Index (anchor-mpp-feature 1.0.0 API)

A B C D E F G H I M O R S T U
All Classes and Interfaces|All Packages|Serialized Form

A

add(double) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Adds a value to the total energy.
add(String, EnergyScheme) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Adds a new EnergyScheme to the set with the given name.
add(EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Adds a new energy total to the list and updates the total energy.
add(EnergySavedIndividual, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Adds a new mark to the list and calculates its energy.
add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Adds a new mark to the collection and updates energies.
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Adds a voxelized mark to the collection.
add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Appends the specified element to the end of this list.
addAll(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Adds all elements from another MemoForIndex to this list.
AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: Criteria for adding edges between marks in a graph-based model.
AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria: Implements AddCriteria for energy pairs, combining energy calculations with additional criteria.
AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair: Creates an AddCriteriaEnergyPair with specified energy pairs and add criteria.
AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria: An implementation of AddCriteria that never adds an edge between marks.
AddCriteriaNever() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria: An AddCriteriaPair that combines multiple criteria using a logical OR operation.
AddCriteriaOr() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria: Abstract base class for criteria used to determine if a pair of marks should be included.
AddCriteriaPair() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria: If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
ArbitraryPointCommon() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
asMarks() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Converts the energy memo list to a collection of marks.
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Asserts that the energy calculations are valid.
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Asserts that the total energy is valid (not NaN).
assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Asserts that the total energy is valid (not NaN).
AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element: Extracts one of the memos from the pair, and processes as a FeatureSingleMemo
AsSingle() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle

B

BoundingBoxIntersection - Class in org.anchoranalysis.mpp.feature.addcriteria: An AddCriteriaPair that includes marks if their bounding boxes intersect.
BoundingBoxIntersection() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection

C

calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Calculates the total energy for all items using the provided energy scheme and stack.
calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element: Derives a FeatureInputSingleMemo from a FeatureInputPairMemo.
CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair: Creates a new CalculateDeriveSingleMemoFromPair instance.
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo
canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
clean() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Cleans up the energy memo list by setting the list to null.
containsMark(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Checks if the collection contains a specific mark.
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator: Creates an EnergyScheme instance.
create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
create(EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.DictionaryForImageCreator: Creates a dictionary containing calculated image features for a given energy stack.
createAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Creates an AddCriteriaEnergyPair based on the energy scheme.
createDictionary() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Creates and returns the associated Dictionary or an empty dictionary if none is associated.
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a set of unique pairs from the graph.
createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a set of unique energy pairs.

D

deepCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a deep copy of this RandomCollectionWithAddCriteria.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Creates a deep copy of this EnergyTotal instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Makes a deep copy of this instance (except the energyScheme which is reused).
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Creates a deep copy of this instance.
deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a deep copy of this instance.
describeBean() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
describeBean() - Method in class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
describeMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Generates a string description of the marks and their associated energies.
describeParameters() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
DictionaryForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme: Creates a Dictionary for a particular EnergyStack that is associated with an EnergyScheme.
DictionaryForImageCreator(EnergyScheme, SharedFeatures, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.DictionaryForImageCreator: Creates a new DictionaryForImageCreator instance.
dimensions() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection: Gets the optional dimensions associated with the mark collection.

