolution associated with the energy-stack.
ResolvedPart<S,T> - Class in org.anchoranalysis.feature.calculate.cache.part: Like a CalculationPart but has been resolved against a cache to reuse any existing identical instance.
ResolvedPart(CalculationPart<S, T>) - Constructor for class org.anchoranalysis.feature.calculate.cache.part.ResolvedPart: Creates a new ResolvedPart instance.
ResolvedPartMap<S,T,U> - Class in org.anchoranalysis.feature.calculate.cache.part: A CalculationPartMap that has been resolved against a cache.
ResolvedPartMap(CalculationPartMap<S, T, U, FeatureCalculationException>) - Constructor for class org.anchoranalysis.feature.calculate.cache.part.ResolvedPartMap: Creates with a map.
resolveFeatureIdentifier(String) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator: Resolves an identifier to a unique-string, suitable for FeatureSymbolCalculator.calculateFeatureByIdentifier(String, FeatureCalculationInput).
resolver() - Method in interface org.anchoranalysis.feature.calculate.FeatureCalculationInput: A resolver for calculations.
ResultsVector - Class in org.anchoranalysis.feature.results: A vector of results of applying a feature-calculations to many entities.
ResultsVector(int) - Constructor for class org.anchoranalysis.feature.results.ResultsVector: Creates with a particular size.
ResultsVectorList - Class in org.anchoranalysis.feature.results: A list of elements of type ResultsVector.
ResultsVectorList() - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
ResultsVectorList(ResultsVector) - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList: Creates with the list containing a single item.

