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

Class BlockImpl

java.lang.Object

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

org.biojava.nbio.structure.align.multiple.BlockImpl

All Implemented Interfaces:

Serializable, Cloneable, Block, ScoresCache

public class BlockImpl
extends AbstractScoresCache
implements Serializable, Block, Cloneable

General implementation of a Block that supports any type of sequential alignment with gaps.

Since:

4.1.0

Author:

Aleix Lafita

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
BlockImpl(BlockImpl b)	Copy constructor.
BlockImpl(BlockSet blockSet)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	clear()	Clear the cached scores.
Block	clone()	Creates and returns an identical copy of this block.
List<List<Integer>>	getAlignRes()	Returns the double List containing the aligned residues for each structure.
List<Integer>	getAlignResCounts()	Returns the number of non null positions (residues) of each structure in the alignment Block.
BlockSet	getBlockSet()	Returns the parent BlockSet of the Block.
int	getCoreLength()	Returns the number of aligned positions (columns) without gaps in the Block.
int	getFinalIndex(int str)	Calculates and returns the last position of the specified structure in the alignment that is not null.
int	getFinalResidue(int str)	Calculates and returns the last residue of the specified structure in the alignment that is not null.
int	getStartIndex(int str)	Calculates and returns the first position of the specified structure in the alignment that is not null.
int	getStartResidue(int str)	Calculates and returns the first residue of the specified structure in the alignment that is not null.
int	length()	Returns the total number of aligned positions (columns) in the Block.
void	setAlignRes(List<List<Integer>> alignRes)	Set the double List containing the aligned residues for each structure.
void	setBlockSet(BlockSet parent)	Set the back-reference to its parent BlockSet.
int	size()	Returns the number of aligned structures (rows) in the Block.
String	toString()
protected void	updateCoreLength()

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 Detail

BlockImpl

public BlockImpl(BlockSet blockSet)

Constructor. Links also the parent to this instance, by adding the Block to the parent's list.

Parameters:

blockSet - the parent BlockSet of the BlockImpl instance.

BlockImpl

public BlockImpl(BlockImpl b)

Copy constructor.

Parameters:

b - BlockImpl object to be copied.

Method Detail

clone

public Block clone()

Description copied from interface: Block

Creates and returns an identical copy of this block.

Specified by:

clone in interface Block

Overrides:

clone in class Object

Returns:

Block identical copy of this object.

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 Block

Overrides:

clear in class AbstractScoresCache

toString

public String toString()

Overrides:

toString in class Object

setBlockSet

public void setBlockSet(BlockSet parent)

Description copied from interface: Block

Set the back-reference to its parent BlockSet.

Specified by:

setBlockSet in interface Block

Parameters:

parent - the parent BlockSet.

See Also:

Block.getBlockSet()

getBlockSet

public BlockSet getBlockSet()

Description copied from interface: Block

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

Specified by:

getBlockSet in interface Block

Returns:

BlockSet the parent BlockSet of the Block, or null.

See Also:

Block.setBlockSet(BlockSet)

getAlignRes

public List<List<Integer>> getAlignRes()

Description copied from interface: Block

Returns the double List containing the aligned residues for each structure.

alignRes.get(structure).get(residue) = alignRes.get(size).get(length).

Specified by:

getAlignRes in interface Block

Returns:

List a double List of aligned residues for each structure.

See Also:

#setAlignRes()

setAlignRes

public void setAlignRes(List<List<Integer>> alignRes)

Description copied from interface: Block

Set the double List containing the aligned residues for each structure.

Specified by:

setAlignRes in interface Block

Parameters:

alignRes - a double List of Integers with the aligned residues.

See Also:

Block.getAlignRes()

length

public int length()

Description copied from interface: Block

Returns the total number of aligned positions (columns) in the Block.

Specified by:

length in interface Block

Returns:

int number of aligned residues.

See Also:

Block.size()

size

public int size()

Description copied from interface: Block

Returns the number of aligned structures (rows) in the Block.

Specified by:

size in interface Block

Returns:

int number of aligned structures.

See Also:

Block.length(), Block.getCoreLength()

getCoreLength

public int getCoreLength()

Description copied from interface: Block

Returns the number of aligned positions (columns) without gaps in the Block.

Specified by:

getCoreLength in interface Block

Returns:

int number of aligned residues.

See Also:

#updateCoreLength(), Block.length(), Block.size()

updateCoreLength

protected void updateCoreLength()

getStartIndex

public int getStartIndex(int str)

Description copied from interface: Block

Calculates and returns the first position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.

Specified by:

getStartIndex in interface Block

Parameters:

str - structure index

Returns:

the first non null aligned position of the structure

getStartResidue

public int getStartResidue(int str)

Description copied from interface: Block

Calculates and returns the first residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.

Specified by:

getStartResidue in interface Block

Parameters:

str - structure index

Returns:

the first non null aligned residue of the structure

getFinalIndex

public int getFinalIndex(int str)

Description copied from interface: Block

Calculates and returns the last position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.

Specified by:

getFinalIndex in interface Block

Parameters:

str - structure index

Returns:

the last non null aligned position of the structure

getFinalResidue

public int getFinalResidue(int str)

Description copied from interface: Block

Calculates and returns the last residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.

Specified by:

getFinalResidue in interface Block

Parameters:

str - structure index

Returns:

the last non null aligned residue of the structure

getAlignResCounts

public List<Integer> getAlignResCounts()

Description copied from interface: Block

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

Specified by:

getAlignResCounts in interface Block

Returns:

List of residue counts for each structure