Uses of Class
org.anchoranalysis.mpp.mark.Mark

Packages that use Mark

Package	Description
org.anchoranalysis.mpp.bean.mark.factory	Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points	Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter	Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer	Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.mark	Features calculated on a Mark.
org.anchoranalysis.mpp.feature.energy	Non-bean classes pertaining to calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.energy.marks	Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.mark	Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.init	Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic	Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points	Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized	A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo	Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlay	Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair	Pairs of Marks.
org.anchoranalysis.mpp.proposer	Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.fitter	Fitting geometric structures to points.

Uses of Mark in org.anchoranalysis.mpp.bean.mark.factory

Methods in org.anchoranalysis.mpp.bean.mark.factory that return Mark

Modifier and Type	Method	Description
Mark	MarkEllipseFactory.create()
Mark	MarkEllipsoidFactory.create()
abstract Mark	MarkFactory.create()	Creates a new Mark object.
Mark	MarkPointListFactory.create()
Mark	MarkWithIdentifierFactory.newTemplateMark()	Creates a new mark based on the template and assigns it a unique identifier.

Uses of Mark in org.anchoranalysis.mpp.bean.points

Methods in org.anchoranalysis.mpp.bean.points that return types with arguments of type Mark

Modifier and Type	Method	Description
Optional<Mark>	CreateMarkFromPoints.fitMarkToPointsFromMarks(MarkCollection marks, Dimensions dimensions)	Extracts points from marks, creates a new mark, and fits this mark to the extracted points.

Uses of Mark in org.anchoranalysis.mpp.bean.points.fitter

Methods in org.anchoranalysis.mpp.bean.points.fitter with parameters of type Mark

Modifier and Type	Method	Description
abstract void	PointsFitter.fit(List<Point3f> points, Mark mark, Dimensions dimensions)	Fits a mark to a set of points within given dimensions.

Uses of Mark in org.anchoranalysis.mpp.bean.proposer

Methods in org.anchoranalysis.mpp.bean.proposer that return types with arguments of type Mark

Modifier and Type	Method	Description
abstract Optional<Mark>	MarkMergeProposer.propose(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, ProposerContext context)	Proposes a merge between two marks.
abstract Optional<Mark>	MarkFromCollectionProposer.selectMarkFrom(MarkCollection marks, ProposerContext context)	Selects a mark from a collection of marks.

Methods in org.anchoranalysis.mpp.bean.proposer with parameters of type Mark

Modifier and Type	Method	Description
abstract Optional<Orientation>	OrientationProposer.propose(Mark mark, Dimensions dimensions, RandomNumberGenerator randomNumberGenerator)	Proposes an orientation for a given mark.
abstract Optional<List<Point3i>>	PointsProposer.propose(Point3d point, Mark mark, Dimensions dimensions, RandomNumberGenerator randomNumberGenerator, ErrorNode errorNode)	Proposes a list of points based on the given parameters.

Uses of Mark in org.anchoranalysis.mpp.feature.addcriteria

Methods in org.anchoranalysis.mpp.feature.addcriteria that return types with arguments of type Mark

Modifier and Type	Method	Description
Optional<MarkPair<Mark>>	AddCriteriaPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Collection<Mark>	RandomCollectionWithAddCriteria.getMarks()	Gets all marks in the collection.
Collection<TypedEdge<Mark,T>>	RandomCollectionWithAddCriteria.getPairsFor(Mark mark)	Gets all pairs associated with a specific mark.

Methods in org.anchoranalysis.mpp.feature.addcriteria with parameters of type Mark

Modifier and Type	Method	Description
boolean	RandomCollectionWithAddCriteria.containsMark(Mark mark)	Checks if the collection contains a specific mark.
Collection<TypedEdge<Mark,T>>	RandomCollectionWithAddCriteria.getPairsFor(Mark mark)	Gets all pairs associated with a specific mark.

Uses of Mark in org.anchoranalysis.mpp.feature.bean.mark

Methods in org.anchoranalysis.mpp.feature.bean.mark that return Mark

Modifier and Type	Method	Description
Mark	FeatureInputMark.getMark()	The mark associated with this feature input.

