Package org.anchoranalysis.mpp.feature.energy.saved

Class EnergySavedPairs

Object

EnergySavedPairs

All Implemented Interfaces:

UpdatableMarks

public class EnergySavedPairs
extends Object
implements UpdatableMarks

Stores and manages pairwise energy interactions between marks.

This class implements UpdatableMarks to allow for dynamic updates of mark pairs and their energies.

Constructor Summary

Constructors

Constructor	Description
EnergySavedPairs(AddCriteria<EnergyPair> addCriteria)	Creates a new instance with the specified add criteria for energy pairs.

Method Summary

Modifier and Type	Method	Description
void	add(MemoForIndex pxlMarkMemoList, VoxelizedMarkMemo newMark)	Adds a new mark to the existing set of marks.
void	assertValid()	Asserts that the total energy is valid (not NaN).
Set<EnergyPair>	createPairsUnique()	Creates a set of unique energy pairs.
EnergySavedPairs	deepCopy()	Creates a deep copy of this instance.
void	exchange(MemoForIndex memo, VoxelizedMarkMemo oldMark, int indexOldMark, VoxelizedMarkMemo newMark)	Exchanges an existing mark with a new one.
double	getEnergyTotal()	Pairwise energy total
void	initUpdatableMarks(MemoForIndex pxlMarkMemoList, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures)	Initializes the updatable marks with necessary context.
boolean	isMarksSpan(MarkCollection marks)	Checks if the pair collection only contains items from a particular mark configuration.
void	remove(MemoForIndex marksExisting, VoxelizedMarkMemo mark)	Removes a mark from the existing set of marks.
EnergySavedPairs	shallowCopy()	Creates a shallow copy of this instance.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

EnergySavedPairs

public EnergySavedPairs(AddCriteria<EnergyPair> addCriteria)

Creates a new instance with the specified add criteria for energy pairs.

Parameters:

addCriteria - the AddCriteria for EnergyPairs

Method Details

shallowCopy

public EnergySavedPairs shallowCopy()

Creates a shallow copy of this instance.

Returns:

a new EnergySavedPairs with a shallow copy of the pair collection

deepCopy

public EnergySavedPairs deepCopy()

Creates a deep copy of this instance.

Returns:

a new EnergySavedPairs with a deep copy of the pair collection

initUpdatableMarks

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

Description copied from interface: UpdatableMarks

Initializes the updatable marks with necessary context.

Specified by:

initUpdatableMarks in interface UpdatableMarks

Parameters:

pxlMarkMemoList - the memo for indexing

stack - the energy stack

logger - the logger for any logging operations

sharedFeatures - shared features to be used

Throws:

InitializeException - if initialization fails

add

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

Description copied from interface: UpdatableMarks

Adds a new mark to the existing set of marks.

Specified by:

add in interface UpdatableMarks

Parameters:

pxlMarkMemoList - the existing set of marks

newMark - the new mark to be added

Throws:

UpdateMarkSetException - if the addition operation fails

remove

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

Description copied from interface: UpdatableMarks

Removes a mark from the existing set of marks.

Specified by:

remove in interface UpdatableMarks

Parameters:

marksExisting - the existing set of marks

mark - the mark to be removed

Throws:

UpdateMarkSetException - if the removal operation fails

exchange

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

Description copied from interface: UpdatableMarks

Exchanges an existing mark with a new one.

Specified by:

exchange in interface UpdatableMarks

Parameters:

memo - the memo for indexing

oldMark - the mark to be replaced

indexOldMark - the index of the old mark

newMark - the new mark to replace the old one

Throws:

UpdateMarkSetException - if the exchange operation fails

isMarksSpan

public boolean isMarksSpan(MarkCollection marks)

Checks if the pair collection only contains items from a particular mark configuration.

Parameters:

marks - the MarkCollection to check against

Returns:

true if the pair collection only contains marks from the given collection, false otherwise

toString

public String toString()

Overrides:

toString in class Object

assertValid

public void assertValid()

Asserts that the total energy is valid (not NaN).

createPairsUnique

public Set<EnergyPair> createPairsUnique()

Creates a set of unique energy pairs.

Returns:

a Set of unique EnergyPairs

getEnergyTotal

public double getEnergyTotal()

Pairwise energy total