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:

java.io.Serializable, java.lang.Cloneable, MultipleAlignment, ScoresCache

public class MultipleAlignmentImpl
extends AbstractScoresCache
implements java.io.Serializable, MultipleAlignment, java.lang.Cloneable

A general implementation of a MultipleAlignment.

Author:

Aleix Lafita

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentImpl() Default Constructor.
MultipleAlignmentImpl(java.util.List<java.lang.String> structureNames) Constructor that allows creating a MultipleAlignment instance without caring about the ensemble.
MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) Constructor linking to an existing ensemble.
MultipleAlignmentImpl(MultipleAlignmentImpl ma) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	clear() Resets all scores
MultipleAlignmentImpl	clone() Creates and returns an identical copy of this alignment, including a deep clone of all constituent blocks sets.
java.util.List<Block>	getBlocks() Convenience method to get a list of all blocks from all blocksets
java.util.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.
java.util.List<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(java.util.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(java.util.List<Matrix4d> matrices) Set a new superposition for the structures.
int	size() Returns the number of aligned structures in the MultipleAlignment.
java.lang.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 block core lengths
protected void	updateLength() Force recalculation of the length (aligned columns) based on the block 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 Detail

MultipleAlignmentImpl

public MultipleAlignmentImpl()

Default Constructor. Empty alignment. No structures assigned.

MultipleAlignmentImpl

public MultipleAlignmentImpl(java.util.List<java.lang.String> structureNames)

Constructor that allows creating a MultipleAlignment instance without caring about the ensemble. Ideal for dealing with one MultipleAlignment alternative only.

Parameters:

structureNames - List of Structure identifiers.

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.

Parameters:

ma - MultipleAlignmentImpl to copy.

Method Detail

clear

public void clear()

Description copied from class: AbstractScoresCache

Resets all scores

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 clone of all constituent blocks sets.

Specified by:

clone in interface MultipleAlignment

Overrides:

clone in class java.lang.Object

Returns:

MultipleAlignment identical copy of this object.

toString

public java.lang.String toString()

Description copied from interface: MultipleAlignment

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

Specified by:

toString in interface MultipleAlignment

Overrides:

toString in class java.lang.Object

Returns:

String summary of the MultipleAlignment

getBlockSets

public java.util.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:

#getBlockSetNum(), MultipleAlignment.setBlockSets(List)

getBlocks

public java.util.List<Block> getBlocks()

Description copied from interface: MultipleAlignment

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

Specified by:

getBlocks in interface MultipleAlignment

Returns:

List of alignment Blocks

setBlockSets

public void setBlockSets(java.util.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()

getTransformations

public java.util.List<Matrix4d> getTransformations()

Description copied from interface: MultipleAlignment

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().

Specified by:

getTransformations in interface MultipleAlignment

Returns:

the 3D superimposition information of the alignment

setTransformations

public void setTransformations(java.util.List<Matrix4d> matrices)

Description copied from interface: MultipleAlignment

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.

Specified by:

setTransformations in interface MultipleAlignment

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(), #getBlockSetNum()

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:

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

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:

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

updateLength

protected void updateLength()

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

updateCoreLength

protected void updateCoreLength()

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

updateCache

protected void updateCache()

Updates all cached properties

Throws:

StructureException

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:

#setParent(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()