Constructors in org.anchoranalysis.mpp.feature.bean.mark with parameters of type Mark

Modifier	Constructor	Description
	FeatureInputMark(Mark mark, Optional<Dimensions> dimensions)	Constructs a new instance with a mark and optional dimensions.
	FeatureInputMark(Mark mark, Optional<Dimensions> dimensions, Optional<Dictionary> dictionary)	Creates a new FeatureInputMark instance.
	FeatureInputMark(Mark mark, Dimensions dimensions, Dictionary dictionary)	Constructs a new instance with a mark, dimensions, and dictionary.

Uses of Mark in org.anchoranalysis.mpp.feature.energy

Methods in org.anchoranalysis.mpp.feature.energy that return types with arguments of type Mark

Modifier and Type	Method	Description
MarkPair<Mark>	EnergyPair.getPair()	The pair of marks.

Constructor parameters in org.anchoranalysis.mpp.feature.energy with type arguments of type Mark

Modifier	Constructor	Description
	EnergyPair(MarkPair<Mark> pair, EnergyTotal energyTotal)	Creates a new EnergyPair instance.

Uses of Mark in org.anchoranalysis.mpp.feature.energy.marks

Methods in org.anchoranalysis.mpp.feature.energy.marks that return Mark

Modifier and Type	Method	Description
Mark	MarksWithTotalEnergy.get(int index)	Gets the mark at the specified index.

Uses of Mark in org.anchoranalysis.mpp.feature.mark

Methods in org.anchoranalysis.mpp.feature.mark with parameters of type Mark

Modifier and Type	Method	Description
VoxelizedMarkMemo	EnergyMemoList.getMemoForMark(MarkCollection marks, Mark mark)	Gets the memo for a specific mark in the collection.

Uses of Mark in org.anchoranalysis.mpp.init

Methods in org.anchoranalysis.mpp.init that return types with arguments of type Mark

Modifier and Type	Method	Description
NamedProviderStore<RandomCollection<MarkPair<Mark>>>	MarksInitialization.markPairs()	Store for random collections of mark pairs.

Uses of Mark in org.anchoranalysis.mpp.mark

Subclasses of Mark in org.anchoranalysis.mpp.mark

Modifier and Type	Class	Description
class	MarkWithPosition	An abstract base class for marks that have a position in 3D space.

Methods in org.anchoranalysis.mpp.mark that return Mark

Modifier and Type	Method	Description
abstract Mark	Mark.duplicate()	Creates a duplicate of this mark.
Mark	MarkCollection.get(int index)	Gets a mark at a specific index.
final Mark	MarkCollection.randomMark(RandomNumberGenerator randomNumberGenerator)	Gets a random mark from the collection.
Mark	MarkCollection.remove(int index)	Removes a mark at a specific index.
Mark	MarkCollection.set(int index, Mark element)	Replaces the mark at a specific index.

Methods in org.anchoranalysis.mpp.mark that return types with arguments of type Mark

Modifier and Type	Method	Description
Map<Mark,Integer>	MarkCollection.createHashMapToId()	Creates a map of marks to their indices in the collection.
Map<Integer,Mark>	MarkCollection.createIdHashMap()	Creates a map of marks indexed by their IDs.
Set<Mark>	MarkCollection.createSet()	Creates a set of all marks in the collection.
List<Mark>	MarkCollection.getMarks()	The underlying List that stores the Marks in the collection.
Iterator<Mark>	ColoredMarks.iterator()
final Iterator<Mark>	MarkCollection.iterator()