S

search(CalculationPart<S, T>) - Method in interface org.anchoranalysis.feature.calculate.part.CalculationPartResolver: Searches for an equivalent calculation to calculation.
search(CalculationPartMap<S, T, U, FeatureCalculationException>) - Method in interface org.anchoranalysis.feature.calculate.part.CalculationPartResolver: Searches for an equivalent calculation to calculation.
set(int, double) - Method in class org.anchoranalysis.feature.results.ResultsVector: Assigns a result at a particular position.
set(int, ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVector: Assigns many results, starting at a particular position, and incrementing thereafter.
setAsPercentage(boolean) - Method in class org.anchoranalysis.feature.bean.results.Quantile: If true, the quantile is interpreted as a percentage rather than a decimal.
setCustomName(String) - Method in class org.anchoranalysis.feature.bean.Feature: An optional additional name that be associated with the feature (defaults to an empty string).
setEnergyStack(Optional<EnergyStack>) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Assigns an optional EnergyStack to be associated with the input.
setEnergyStack(EnergyStack) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy: Assigns an EnergyStack to be associated with the input.
setError(int, Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector: Set an error state at a particular position.
setErrorAll(Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector: Set an error state at all positions.
setFeature(Feature<T>) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine: The feature to provide.
setId(String) - Method in class org.anchoranalysis.feature.bean.operator.Reference: The identifier that uniquely determines the other feature to reference.
setId(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the feature to reference.
setId(String) - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic: The name of the feature, whose results will provide the statistic.
setIgnoreNaN(boolean) - Method in class org.anchoranalysis.feature.bean.operator.Sum: If true, we ignore any NaN values.
setItem(Feature<S>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
setItem(Feature<T>) - Method in class org.anchoranalysis.feature.bean.list.DefineSingle: The sole feature that forms the list.
setItem(FeatureListProvider<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.list.PrependName: Provides the features and names before any prepending.
setItem1(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the first value for the binary-function.
setItem2(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureBinary: Provides the second value for the binary-function.
setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed: A list of FeatureListProviders with an associated name.
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.Define: The list that specifies features.
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: The list of features.
setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: Assigns the list of features to use.
setList(FeatureList<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureFromList: Assigns the list of features to use.
setParameters(Dictionary) - Method in class org.anchoranalysis.feature.energy.EnergyStack: The associated parameters.
setPrefix(String) - Method in class org.anchoranalysis.feature.bean.list.PrependName: The string to prepend to the custom-name of each feature.
setQuantile(double) - Method in class org.anchoranalysis.feature.bean.results.Quantile: The quantile.
setReferences(StringSet) - Method in class org.anchoranalysis.feature.bean.list.ReferencingFeatureListProvider: The names of other feature-lists, whose features may be referenced by this feature.
setReferencesList(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference: The name of the list in which the feature referenced by id resides.
setValue(double) - Method in class org.anchoranalysis.feature.bean.operator.Constant: The constant value.
shallowDuplicate() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list which contains identical elements.
SharedFeatures - Class in org.anchoranalysis.feature.shared: A group of features made available to other features to reference.
SharedFeatures() - Constructor for class org.anchoranalysis.feature.shared.SharedFeatures: Create empty, without any features.
SharedFeaturesSubset<T> - Class in org.anchoranalysis.feature.shared: A subset of features from SharedFeatures that share a common feature input-type.
SharedFeaturesSubset(NameValueMap<Feature<T>>) - Constructor for class org.anchoranalysis.feature.shared.SharedFeaturesSubset: Creates a new SharedFeaturesSubset instance.
sharedObjectsRequired() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization: Retrieves the shared-objects associated with the initialization, or throws an an exception if they do not exist.
size() - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Returns the number of elements in this list.
size() - Method in class org.anchoranalysis.feature.name.FeatureNameList: The number of names in the list.
size() - Method in class org.anchoranalysis.feature.results.ResultsVector: The number of calculations stored in the vector.
size() - Method in class org.anchoranalysis.feature.results.ResultsVectorList: The number of ResultsVectors in the list.
size() - Method in class org.anchoranalysis.feature.store.NamedFeatureStore: The total number of Features in the store.
sizeFeatures() - Method in interface org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMulti: The number of features that is calculated on each call to FeatureCalculatorMulti.calculate(T), and therefore the size of the returned ResultsVector.
sizeFeatures() - Method in class org.anchoranalysis.feature.calculate.bound.FeatureCalculatorMultiChangeInput
sort(Comparator<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList: Creates a new feature-list sorted in a particular order.
StandardDeviation - Class in org.anchoranalysis.feature.bean.results: The standard-deviation of the results from a particular feature.
StandardDeviation() - Constructor for class org.anchoranalysis.feature.bean.results.StandardDeviation
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.FeatureResultsStatistic: Calculates the statistic for a given list of result-value.
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Maximum
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Mean
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Minimum
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Quantile
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StandardDeviation
statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Sum
stream() - Method in class org.anchoranalysis.feature.results.ResultsVectorList: A stream of ResultsVectors.
subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatures: Extracts the subset of inputs that are compatible with a particular input-type.
Sum<T> - Class in org.anchoranalysis.feature.bean.operator: Sums the results after calculating a list of Features.
Sum - Class in org.anchoranalysis.feature.bean.results: The sum of the results from a particular feature.
Sum() - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
Sum() - Constructor for class org.anchoranalysis.feature.bean.results.Sum
Sum(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.Sum: Create with a list of Features which become summed.

T

toString() - Method in class org.anchoranalysis.feature.bean.Feature
toString() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
toString() - Method in class org.anchoranalysis.feature.initialization.FeatureInitialization
toString() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
toString() - Method in class org.anchoranalysis.feature.name.FeatureNameList
toString() - Method in class org.anchoranalysis.feature.results.ResultsVector
toString() - Method in class org.anchoranalysis.feature.shared.SharedFeatures
total() - Method in class org.anchoranalysis.feature.results.ResultsVector: The total value of all results.

W

withoutParameters() - Method in class org.anchoranalysis.feature.energy.EnergyStack: The energy-stack without associated parameters.
wrapDuplicate(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Wraps an existing list, WITHOUT reusing the list in the internals of the FeatureList i.e.
wrapReuse(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory: Wraps an existing list, reusing the list in the internals of the FeatureList

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