E

EnergyMemoList - Class in org.anchoranalysis.mpp.feature.mark: A collection of memoized marks on which energies can be derived.
EnergyMemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Creates an empty energy memo list.
EnergyMemoList(EnergySavedIndividual, EnergyStackWithoutParameters, MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Creates an energy memo list with the given parameters.
EnergyMemoList(EnergyMemoList) - Constructor for class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Creates a copy of an existing energy memo list.
EnergyPair - Class in org.anchoranalysis.mpp.feature.energy: Represents a pair of Marks with their associated total energy.
EnergyPair(MarkPair<Mark>, EnergyTotal) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyPair: Creates a new EnergyPair instance.
EnergySavedAll - Class in org.anchoranalysis.mpp.feature.energy.saved: Saves and manages the total energy for all items in a collection.
EnergySavedAll() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
EnergySavedIndividual - Class in org.anchoranalysis.mpp.feature.energy.saved: Stores and manages individual energy values for a collection of marks.
EnergySavedIndividual() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual
EnergySavedPairs - Class in org.anchoranalysis.mpp.feature.energy.saved: Stores and manages pairwise energy interactions between marks.
EnergySavedPairs(AddCriteria<EnergyPair>) - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a new instance with the specified add criteria for energy pairs.
EnergyScheme - Class in org.anchoranalysis.mpp.feature.energy.scheme: The energy for a feature-list as factorized into different cliques.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Creates an energy scheme with the specified features and region map.
EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair, Optional<DictionaryProvider>, List<NamedBean<Feature<FeatureInputStack>>>) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Creates an energy scheme with the specified features, region map, and additional options.
EnergySchemeCreator - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme: An abstract class for creating EnergyScheme instances.
EnergySchemeCreator() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
EnergySchemeCreatorByElement - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme: Creates an EnergyScheme by combining individual elements and their interactions.
EnergySchemeCreatorByElement() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
EnergySchemeSet - Class in org.anchoranalysis.mpp.feature.energy.scheme: A set of EnergySchemes, each associated with a unique name.
EnergySchemeSet(SharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Creates a new EnergySchemeSet instance.
EnergySchemeWithSharedFeatures - Class in org.anchoranalysis.mpp.feature.energy.scheme: Combines an EnergyScheme with SharedFeatures for energy calculations.
EnergySchemeWithSharedFeatures(EnergyScheme, SharedFeatures, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Creates a new EnergySchemeWithSharedFeatures.
EnergyTotal - Class in org.anchoranalysis.mpp.feature.energy: Represents the total energy of a system, which can be modified and queried.
EnergyTotal() - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyTotal
EnergyTotal(double) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Creates a new EnergyTotal instance.
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo
equals(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
exchange(int, EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Exchanges an energy total at a specific index with a new one and updates the total energy.
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Exchanges a mark at a specific index with a new mark.
exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Exchanges a mark at a particular index with a new mark.
exchange(EnergySavedIndividual, int, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Exchanges a mark at a specific index with a new mark and recalculates energies.
exchange(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Exchanges a mark at a specific index with a new mark and updates energies.
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair

F

FeatureAllMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element: An abstract base class for features that operate on FeatureInputAllMemo.
FeatureAllMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
FeatureInputAllMemo - Class in org.anchoranalysis.mpp.feature.input: Feature input that contains a list of memoized energy calculations for all marks.
FeatureInputAllMemo(EnergyMemoList, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo: Creates a new instance with a list of memoized energy calculations and an energy stack.
FeatureInputMark - Class in org.anchoranalysis.mpp.feature.bean.mark: A feature input that wraps a Mark along with optional dimensions and dictionary.
FeatureInputMark(Mark, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Constructs a new instance with a mark and optional dimensions.
FeatureInputMark(Mark, Optional<Dimensions>, Optional<Dictionary>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Creates a new FeatureInputMark instance.
FeatureInputMark(Mark, Dimensions, Dictionary) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Constructs a new instance with a mark, dimensions, and dictionary.
FeatureInputMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection: Feature input that contains a collection of marks and optional dimensions.
FeatureInputMarkCollection(MarkCollection, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection: Creates a new FeatureInputMarkCollection instance.
FeatureInputPairMemo - Class in org.anchoranalysis.mpp.feature.input: Feature input that contains a pair of memoized voxelized marks and an energy stack.
FeatureInputPairMemo(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo: Creates a new instance with two memoized voxelized marks and an energy stack.
FeatureInputSingleMemo - Class in org.anchoranalysis.mpp.feature.input: Feature input that contains a single memoized voxelized mark and an optional energy stack.
FeatureInputSingleMemo(VoxelizedMarkMemo, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: Creates a new instance with a memoized voxelized mark and an optional energy stack.
FeatureInputSingleMemo(VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: Creates a new instance with a memoized voxelized mark and a non-optional energy stack.
FeaturePairMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element: An abstract base class for features that operate on pairs of memoized objects.
FeaturePairMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
FeatureSingleMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element: An abstract base class for features that operate on a single memoized object.
FeatureSingleMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo

