Package org.biojava.nbio.structure.align.multiple

Class MultipleAlignmentImpl

java.lang.Object

org.biojava.nbio.structure.align.multiple.AbstractScoresCache

org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

All Implemented Interfaces:

Serializable, Cloneable, MultipleAlignment, ScoresCache

public class MultipleAlignmentImpl
extends AbstractScoresCache
implements Serializable, MultipleAlignment, Cloneable

A general implementation of a MultipleAlignment.

Since:

4.1.0

Author:

Aleix Lafita

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentImpl()	Default Constructor.
MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble)	Constructor linking to an existing ensemble.
MultipleAlignmentImpl(MultipleAlignmentImpl ma)	Copy constructor.

Method Summary

Modifier and Type	Method	Description
void	clear()	Clear the cached scores.
MultipleAlignmentImpl	clone()	Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
List<Integer>	getAlignResCounts()	Returns the number of non null positions (residues) of each structure in the alignment.
List<Atom[]>	getAtomArrays()	Returns the array of Atoms for each structure from its parent Ensemble.
Block	getBlock(int index)	Returns the Block with the specified index of the MultipleAlignment.
List<Block>	getBlocks()	Convenience method to get a List of all Blocks from all BlockSets.
BlockSet	getBlockSet(int index)	Returns the BlockSet with the specified index of the MultipleAlignment.
List<BlockSet>	getBlockSets()	Returns the BlockSet List of the multiple structure alignment.
int	getCoreLength()	Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.
List<Double>	getCoverages()	Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.
MultipleAlignmentEnsemble	getEnsemble()	Returns the parent Ensemble of the MultipleAlignment.
StructureIdentifier	getStructureIdentifier(int index)	Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
int	length()	Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
void	setBlockSets(List<BlockSet> blockSets)	Sets the List of BlockSet List of the specified alignment.
void	setEnsemble(MultipleAlignmentEnsemble parent)	Set the back-reference to its parent Ensemble.
int	size()	Returns the number of aligned structures in the MultipleAlignment.
String	toString()	Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.
protected void	updateCache()	Updates all cached properties
protected void	updateCoreLength()	Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.
protected void	updateLength()	Force recalculation of the length (aligned columns) based on the BlockSet lengths.

Methods inherited from class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

clone, getScore, getScores, putScore

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.nbio.structure.align.multiple.ScoresCache

getScore, getScores, putScore

Constructor Details

MultipleAlignmentImpl

public MultipleAlignmentImpl()

Default Constructor. Empty alignment. No structures assigned.

MultipleAlignmentImpl

public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble)

Constructor linking to an existing ensemble. Automatically adds this alignment to the parent ensemble.

Parameters:

ensemble - parent MultipleAlignmentEnsemble.

MultipleAlignmentImpl

public MultipleAlignmentImpl(MultipleAlignmentImpl ma)

Copy constructor. Recursively copies member BlockSets.

Parameters:

ma - MultipleAlignmentImpl to copy.

Method Details

clear

public void clear()

Description copied from class: AbstractScoresCache

Clear the cached scores. This frees memory after the alignment changed.

Specified by:

clear in interface MultipleAlignment

Overrides:

clear in class AbstractScoresCache

clone

public MultipleAlignmentImpl clone()

Description copied from interface: MultipleAlignment

Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.

Specified by:

clone in interface MultipleAlignment

Overrides:

clone in class Object

Returns:

MultipleAlignment identical copy of this object.

toString

public String toString()

Description copied from interface: MultipleAlignment

Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores. Can be used as a header for the differnt display options.

Specified by:

toString in interface MultipleAlignment

Overrides:

toString in class Object

Returns:

String header summary of the MultipleAlignment

getBlockSets

public List<BlockSet> getBlockSets()

Description copied from interface: MultipleAlignment

Returns the BlockSet List of the multiple structure alignment. Initializes the variable if it is null.

Specified by:

getBlockSets in interface MultipleAlignment

Returns:

List of BlockSets that describe the aligned residues of all the structures.

See Also:

• MultipleAlignment.getBlocks()
• MultipleAlignment.setBlockSets(List)

getBlocks

public List<Block> getBlocks()

Description copied from interface: MultipleAlignment

Convenience method to get a List of all Blocks from all BlockSets. Modifications of this List will not alter the MultipleAlignment, but modifications to the Blocks will.

Specified by:

getBlocks in interface MultipleAlignment

Returns:

List of Blocks

See Also:

• MultipleAlignment.getBlockSets()

setBlockSets

public void setBlockSets(List<BlockSet> blockSets)

Description copied from interface: MultipleAlignment

Sets the List of BlockSet List of the specified alignment.

