Package org.anchoranalysis.mpp.feature.energy.marks

Class MarksWithEnergyBreakdown

Object

org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown

All Implemented Interfaces:

Serializable

public class MarksWithEnergyBreakdown
extends Object
implements Serializable

Marks with both the total energy and a breakdown by clique.

This class provides functionality to manage and calculate energies for a collection of marks, including individual, pair, and all-mark energies.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
MarksWithEnergyBreakdown(MarksWithTotalEnergy marks)	Creates a new instance with the given marks and total energy.
MarksWithEnergyBreakdown(MarksWithTotalEnergy marks, EnergySavedIndividual individual, EnergySavedPairs pair, EnergySavedAll all)

Method Summary

Modifier and Type	Method	Description
void	add(EnergyMemoList wrapperInd, VoxelizedMarkMemo newPxlMarkMemo, EnergyStackWithoutParameters stack)	Adds a new mark to the collection and updates energies.
void	assertValid()	Asserts that the energy calculations are valid.
MarksWithEnergyBreakdown	deepCopy()	Creates a deep copy of this instance.
void	exchange(int index, VoxelizedMarkMemo newMark)	Exchanges a mark at a specific index with a new mark.
void	exchange(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo newMark, EnergyStack energyStack)	Exchanges a mark at a specific index with a new mark and updates energies.
EnergySavedAll	getAll()	Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.
EnergySchemeWithSharedFeatures	getEnergyScheme()	Gets the energy scheme with shared features.
double	getEnergyTotal()	Gets the total energy of all marks.
EnergySavedIndividual	getIndividual()	Energy saved for individual marks.
MarkCollection	getMarks()	Gets the collection of marks.
MarksWithTotalEnergy	getMarksWithTotalEnergy()	Gets the marks with their total energy.
EnergySavedPairs	getPair()	Every combination of interactions between marks and the associated energy.
void	initialize()	Initializes the energy calculations.
void	remove(int index)	Removes a mark at a specific index from the collection.
void	remove(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo markToRemove, EnergyStackWithoutParameters stack)	Removes a mark at a specific index from the collection and updates energies.
void	remove(EnergyMemoList wrapperInd, VoxelizedMarkMemo markToRemove, EnergyStackWithoutParameters stack)	Removes a specific mark from the collection and updates energies.
void	removeTwo(EnergyMemoList wrapperInd, int index1, int index2, EnergyStackWithoutParameters energyStack)	Removes two marks at specific indices from the collection and updates energies.
void	setAll(EnergySavedAll all)	Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.
MarksWithEnergyBreakdown	shallowCopy()	Creates a shallow copy of this instance.
int	size()	Gets the number of marks in the collection.
String	toString()	Returns a string representation of the object.
void	updateTotal(EnergyMemoList pxlMarkMemoList, EnergyStackWithoutParameters stack)	Updates the total energy based on the current state.

Methods inherited from class java.lang.Object

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

Constructor Details

MarksWithEnergyBreakdown

public MarksWithEnergyBreakdown(MarksWithTotalEnergy marks)

Creates a new instance with the given marks and total energy.

Parameters:

marks - the MarksWithTotalEnergy containing marks with their total energy

MarksWithEnergyBreakdown

public MarksWithEnergyBreakdown(MarksWithTotalEnergy marks, EnergySavedIndividual individual, EnergySavedPairs pair, EnergySavedAll all)

Method Details

initialize

public void initialize() throws NamedFeatureCalculateException

Initializes the energy calculations.

Throws:

NamedFeatureCalculateException - if there's an error during initialization

assertValid

public void assertValid()

Asserts that the energy calculations are valid.

getMarksWithTotalEnergy

public MarksWithTotalEnergy getMarksWithTotalEnergy()

Gets the marks with their total energy.

Returns:

the MarksWithTotalEnergy containing marks with total energy

updateTotal

public void updateTotal(EnergyMemoList pxlMarkMemoList, EnergyStackWithoutParameters stack) throws NamedFeatureCalculateException

Updates the total energy based on the current state.

Parameters:

pxlMarkMemoList - the EnergyMemoList containing energy memos

stack - the EnergyStackWithoutParameters for energy calculations

Throws:

NamedFeatureCalculateException - if there's an error during calculation

shallowCopy

public MarksWithEnergyBreakdown shallowCopy()

Creates a shallow copy of this instance.

