org.biojava.nbio.structure.align.multiple

Interface BlockSet

All Superinterfaces:

ScoresCache

All Known Implementing Classes:

BlockSetImpl

public interface BlockSet
extends ScoresCache

A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment as a collection of Blocks.

It allows non-sequential alignments and circular permutations, thanks to the multiple Block format.

Every BlockSet has a unique transformation 4D matrix, which describes the 3D superimposition of the structures in this particular region of the alignment.

A collection of BlockSets, in a MultipleAlignment, allows the description of multiple alignments with various flexible parts. Every BlockSet object is part of a MultipleAlignment instance, its parent.

Author:

Aleix Lafita, Spencer Bliven

Method Summary

Methods

Modifier and Type	Method and Description
void	clear() Clear scores and other properties which depend on the specific alignment.
BlockSet	clone() Creates and returns an identical copy of this blockset, including a deep clone of all constituent Blocks.
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.

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

getScore, getScores, putScore

Method Detail

clone

BlockSet clone()

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

Returns:

BlockSet identical copy of this object.

getMultipleAlignment

MultipleAlignment getMultipleAlignment()

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

Returns:

MultipleAlignment the parent MultipleAlignment of the BlockSet, or null.

See Also:

setMultipleAlignment(MultipleAlignment)

setMultipleAlignment

void setMultipleAlignment(MultipleAlignment parent)

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.

Parameters:

parent - the parent MultipleAlignment.

See Also:

getMultipleAlignment()

getBlocks

List<Block> getBlocks()

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

Returns:

List of alignment Blocks.

See Also:

setBlocks(List)

setBlocks

void setBlocks(List<Block> blocks)

Set the List of alignment Blocks of the BlockSet.

Also calls Block.setBlockSet(BlockSet) for each argument

Parameters:

blocks - List of alignment Blocks.

See Also:

getBlocks()

getTransformations

List<javax.vecmath.Matrix4d> getTransformations()

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

Returns:

the 3D superimposition information of the alignment

setTransformations

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

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

Parameters:

matrices -

length

int length()

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

Returns:

int the total number of aligned residues.

See Also:

#updateLength(), getCoreLength(), size(), #getBlockNum()

getCoreLength

int getCoreLength()

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

Returns:

int the total number of aligned residues.

See Also:

#updateCoreLength(), length(), size(), #getBlockNum()

size

int size()

Returns the number of aligned structures in the BlockSet.

Returns:

int number of aligned structures

See Also:

length(), #getBlockNum()

clear

void clear()

Clear scores and other properties which depend on the specific alignment.

Recursively clears the memeber Blocks.