Specified by:

setBlockSets in interface MultipleAlignment

Parameters:

blockSets - the List of BlockSets that describe the aligned residues.

See Also:

• MultipleAlignment.getBlockSets()

getBlockSet

public BlockSet getBlockSet(int index)

Description copied from interface: MultipleAlignment

Returns the BlockSet with the specified index of the MultipleAlignment. Throws an Exception if the index is out of bounds, like accessing a normal List.

Specified by:

getBlockSet in interface MultipleAlignment

Parameters:

index - of the BlockSet

Returns:

BlockSets at the specified index

See Also:

• MultipleAlignment.getBlocks()
• MultipleAlignment.getBlockSets()

getBlock

public Block getBlock(int index)

Description copied from interface: MultipleAlignment

Returns the Block with the specified index of the MultipleAlignment. Throws an Exception if the index is out of bounds, like accessing a normal List.

Specified by:

getBlock in interface MultipleAlignment

Parameters:

index - of the BlockSet

Returns:

Block at the specified index

See Also:

• MultipleAlignment.getBlocks()
• MultipleAlignment.getBlockSets()

getAtomArrays

public List<Atom[]> getAtomArrays()

Description copied from interface: MultipleAlignment

Returns the array of Atoms for each structure from its parent Ensemble. Throws an Exception if the parent ensemble is null or the Atom variables are not previously set.

Specified by:

getAtomArrays in interface MultipleAlignment

Returns:

List of Atom arrays

See Also:

• MultipleAlignment.getEnsemble()

getStructureIdentifier

public StructureIdentifier getStructureIdentifier(int index)

Description copied from interface: MultipleAlignment

Returns the StructureIdentifier associated with the structure index from its parent Ensemble. Throws an Exception if the parent ensemble is null or the StructureIdentifiers are not previously set.

Specified by:

getStructureIdentifier in interface MultipleAlignment

Returns:

StructureIdentifier

See Also:

• MultipleAlignment.getEnsemble()

size

public int size()

Description copied from interface: MultipleAlignment

Returns the number of aligned structures in the MultipleAlignment.

Specified by:

size in interface MultipleAlignment

Returns:

int number of aligned structures

See Also:

• MultipleAlignment.length()
• MultipleAlignment.getCoreLength()

length

public int length()

Description copied from interface: MultipleAlignment

Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.

Specified by:

length in interface MultipleAlignment

Returns:

int the total number of aligned residues in the alignment.

See Also:

• MultipleAlignment.getCoreLength()
• MultipleAlignment.size()

getCoreLength

public int getCoreLength()

Description copied from interface: MultipleAlignment

Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.

Specified by:

getCoreLength in interface MultipleAlignment

Returns:

int the total number of aligned residues.

See Also:

• MultipleAlignment.length()
• MultipleAlignment.size()

updateLength

protected void updateLength()

Force recalculation of the length (aligned columns) based on the BlockSet lengths.

updateCoreLength

protected void updateCoreLength()

Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.

updateCache

protected void updateCache()

Updates all cached properties

getEnsemble

public MultipleAlignmentEnsemble getEnsemble()

Description copied from interface: MultipleAlignment

Returns the parent Ensemble of the MultipleAlignment. Returns null if there is no referenced object.

Specified by:

getEnsemble in interface MultipleAlignment

Returns:

MultipleAlignmentEnsemble the parent MultipleAlignment of the BlockSet, or null.

See Also:

• MultipleAlignment.setEnsemble(MultipleAlignmentEnsemble)

setEnsemble

public void setEnsemble(MultipleAlignmentEnsemble parent)

Description copied from interface: MultipleAlignment

Set the back-reference to its parent Ensemble.

Neither removes this alignment from its previous ensemble, if any, nor adds it to the new parent. Calling code should assure that links to and from the ensemble are consistent and free of memory leaks.

Specified by:

setEnsemble in interface MultipleAlignment

Parameters:

parent - the parent MultipleAlignmentEnsemble.

See Also:

• MultipleAlignment.getEnsemble()

getAlignResCounts

public List<Integer> getAlignResCounts()

Description copied from interface: MultipleAlignment

Returns the number of non null positions (residues) of each structure in the alignment. The values can be used to compute the coverages.

Specified by:

getAlignResCounts in interface MultipleAlignment

Returns:

List of residue counts for each structure

getCoverages

public List<Double> getCoverages()

Description copied from interface: MultipleAlignment

Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.

Specified by:

getCoverages in interface MultipleAlignment

Returns:

List coverage for each structure