Returns:

a new MarksWithEnergyBreakdown instance with shallow copies of the internal state

deepCopy

public MarksWithEnergyBreakdown deepCopy()

Creates a deep copy of this instance.

Returns:

a new MarksWithEnergyBreakdown instance with deep copies of the internal state

getEnergyTotal

public double getEnergyTotal()

Gets the total energy of all marks.

Returns:

the total energy as a double

getMarks

public MarkCollection getMarks()

Gets the collection of marks.

Returns:

the MarkCollection containing all marks

getEnergyScheme

public EnergySchemeWithSharedFeatures getEnergyScheme()

Gets the energy scheme with shared features.

Returns:

the EnergySchemeWithSharedFeatures used for energy calculations

add

public void add(EnergyMemoList wrapperInd, VoxelizedMarkMemo newPxlMarkMemo, EnergyStackWithoutParameters stack) throws NamedFeatureCalculateException

Adds a new mark to the collection and updates energies.

Parameters:

wrapperInd - the EnergyMemoList containing energy memos

newPxlMarkMemo - the new VoxelizedMarkMemo to add

stack - the EnergyStackWithoutParameters for energy calculations

Throws:

NamedFeatureCalculateException - if there's an error during calculation

remove

public void remove(EnergyMemoList wrapperInd, VoxelizedMarkMemo markToRemove, EnergyStackWithoutParameters stack) throws NamedFeatureCalculateException

Removes a specific mark from the collection and updates energies.

Parameters:

wrapperInd - the EnergyMemoList containing energy memos

markToRemove - the VoxelizedMarkMemo to remove

stack - the EnergyStackWithoutParameters for energy calculations

Throws:

NamedFeatureCalculateException - if there's an error during calculation

remove

public void remove(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo markToRemove, EnergyStackWithoutParameters stack) throws NamedFeatureCalculateException

Removes a mark at a specific index from the collection and updates energies.

Parameters:

wrapperInd - the EnergyMemoList containing energy memos

index - the index of the mark to remove

markToRemove - the VoxelizedMarkMemo to remove

stack - the EnergyStackWithoutParameters for energy calculations

Throws:

NamedFeatureCalculateException - if there's an error during calculation

removeTwo

public void removeTwo(EnergyMemoList wrapperInd, int index1, int index2, EnergyStackWithoutParameters energyStack) throws NamedFeatureCalculateException

Removes two marks at specific indices from the collection and updates energies.

Parameters:

wrapperInd - the EnergyMemoList containing energy memos

index1 - the index of the first mark to remove

index2 - the index of the second mark to remove

energyStack - the EnergyStackWithoutParameters for energy calculations

Throws:

NamedFeatureCalculateException - if there's an error during calculation

exchange

public void exchange(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo newMark, EnergyStack energyStack) throws NamedFeatureCalculateException

Exchanges a mark at a specific index with a new mark and updates energies.

Parameters:

wrapperInd - the EnergyMemoList containing energy memos

index - the index of the mark to exchange

newMark - the new VoxelizedMarkMemo to replace the existing mark

energyStack - the EnergyStack for energy calculations

Throws:

NamedFeatureCalculateException - if there's an error during calculation

remove

public void remove(int index)

Removes a mark at a specific index from the collection.

Parameters:

index - the index of the mark to remove

exchange

public void exchange(int index, VoxelizedMarkMemo newMark)

Exchanges a mark at a specific index with a new mark.

Parameters:

index - the index of the mark to exchange

newMark - the new VoxelizedMarkMemo to replace the existing mark

toString

public String toString()

Returns a string representation of the object.

Overrides:

toString in class Object

Returns:

a string representation of the object

size

public final int size()

Gets the number of marks in the collection.

Returns:

the number of marks as an int

getIndividual

public EnergySavedIndividual getIndividual()

Energy saved for individual marks.

getPair

public EnergySavedPairs getPair()

Every combination of interactions between marks and the associated energy.

getAll

public EnergySavedAll getAll()

Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.

setAll

public void setAll(EnergySavedAll all)

Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component.