Methods in org.anchoranalysis.mpp.mark with parameters of type Mark

Modifier and Type	Method	Description
void	ColoredMarks.add(Mark mark, Color color)	Adds a mark with an associated color.
void	ColoredMarks.add(Mark mark, RGBColor color)	Adds a mark with an associated RGBColor.
boolean	MarkCollection.add(Mark mark)	Adds a mark to the collection.
void	ColoredMarks.addChangeID(Mark mark, Color color)	Adds a mark, changes its ID, and associates it with a color.
void	ColoredMarks.addChangeID(Mark mark, RGBColor color)	Adds a mark, changes its ID, and associates it with an RGBColor.
ObjectMask	MarkToObjectConverter.convert(Mark mark)	Converts a Mark to an equivalent ObjectMask.
boolean	Mark.equalsDeep(Mark mark)	Checks if this mark is deeply equal to another mark.
boolean	MarkWithPosition.equalsDeep(Mark m)	Checks if this mark is equal to another mark by comparing all attributes.
final void	MarkCollection.exchange(int index, Mark markToAssign)	Replaces the mark at a specific index.
int	MarkCollection.indexOf(Mark mark)	Finds the index of a specific mark in the collection.
boolean	CompatibleWithMark.isCompatibleWith(Mark testMark)	Tests if the implementing object is compatible with a mark of a particular type.
boolean	QuickOverlapCalculation.noOverlapWith(Mark mark, int regionID)	A quick (computationally-efficient) test to see if we can reject the possibility of overlap
Mark	MarkCollection.set(int index, Mark element)	Replaces the mark at a specific index.

Constructors in org.anchoranalysis.mpp.mark with parameters of type Mark

Modifier	Constructor	Description
	ColoredMarks(Mark mark, RGBColor color)	Creates a ColoredMarks instance with a single mark and color.
protected	Mark(Mark source)	Copy constructor.
	MarkCollection(Mark mark)	Creates from a single Mark.

Constructor parameters in org.anchoranalysis.mpp.mark with type arguments of type Mark

Modifier	Constructor	Description
	ColoredMarks(MarkCollection marks, ColorIndex colorIndex, IdentifierGetter<Mark> colorIDGetter)	Creates a ColoredMarks instance from a MarkCollection and assigns colors based on a ColorIndex.
	MarkCollection(List<Mark> marks)	Creates a new MarkCollection instance.
	MarkCollection(Stream<Mark> stream)	Creates from a stream of Marks.

Uses of Mark in org.anchoranalysis.mpp.mark.conic

Subclasses of Mark in org.anchoranalysis.mpp.mark.conic

Modifier and Type	Class	Description
class	Circle	Represents a 2D circle mark.
class	ConicBase	Abstract base class for conic marks (e.g., ellipsoids, spheres).
class	Ellipse	Represents a 2D ellipse mark.
class	Ellipsoid	Represents a 3D ellipsoid mark with multiple sub-regions.
class	MarkWithPositionAndSingleRadius	Base-class for a conic that has a single radius (circle, sphere etc.)
class	Sphere	Represents a 3D sphere mark.

Methods in org.anchoranalysis.mpp.mark.conic that return Mark

Modifier and Type	Method	Description
static Mark	MarkConicFactory.createMarkFromPoint(Point3d point, int size, boolean do3D)	Creates a mark from a double-precision 3D point.
static Mark	MarkConicFactory.createMarkFromPoint(Point3i point, int size, boolean do3D)	Creates a mark from an integer 3D point.
Mark	Circle.duplicate()
Mark	Ellipsoid.duplicate()
Mark	Sphere.duplicate()

Methods in org.anchoranalysis.mpp.mark.conic with parameters of type Mark

Modifier and Type	Method	Description
boolean	Ellipse.equalsDeep(Mark mark)
boolean	Ellipsoid.equalsDeep(Mark m)
boolean	MarkWithPositionAndSingleRadius.equalsDeep(Mark mark)

Uses of Mark in org.anchoranalysis.mpp.mark.points

Subclasses of Mark in org.anchoranalysis.mpp.mark.points

Modifier and Type	Class	Description
class	LineSegment	Represents a line segment in 3D space as a Mark.
class	PointList	A a list of 3D points.
class	PointListBase	A base class for marks that consist of a list of 3D points.
class	Polygon	Represents a polygon in 2D space as a Mark.
class	PolygonCurve	Represents a polygon curve in 3D space as a Mark.
class	RotatableBoundingBox	A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.

Methods in org.anchoranalysis.mpp.mark.points that return Mark

Modifier and Type	Method	Description
Mark	LineSegment.duplicate()
Mark	PointList.duplicate()
Mark	Polygon.duplicate()
Mark	PolygonCurve.duplicate()
Mark	RotatableBoundingBox.duplicate()

Methods in org.anchoranalysis.mpp.mark.points with parameters of type Mark

Modifier and Type	Method	Description
boolean	PointListBase.equalsDeep(Mark mark)

Uses of Mark in org.anchoranalysis.mpp.mark.voxelized

Methods in org.anchoranalysis.mpp.mark.voxelized with parameters of type Mark

Modifier and Type	Method	Description
static VoxelizedMarkHistogram	VoxelizedMarkFactory.create(Mark mark, EnergyStackWithoutParameters stack, RegionMap regionMap)	Creates a new VoxelizedMarkHistogram instance.