G

generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface org.anchoranalysis.mpp.feature.addcriteria.AddCriteria: Generates an edge between two marks based on the defined criteria.
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Gets the mark at the specified index.
get(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Gets the energy total at a specific index.
get(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Returns the element at the specified position in this list.
get(String) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Retrieves an EnergyScheme by its name.
getAddCriteria() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The criteria used to determine which marks to add.
getAll() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.
getAll() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Features for all elements together.
getCalculations() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo: The list of memoized energy calculations for all marks.
getDefine() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Defines additional configuration for the evaluation process.
getDictionary() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional dictionary provider.
getDictionaryOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getDimensionsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Gets the optional dimensions associated with this feature input.
getDimensionsRequired() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: Gets the dimensions associated with this feature input, throwing an exception if not present.
getElemAllCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional creator for features considering all elements.
getElemByCliqueSize(int) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Gets the feature list for a specific clique size.
getElemIndCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for individual elements.
getElemPairCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for pairs of elements.
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the energy scheme with shared features.
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Associated Energy Scheme, which should include the EnergySavedPairs.
getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: The energy scheme used for calculations.
getEnergySchemeCreator() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Creator for the energy scheme used in mark evaluation.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair: The total energy associated with the pair of marks.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the total energy of all marks.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The pre-annealed total energy.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Gets the total energy for all items.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: The total energy of all individual marks.
getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Pairwise energy total
getIndexForMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the index for a specific memo.
getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Energy saved for individual marks.
getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Features for individual elements (clique-size==1).
getList() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr: List of AddCriteriaPair to be combined with OR operation.
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: List of named feature providers for image-based features.
getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: A list of features of the image that are calculated first, and exposed to the other features as parameters.
getMark() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark: The mark associated with this feature input.
getMarkFactory() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Factory for creating marks with identifiers.
getMarks() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Gets all marks in the collection.
getMarks() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection: The collection of marks.
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy: The marks with their energy breakdown.
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the collection of marks.
getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The marks in the collection.
getMarksWithTotalEnergy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the marks with their total energy.
getMemo() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: The memoized voxelized mark.
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the memo for a specific index.
getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
getMemoForMark(MarkCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the memo for a specific mark in the collection.
getObject1() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo: The first memoized voxelized mark.
getObject2() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo: The second memoized voxelized mark.
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair: The pair of marks.
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Every combination of interactions between marks and the associated energy.
getPair() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Features for pairs of elements (clique-size==2).
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Criteria for adding pairs of elements.
getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: Criteria for adding pairs to the energy calculation.
getPairsFor(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Gets all pairs associated with a specific mark.
getPairTypeClass() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The class type of the pair.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Mapping of regions.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme: The region map used in the energy scheme.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Gets the region map from the energy scheme.
getRegionMap() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Gets the region map associated with this energy memo list.
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet: Shared features associated with all energy schemes in the set.
getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Shared features used across calculations.
getTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal: Gets the current total energy value.

H

hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo
hashCode() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList

I

includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair: Determines whether to include a pair of marks based on specific criteria.
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
IncludeMarksFailureException - Exception Class in org.anchoranalysis.mpp.feature.addcriteria: Exception thrown when there's a failure in including marks during the add criteria process.
IncludeMarksFailureException(Exception) - Constructor for exception class org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException: Constructs a new exception with the specified cause.
IncludeMarksFailureException(String) - Constructor for exception class org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException: Constructs a new exception with the specified detail message.
IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy: An Indexable object that contains MarksWithEnergyBreakdown.
IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy: Creates a new IndexableMarksWithEnergy.
initialize() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Initializes the energy calculations.
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
isFirst() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle: Iff true, first object is used, otherwise the second
isIncludeFeatureNames() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features.
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Checks if the given MarkCollection spans all marks in this collection.
isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Checks if the pair collection only contains items from a particular mark configuration.
isSuppressZ() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection: If true, the Z dimension is ignored when checking for intersection.
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual
iterator() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
iterator() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList

M

MarkEvaluator - Class in org.anchoranalysis.mpp.feature.bean.mark: A bean for evaluating marks using features and energy schemes.
MarkEvaluator() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
MarkPairCollection - Class in org.anchoranalysis.mpp.feature.mark: A collection of MarkPairs with Marks as the underlying type.
MarkPairCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MarkPairCollection: Creates a new MarkPairCollection.
MarksWithEnergyBreakdown - Class in org.anchoranalysis.mpp.feature.energy.marks: Marks with both the total energy and a breakdown by clique.
MarksWithEnergyBreakdown(MarksWithTotalEnergy) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a new instance with the given marks and total energy.
MarksWithEnergyBreakdown(MarksWithTotalEnergy, EnergySavedIndividual, EnergySavedPairs, EnergySavedAll) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a new MarksWithEnergyBreakdown instance.
MarksWithTotalEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks: A collection of marks with an associated (total) energy.
MarksWithTotalEnergy(MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Creates a new instance with the given marks and energy scheme.
MemoList - Class in org.anchoranalysis.mpp.feature.mark: A list of VoxelizedMarkMemo objects that implements MemoForIndex and Iterable.
MemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoList

