Package org.anchoranalysis.mpp.feature.mark

Class EnergyMemoList

Object

org.anchoranalysis.mpp.feature.mark.EnergyMemoList

All Implemented Interfaces:

Serializable, MemoForIndex

public class EnergyMemoList
extends Object
implements Serializable, MemoForIndex

A collection of memoized marks on which energies can be derived.

This class implements Serializable for persistence and MemoForIndex for indexing operations.

Author:

Owen Feehan

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
EnergyMemoList()	Creates an empty energy memo list.
EnergyMemoList(EnergySavedIndividual savedInd, EnergyStackWithoutParameters energyStack, MarkCollection marks, EnergySchemeWithSharedFeatures energySchemeTotal)	Creates an energy memo list with the given parameters.
EnergyMemoList(EnergyMemoList source)	Creates a copy of an existing energy memo list.

Method Summary

Modifier and Type	Method	Description
VoxelizedMarkMemo	add(EnergySavedIndividual energySavedInd, VoxelizedMarkMemo memo, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energyScheme)	Adds a new mark to the list and calculates its energy.
MarkCollection	asMarks()	Converts the energy memo list to a collection of marks.
void	clean()	Cleans up the energy memo list by setting the list to null.
VoxelizedMarkMemo	exchange(EnergySavedIndividual energySavedInd, int index, VoxelizedMarkMemo newMark, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energySchemeTotal)	Exchanges a mark at a specific index with a new mark and recalculates energies.
int	getIndexForMemo(VoxelizedMarkMemo memo)	Gets the index for a specific memo.
VoxelizedMarkMemo	getMemoForIndex(int index)	Gets the memo for a specific index.
VoxelizedMarkMemo	getMemoForMark(MarkCollection marks, Mark mark)	Gets the memo for a specific mark in the collection.
RegionMap	getRegionMap()	Gets the region map associated with this energy memo list.
void	remove(EnergySavedIndividual energySavedInd, int index)	Removes a mark at a specific index and updates energies.
void	removeTwo(EnergySavedIndividual energySavedInd, int index1, int index2)	Removes two marks at specific indices and updates energies.
int	size()

Methods inherited from class java.lang.Object

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

Constructor Details

EnergyMemoList

public EnergyMemoList()

Creates an empty energy memo list.

EnergyMemoList

public EnergyMemoList(EnergySavedIndividual savedInd, EnergyStackWithoutParameters energyStack, MarkCollection marks, EnergySchemeWithSharedFeatures energySchemeTotal) throws NamedFeatureCalculateException

Creates an energy memo list with the given parameters.

Parameters:

savedInd - the saved individual energies

energyStack - the energy stack without parameters

marks - the collection of marks

energySchemeTotal - the energy scheme with shared features

Throws:

NamedFeatureCalculateException - if there's an error calculating named features

EnergyMemoList

public EnergyMemoList(EnergyMemoList source)

Creates a copy of an existing energy memo list.

Parameters:

source - the source energy memo list to copy

Method Details

clean

public void clean()

Cleans up the energy memo list by setting the list to null.

size

public int size()

Specified by:

size in interface MemoForIndex

getRegionMap

public RegionMap getRegionMap()

Gets the region map associated with this energy memo list.

Returns:

the RegionMap

getMemoForMark

public VoxelizedMarkMemo getMemoForMark(MarkCollection marks, Mark mark)

Gets the memo for a specific mark in the collection.

Parameters:

marks - the collection of marks

mark - the specific mark to find

Returns:

the VoxelizedMarkMemo for the given mark

Throws:

AnchorFriendlyRuntimeException - if the mark doesn't exist in the collection

getMemoForIndex

public VoxelizedMarkMemo getMemoForIndex(int index)

Gets the memo for a specific index.

Specified by:

getMemoForIndex in interface MemoForIndex

Parameters:

index - the index of the memo

Returns:

the VoxelizedMarkMemo at the given index

getIndexForMemo

public int getIndexForMemo(VoxelizedMarkMemo memo)

Gets the index for a specific memo.

Parameters:

memo - the memo to find

Returns:

the index of the memo, or -1 if not found

exchange

public VoxelizedMarkMemo exchange(EnergySavedIndividual energySavedInd, int index, VoxelizedMarkMemo newMark, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energySchemeTotal) throws NamedFeatureCalculateException

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

Parameters:

energySavedInd - the saved individual energies

index - the index of the mark to exchange

newMark - the new mark to insert

stack - the energy stack without parameters

energySchemeTotal - the energy scheme with shared features

Returns:

the VoxelizedMarkMemo for the new mark

Throws:

NamedFeatureCalculateException - if there's an error calculating named features

add

public VoxelizedMarkMemo add(EnergySavedIndividual energySavedInd, VoxelizedMarkMemo memo, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energyScheme) throws NamedFeatureCalculateException

Adds a new mark to the list and calculates its energy.

Parameters:

energySavedInd - the saved individual energies

memo - the memo for the new mark

stack - the energy stack without parameters

energyScheme - the energy scheme with shared features

Returns:

the VoxelizedMarkMemo for the added mark

Throws:

NamedFeatureCalculateException - if there's an error calculating named features

remove

public void remove(EnergySavedIndividual energySavedInd, int index)

Removes a mark at a specific index and updates energies.

Parameters:

energySavedInd - the saved individual energies

index - the index of the mark to remove

removeTwo

public void removeTwo(EnergySavedIndividual energySavedInd, int index1, int index2)

Removes two marks at specific indices and updates energies.

Parameters:

energySavedInd - the saved individual energies

index1 - the index of the first mark to remove

index2 - the index of the second mark to remove

asMarks

public MarkCollection asMarks()

Converts the energy memo list to a collection of marks.

Returns:

a MarkCollection containing all the marks in this list