Uses of Mark in org.anchoranalysis.mpp.mark.voxelized.memo

Methods in org.anchoranalysis.mpp.mark.voxelized.memo that return Mark

Modifier and Type	Method	Description
Mark	VoxelizedMarkMemo.getMark()	The associated mark.

Methods in org.anchoranalysis.mpp.mark.voxelized.memo with parameters of type Mark

Modifier and Type	Method	Description
void	VoxelizedMarkMemo.assignFrom(Mark mark)	Assigns a new mark to replace the existing mark.
static VoxelizedMarkMemo	VoxelizedMarkMemoFactory.create(Mark mark, EnergyStackWithoutParameters stack, RegionMap regionMap)	Creates a new VoxelizedMarkMemo instance.

Constructors in org.anchoranalysis.mpp.mark.voxelized.memo with parameters of type Mark

Modifier	Constructor	Description
	VoxelizedMarkMemo(Mark mark, EnergyStackWithoutParameters stack, RegionMap regionMap)	Creates a new VoxelizedMarkMemo.

Uses of Mark in org.anchoranalysis.mpp.overlay

Methods in org.anchoranalysis.mpp.overlay that return Mark

Modifier and Type	Method	Description
Mark	OverlayMark.getMark()	The Mark to overlay.

Constructors in org.anchoranalysis.mpp.overlay with parameters of type Mark

Modifier	Constructor	Description
	OverlayMark(Mark mark, RegionMembershipWithFlags regionMembership)	Creates a new OverlayMark instance.

Uses of Mark in org.anchoranalysis.mpp.pair

Classes in org.anchoranalysis.mpp.pair with type parameters of type Mark

Modifier and Type	Class	Description
class	MarkPair<T extends Mark>	Represents a pair of marks, with a source and destination.

Uses of Mark in org.anchoranalysis.mpp.proposer

Methods in org.anchoranalysis.mpp.proposer with parameters of type Mark

Modifier and Type	Method	Description
VoxelizedMarkMemo	ProposerContext.create(Mark mark)	Creates a VoxelizedMarkMemo for the given mark.

Uses of Mark in org.anchoranalysis.plugin.points.bean

Methods in org.anchoranalysis.plugin.points.bean with parameters of type Mark

Modifier and Type	Method	Description
boolean	FitPoints.isCompatibleWith(Mark testMark)

Uses of Mark in org.anchoranalysis.plugin.points.bean.fitter

Methods in org.anchoranalysis.plugin.points.bean.fitter with parameters of type Mark

Modifier and Type	Method	Description
protected abstract void	LinearLeastSquaresViaNormalEquationBase.applyCoefficientsToMark(cern.colt.matrix.DoubleMatrix2D matrixV, Mark mark, Dimensions dimensions)	Applies the calculated coefficients to the mark.
void	LinearLeastSquaresEllipseFitter.fit(List<Point3f> points, Mark mark, Dimensions dimensions)
void	LinearLeastSquaresEllipsoidFitter.fit(List<Point3f> points, Mark mark, Dimensions dimensions)
void	LinearLeastSquaresViaNormalEquationBase.fit(List<Point3f> points, Mark mark, Dimensions dimensions)
void	Reference.fit(List<Point3f> points, Mark mark, Dimensions dimensions)
void	ReflectInAxesWithinDistance.fit(List<Point3f> points, Mark mark, Dimensions dimensions)
void	PointsFitterToMark.fitPointsToMark(List<Point3f> pointsForFitter, Mark mark, Dimensions dim)	Fits a list of points to a mark using the specified points fitter.
boolean	LinearLeastSquaresEllipseFitter.isCompatibleWith(Mark testMark)
boolean	LinearLeastSquaresEllipsoidFitter.isCompatibleWith(Mark testMark)
boolean	Reference.isCompatibleWith(Mark testMark)
boolean	ReflectInAxesWithinDistance.isCompatibleWith(Mark testMark)