O

OrderedFeatureList<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria: An interface for providing an ordered list of features.
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
orderedListOfFeatures() - Method in interface org.anchoranalysis.mpp.feature.addcriteria.OrderedFeatureList: Retrieves an ordered list of features used to determine the AddCriteria.
org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria: Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element: Implementations and helper classes for calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme: Creating EnergySchemes.
org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark: Features calculated on a Mark.
org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection: Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy: Non-bean classes pertaining to calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks: Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved: Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme: Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.input - package org.anchoranalysis.mpp.feature.input: Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark: Non-bean classes for calculating feature-values related to Marks.

R

RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria: An implementation of a RandomCollection that uses AddCriteria to determine which marks to add.
RandomCollectionWithAddCriteria(Class<?>) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a new instance with the specified pair type class.
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes a mark at a specific index from the collection.
remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Removes a mark at the specified index from the collection.
remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Removes the element at the specified position in this list.
remove(EnergySavedIndividual, int) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Removes a mark at a specific index and updates energies.
remove(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes a mark at a specific index from the collection and updates energies.
remove(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes a specific mark from the collection and updates energies.
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
remove(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Removes the first occurrence of the specified element from this list, if it is present.
removeTwo(EnergySavedIndividual, int, int) - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList: Removes two marks at specific indices and updates energies.
removeTwo(EnergyMemoList, int, int, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Removes two marks at specific indices from the collection and updates energies.
resetInd() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Resets the list of individual energy totals.
rmv(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Removes an energy total at a specific index and updates the total energy.

S

sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
set(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Replaces the element at the specified position in this list with the specified element.
setAddCriteria(AddCriteria<T>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The criteria used to determine which marks to add.
setAll(EnergySavedAll) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.
setCalculations(EnergyMemoList) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputAllMemo: The list of memoized energy calculations for all marks.
setDefine(Define) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Defines additional configuration for the evaluation process.
setDictionary(DictionaryProvider) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional dictionary provider.
setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Optional creator for features considering all elements.
setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for individual elements.
setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Creates features for pairs of elements.
setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Creator for the energy scheme used in mark evaluation.
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The pre-annealed total energy.
setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: The total energy of all individual marks.
setFirst(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle: Iff true, first object is used, otherwise the second
setIncludeFeatureNames(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features.
setList(List<AddCriteriaPair>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr: List of AddCriteriaPair to be combined with OR operation.
setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: List of named feature providers for image-based features.
setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator: Factory for creating marks with identifiers.
setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: The marks in the collection.
setMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputSingleMemo: The memoized voxelized mark.
setPairAddCriteria(AddCriteriaPair) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Criteria for adding pairs of elements.
setPairTypeClass(Class<?>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: The class type of the pair.
setRegionMap(RegionMap) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement: Mapping of regions.
setSuppressZ(boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection: If true, the Z dimension is ignored when checking for intersection.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria: Creates a shallow copy of this RandomCollectionWithAddCriteria.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Makes a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Creates a shallow copy of this instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs: Creates a shallow copy of this instance.
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Gets the number of marks in the collection.
size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy: Gets the number of marks in the collection.
size() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedIndividual: Gets the number of individual energy totals stored.
size() - Method in class org.anchoranalysis.mpp.feature.mark.EnergyMemoList
size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList: Returns the number of elements in this list.

T

toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyTotal
toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Returns a string representation of the object.
toString() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
toString() - Method in class org.anchoranalysis.mpp.feature.input.FeatureInputPairMemo
totalAll(EnergyMemoList, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Calculates the total energy for all marks in the list.
totalIndividual(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures: Calculates the total energy for an individual mark.

U

updateTotal(EnergyMemoList, EnergyStackWithoutParameters) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown: Updates the total energy based on the current state.

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