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

Class BlockSetImpl

java.lang.Object

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

org.biojava.nbio.structure.align.multiple.BlockSetImpl

All Implemented Interfaces:

Serializable, Cloneable, BlockSet, ScoresCache

public class BlockSetImpl
extends AbstractScoresCache
implements Serializable, BlockSet, Cloneable

A general implementation of a BlockSet to store a flexible part of a multiple alignment.

Since:

4.1.0

Author:

Aleix Lafita

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
BlockSetImpl(BlockSetImpl bs)	Copy constructor.
BlockSetImpl(MultipleAlignment alignment)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	clear()	Clear the cached scores.
BlockSetImpl	clone()	Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
List<Integer>	getAlignResCounts()	Returns the number of non null positions (residues) of each structure in the alignment Block Set.
List<Block>	getBlocks()	Returns the List of alignment Blocks of the BlockSet.
int	getCoreLength()	Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
MultipleAlignment	getMultipleAlignment()	Returns the parent MultipleAlignment of the BlockSet.
List<javax.vecmath.Matrix4d>	getTransformations()	Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.
int	length()	Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.
void	setBlocks(List<Block> blocks)	Set the List of alignment Blocks of the BlockSet.
void	setMultipleAlignment(MultipleAlignment parent)	Set the back-reference to its parent MultipleAlignment.
void	setTransformations(List<javax.vecmath.Matrix4d> transformations)	Set a new superposition for the structures.
int	size()	Returns the number of aligned structures in the BlockSet.
String	toString()
protected void	updateCache()
protected void	updateCoreLength()
protected void	updateLength()

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

BlockSetImpl

public BlockSetImpl(MultipleAlignment alignment)

Constructor. Links also the parent to this instance by adding the BlockSet to the parent's List.

Parameters:

alignment - MultipleAlignment parent of the BlockSet.

BlockSetImpl

public BlockSetImpl(BlockSetImpl bs)

Copy constructor. Makes also a deep copy of all constituent Block s.

Parameters:

bs - BlockSet object to be copied.

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 BlockSet

Overrides:

clear in class AbstractScoresCache

clone

public BlockSetImpl clone()

Description copied from interface: BlockSet

Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.

Specified by:

clone in interface BlockSet

Overrides:

clone in class Object

Returns:

BlockSet identical copy of this object.

toString

public String toString()

Overrides:

toString in class Object

getMultipleAlignment

public MultipleAlignment getMultipleAlignment()

Description copied from interface: BlockSet

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

Specified by:

getMultipleAlignment in interface BlockSet

Returns:

MultipleAlignment the parent MultipleAlignment of the BlockSet, or null.

See Also:

• BlockSet.setMultipleAlignment(MultipleAlignment)

setMultipleAlignment

public void setMultipleAlignment(MultipleAlignment parent)

Description copied from interface: BlockSet

Set the back-reference to its parent MultipleAlignment.

Neither removes this BlockSet from its previous alignment, 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:

setMultipleAlignment in interface BlockSet

Parameters:

parent - the parent MultipleAlignment.

See Also:

• BlockSet.getMultipleAlignment()

getBlocks

public List<Block> getBlocks()

Description copied from interface: BlockSet

Returns the List of alignment Blocks of the BlockSet. It initializes a new List of Blocks if it is null.

Specified by:

getBlocks in interface BlockSet

Returns:

List of alignment Blocks.

See Also:

• BlockSet.setBlocks(List)

setBlocks

public void setBlocks(List<Block> blocks)

Description copied from interface: BlockSet

Set the List of alignment Blocks of the BlockSet.

Also calls Block.setBlockSet(BlockSet) for each argument

Specified by:

setBlocks in interface BlockSet

Parameters:

blocks - List of alignment Blocks.

See Also:

• BlockSet.getBlocks()

getTransformations

public List<javax.vecmath.Matrix4d> getTransformations()

Description copied from interface: BlockSet

Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.

Specified by:

getTransformations in interface BlockSet

Returns:

the 3D superimposition information of the alignment

setTransformations

public void setTransformations(List<javax.vecmath.Matrix4d> transformations)

Description copied from interface: BlockSet

Set a new superposition for the structures. This may trigger other properties to update which depend on the superposition.

Specified by:

setTransformations in interface BlockSet

Parameters:

transformations -

length

public int length()

Description copied from interface: BlockSet

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

Specified by:

length in interface BlockSet

Returns:

int the total number of aligned residues.

See Also:

• BlockSet.getCoreLength()
• BlockSet.size()

size

public int size()

Description copied from interface: BlockSet

Returns the number of aligned structures in the BlockSet.

Specified by:

size in interface BlockSet

Returns:

int number of aligned structures

See Also:

• BlockSet.length()
• BlockSet.getCoreLength()

getCoreLength

public int getCoreLength()

Description copied from interface: BlockSet

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

Specified by:

getCoreLength in interface BlockSet

Returns:

int the total number of aligned residues.

See Also:

• BlockSet.length()
• BlockSet.size()

updateLength

protected void updateLength()

updateCoreLength

protected void updateCoreLength()

updateCache

protected void updateCache()

getAlignResCounts

public List<Integer> getAlignResCounts()

Description copied from interface: BlockSet

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

Specified by:

getAlignResCounts in interface BlockSet

Returns:

List of residue counts for each structure