org.biojava.nbio.structure.align.multiple

Interface MultipleAlignment

All Superinterfaces:

ScoresCache

All Known Implementing Classes:

MultipleAlignmentImpl

public interface MultipleAlignment
extends ScoresCache

A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type.

Each alignment is described as a collection of:

• BlockSets that define the aligned positions,
• Structure identifiers (i,e. Atom arrays, structure names),
• Information about the 3D superimposition in a 4D transformation matrix,
• Creation properties (algorithm, version, etc).

A collection of MultipleAlignments that share the same structures and creation properties are part of the same MultipleAlignmentEnsemble. Every MultipleAlignment has a MultipleAlignmentEnsemble as its parent, which contains this information

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.
MultipleAlignment	clone() Creates and returns an identical copy of this alignment, including a deep clone of all constituent blocks sets.
List<Block>	getBlocks() Convenience method to get a list of all blocks from all blocksets
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.
MultipleAlignmentEnsemble	getEnsemble() Returns the parent Ensemble of the MultipleAlignment.
List<javax.vecmath.Matrix4d>	getTransformations() Returns a transformation 4D 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 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.
void	setTransformations(List<javax.vecmath.Matrix4d> transformations) Set a new superposition for the structures.
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.

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

getScore, getScores, putScore

Method Detail

clone

MultipleAlignment clone()

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

Returns:

MultipleAlignment identical copy of this object.

getEnsemble

MultipleAlignmentEnsemble getEnsemble()

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

Returns:

MultipleAlignmentEnsemble the parent MultipleAlignment of the BlockSet, or null.

See Also:

#setParent(MultipleAlignmentEnsemble)

setEnsemble

void setEnsemble(MultipleAlignmentEnsemble parent)

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.

Parameters:

parent - the parent MultipleAlignmentEnsemble.

See Also:

getEnsemble()

getBlockSets

List<BlockSet> getBlockSets()

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

Returns:

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

See Also:

#getBlockSetNum(), setBlockSets(List)

setBlockSets

void setBlockSets(List<BlockSet> blockSets)

Sets the List of BlockSet List of the specified alignment.

Parameters:

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

See Also:

getBlockSets()

getBlocks

List<Block> getBlocks()

Convenience method to get a list of all blocks from all blocksets

Returns:

List of alignment Blocks

getTransformations

List<javax.vecmath.Matrix4d> getTransformations()

Returns a transformation 4D matrix for each structure giving the 3D superimposition information of the multiple structure alignment.

Individual BlockSets may override the transformation matrix for particular substructures. Flexible alignments will generally return null from this method, while rigid-body methods would typically store the global matrices here and return null for BlockSet.getTransformations().

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. In particular, the list of scores should be reset by implementations after changing the transformation matrices.

Parameters:

matrices - 4D

Throws:

IllegalArgumentException - when the size of the alignment and the size of transformations do not match.

size

int size()

Returns the number of aligned structures in the MultipleAlignment.

Returns:

int number of aligned structures

See Also:

length(), getCoreLength(), #getBlockSetNum()

length

int length()

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

Returns:

int the total number of aligned residues in the alignment.

See Also:

#updateLength(), getCoreLength(), size(), #getBlockSetNum()

getCoreLength

int getCoreLength()

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

Returns:

int the total number of aligned residues.

See Also:

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

clear

void clear()

Clear scores and other properties which depend on the specific alignment. Recursively clears member BlockSets.

This frees memory and ensures consistency for cached variables.

toString

String toString()

Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.

Overrides:

toString in class Object

Returns:

String summary of the MultipleAlignment