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

Class MarksWithTotalEnergy

Object

org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy

All Implemented Interfaces:

Serializable

public class MarksWithTotalEnergy
extends Object
implements Serializable

A collection of marks with an associated (total) energy.

Author:

Owen Feehan

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
MarksWithTotalEnergy(MarkCollection marks, EnergySchemeWithSharedFeatures energyScheme)	Creates a new instance with the given marks and energy scheme.

Method Summary

Modifier and Type	Method	Description
void	add(VoxelizedMarkMemo voxelizedMark)	Adds a voxelized mark to the collection.
MarksWithTotalEnergy	deepCopy()	Makes a deep copy of this instance (except the energyScheme which is reused).
void	exchange(int index, VoxelizedMarkMemo newMark)	Exchanges a mark at a particular index with a new mark.
Mark	get(int index)	Gets the mark at the specified index.
EnergySchemeWithSharedFeatures	getEnergyScheme()	Associated Energy Scheme, which should include the EnergySavedPairs.
double	getEnergyTotal()	The pre-annealed total energy.
MarkCollection	getMarks()	The marks in the collection.
void	remove(int index)	Removes a mark at the specified index from the collection.
void	setEnergyTotal(double energyTotal)	The pre-annealed total energy.
void	setMarks(MarkCollection marks)	The marks in the collection.
MarksWithTotalEnergy	shallowCopy()	Makes a shallow copy of this instance.
int	size()	Gets the number of marks in the collection.

Methods inherited from class java.lang.Object

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

Constructor Details

MarksWithTotalEnergy

public MarksWithTotalEnergy(MarkCollection marks, EnergySchemeWithSharedFeatures energyScheme)

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

Parameters:

marks - the collection of marks

energyScheme - the energy scheme with shared features

Method Details

shallowCopy

public MarksWithTotalEnergy shallowCopy()

Makes a shallow copy of this instance.

Returns:

a newly created object with identical contents (all member fields reused)

deepCopy

public MarksWithTotalEnergy deepCopy()

Makes a deep copy of this instance (except the energyScheme which is reused).

Returns:

a newly created object with identical contents (some member fields duplicated, some reused)

add

public void add(VoxelizedMarkMemo voxelizedMark)

Adds a voxelized mark to the collection.

Parameters:

voxelizedMark - the voxelized mark to add

remove

public void remove(int index)

Removes a mark at the specified 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 particular index with a new mark.

Parameters:

index - the index of the mark to exchange

newMark - the new voxelized mark to replace the existing mark

size

public final int size()

Gets the number of marks in the collection.

Returns:

the number of marks

get

public Mark get(int index)

Gets the mark at the specified index.

Parameters:

index - the index of the mark to retrieve

Returns:

the Mark at the specified index

getMarks

public MarkCollection getMarks()

The marks in the collection.

setMarks

public void setMarks(MarkCollection marks)

The marks in the collection.

getEnergyScheme

public EnergySchemeWithSharedFeatures getEnergyScheme()

Associated Energy Scheme, which should include the EnergySavedPairs.

getEnergyTotal

public double getEnergyTotal()

The pre-annealed total energy.

setEnergyTotal

public void setEnergyTotal(double energyTotal)

The pre-annealed total energy.