Package org.anchoranalysis.mpp.feature.addcriteria

Class RandomCollectionWithAddCriteria<T>

Object

org.anchoranalysis.bean.AnchorBean<RandomCollection<T>>

org.anchoranalysis.mpp.pair.RandomCollection<T>

org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria<T>

Type Parameters:

T - type of the pair

All Implemented Interfaces:

UpdatableMarks

Direct Known Subclasses:

MarkPairCollection

public class RandomCollectionWithAddCriteria<T>
extends RandomCollection<T>

An implementation of a RandomCollection that uses AddCriteria to determine which marks to add.

This class is not a valid bean on its own, as it lacks a default public constructor. To use it in BeanXML, it must be subclassed with such a constructor. However, it is a valid (non-bean) class on its own.

The class is kept non-abstract to allow instantiation when copy methods (shallowCopy, deepCopy, etc.) are called.

Constructor Summary

Constructors

Constructor	Description
RandomCollectionWithAddCriteria(Class<?> pairTypeClass)	Creates a new instance with the specified pair type class.

Method Summary

Modifier and Type	Method	Description
void	add(MemoForIndex marksExisting, VoxelizedMarkMemo newMark)
boolean	containsMark(Mark mark)	Checks if the collection contains a specific mark.
Set<T>	createPairsUnique()	Creates a set of unique pairs from the graph.
RandomCollectionWithAddCriteria<T>	deepCopy()	Creates a deep copy of this RandomCollectionWithAddCriteria.
void	exchange(MemoForIndex memo, VoxelizedMarkMemo oldMark, int indexOldMark, VoxelizedMarkMemo newMark)
AddCriteria<T>	getAddCriteria()	The criteria used to determine which marks to add.
Collection<Mark>	getMarks()	Gets all marks in the collection.
Collection<TypedEdge<Mark,T>>	getPairsFor(Mark mark)	Gets all pairs associated with a specific mark.
Class<?>	getPairTypeClass()	The class type of the pair.
void	initUpdatableMarks(MemoForIndex marks, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures)
boolean	isMarksSpan(MarkCollection marks)	Checks if the given MarkCollection spans all marks in this collection.
void	remove(MemoForIndex marksExisting, VoxelizedMarkMemo mark)
T	sampleRandomPairNonUniform(RandomNumberGenerator randomNumberGenerator)
void	setAddCriteria(AddCriteria<T> addCriteria)	The criteria used to determine which marks to add.
void	setPairTypeClass(Class<?> pairTypeClass)	The class type of the pair.
RandomCollectionWithAddCriteria<T>	shallowCopy()	Creates a shallow copy of this RandomCollectionWithAddCriteria.

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

RandomCollectionWithAddCriteria

public RandomCollectionWithAddCriteria(Class<?> pairTypeClass)

Creates a new instance with the specified pair type class.

Parameters:

pairTypeClass - the class type of the pair

Method Details

shallowCopy

public RandomCollectionWithAddCriteria<T> shallowCopy()

Creates a shallow copy of this RandomCollectionWithAddCriteria.

This method creates a new instance with the same pairTypeClass and addCriteria, and copies references to the graph, energyStack, logger, and sharedFeatures.

Returns:

a new RandomCollectionWithAddCriteria instance with shallow-copied properties

deepCopy

public RandomCollectionWithAddCriteria<T> deepCopy()

Creates a deep copy of this RandomCollectionWithAddCriteria.

This method creates a new instance with the same pairTypeClass and addCriteria, and copies references to the graph, energyStack, logger, and sharedFeatures.

Returns:

a new RandomCollectionWithAddCriteria instance with deep-copied properties

initUpdatableMarks

public void initUpdatableMarks(MemoForIndex marks, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures) throws InitializeException

Throws:

InitializeException

add

public void add(MemoForIndex marksExisting, VoxelizedMarkMemo newMark) throws UpdateMarkSetException

Throws:

UpdateMarkSetException

exchange

public void exchange(MemoForIndex memo, VoxelizedMarkMemo oldMark, int indexOldMark, VoxelizedMarkMemo newMark) throws UpdateMarkSetException

Throws:

UpdateMarkSetException

remove

public void remove(MemoForIndex marksExisting, VoxelizedMarkMemo mark) throws UpdateMarkSetException

Throws:

UpdateMarkSetException

createPairsUnique

public Set<T> createPairsUnique()

Creates a set of unique pairs from the graph.

Returns:

a Set of unique pairs

getPairsFor

public Collection<TypedEdge<Mark,T>> getPairsFor(Mark mark)

Gets all pairs associated with a specific mark.

Parameters:

mark - the Mark to get pairs for

Returns:

a Collection of edges (pairs) associated with the mark

containsMark

public boolean containsMark(Mark mark)

Checks if the collection contains a specific mark.

Parameters:

mark - the Mark to check for

Returns:

true if the mark is present in the collection, false otherwise

getMarks

public Collection<Mark> getMarks()

Gets all marks in the collection.

Returns:

a Collection of all Marks in the graph

isMarksSpan

public boolean isMarksSpan(MarkCollection marks)

Checks if the given MarkCollection spans all marks in this collection.

This method verifies that all marks in the given collection are present in this collection, and that this collection doesn't contain any additional marks.

Parameters:

marks - the MarkCollection to check against

Returns:

true if the given collection spans all marks in this collection, false otherwise

sampleRandomPairNonUniform

public T sampleRandomPairNonUniform(RandomNumberGenerator randomNumberGenerator)

Specified by:

sampleRandomPairNonUniform in class RandomCollection<T>

getPairTypeClass

public Class<?> getPairTypeClass()

The class type of the pair.

setPairTypeClass

public void setPairTypeClass(Class<?> pairTypeClass)

The class type of the pair.

getAddCriteria

public AddCriteria<T> getAddCriteria()

The criteria used to determine which marks to add.

setAddCriteria

public void setAddCriteria(AddCriteria<T> addCriteria)

The criteria used to determine which marks to add.