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

Class MultipleAlignmentEnsembleImpl

java.lang.Object

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

org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl

All Implemented Interfaces:

Serializable, Cloneable, MultipleAlignmentEnsemble, ScoresCache

public class MultipleAlignmentEnsembleImpl
extends AbstractScoresCache
implements MultipleAlignmentEnsemble, Serializable, Cloneable

A general implementation of a MultipleAlignmentEnsemble.

Since:

4.1.0

Author:

Aleix Lafita

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentEnsembleImpl()	Default Constructor.
MultipleAlignmentEnsembleImpl(List<StructureIdentifier> structureIdentifiers)	Constructor using structure identifiers.
MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2, boolean flexible)	Constructor from an AFPChain instance.
MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e)	Copy constructor.

Method Summary

Modifier and Type	Method	Description
void	addMultipleAlignment(MultipleAlignment alignment)	Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.
void	clear()	Clear the cached scores.
MultipleAlignmentEnsembleImpl	clone()	Creates and returns an identical copy of this ensemble, including a deep clone of all constituent alignments.
String	getAlgorithmName()	Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
List<Atom[]>	getAtomArrays()	Get an array of representative atoms for each structure (CA atoms for proteins).
Long	getCalculationTime()	Returns the running time of the structure alignment calculation, in milliseconds.
List<Matrix>	getDistanceMatrix()	Returns the List containing the interatomic distance Matrix of each structure.
Long	getIoTime()	Returns the io time for this object, in milliseconds.
MultipleAlignment	getMultipleAlignment(int index)	Returns the MultipleAlignments at the specified index in the ensemble.
List<MultipleAlignment>	getMultipleAlignments()	Returns the List of MultipleAlignments in the ensemble.
List<StructureIdentifier>	getStructureIdentifiers()	Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
String	getVersion()	Returns the version of the algorithm used to generate the MultipleAlignment objects.
void	setAlgorithmName(String algorithmName)	Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.
void	setAtomArrays(List<Atom[]> atomArrays)	Sets the List of Atom arrays.
void	setCalculationTime(Long millis)	Set the running time spent to calculate this alignment.
void	setIoTime(Long millis)	Set the IO time to load this object
void	setMultipleAlignments(List<MultipleAlignment> alignments)	Set the List of MultipleAlignments in the ensemble.
void	setStructureIdentifiers(List<StructureIdentifier> structureNames)	Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).
void	setVersion(String version)	Sets the version of the algorithm used to generate the MultipleAlignment objects.
int	size()	Returns the number of aligned structures in the MultipleAlignments.
void	updateAtomArrays()	Force the atom arrays to regenerate based on getStructureIdentifiers().
void	updateDistanceMatrix()	Force recalculation of the distance matrices.

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, toString, wait, wait, wait

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

getScore, getScores, putScore

Constructor Details

MultipleAlignmentEnsembleImpl

public MultipleAlignmentEnsembleImpl()

Default Constructor. Empty ensemble, no structures assigned.

MultipleAlignmentEnsembleImpl

public MultipleAlignmentEnsembleImpl(List<StructureIdentifier> structureIdentifiers)

Constructor using structure identifiers.

Parameters:

structureIdentifiers - List of Structure names, that can be parsed by AtomCache.

MultipleAlignmentEnsembleImpl

public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e)

Copy constructor. This copies recursively all member variables, including MultipleAlignments, Atom arrays and cached variables.

Parameters:

e - MultipleAlignmentEnsemble to copy.

MultipleAlignmentEnsembleImpl

public MultipleAlignmentEnsembleImpl(AFPChain afp,
 Atom[] ca1,
 Atom[] ca2,
 boolean flexible)

Constructor from an AFPChain instance. Creates an equivalent pairwise alignment, but in the MultipleAlignment format.

Parameters:

afp - pairwise alignment

ca1 - Atoms of the first strcuture

ca2 - Atoms of the second structure

flexible - true if the alignment is flexible (use BlockSets)

Method Details

clone

public MultipleAlignmentEnsembleImpl clone()

Description copied from interface: MultipleAlignmentEnsemble

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

Specified by:

clone in interface MultipleAlignmentEnsemble

Overrides:

clone in class Object

Returns:

MultipleAlignmentEnsemble identical copy of this object.

getAlgorithmName

public String getAlgorithmName()

Description copied from interface: MultipleAlignmentEnsemble

Returns the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.

Specified by:

getAlgorithmName in interface MultipleAlignmentEnsemble

Returns:

String name of the algorithm.

See Also:

• MultipleAlignmentEnsemble.setAlgorithmName(String)

setAlgorithmName

public void setAlgorithmName(String algorithmName)

Description copied from interface: MultipleAlignmentEnsemble

Set the name of the multiple structure alignment algorithm that created the MultipleAlignment objects.

Specified by:

setAlgorithmName in interface MultipleAlignmentEnsemble

Parameters:

algorithmName - name of the algorithm.

See Also:

• MultipleAlignmentEnsemble.getAlgorithmName()

getVersion

public String getVersion()

Description copied from interface: MultipleAlignmentEnsemble

Returns the version of the algorithm used to generate the MultipleAlignment objects.

Specified by:

getVersion in interface MultipleAlignmentEnsemble

Returns:

String version of the algorithm.

See Also:

• MultipleAlignmentEnsemble.setVersion(String)

setVersion

public void setVersion(String version)

Description copied from interface: MultipleAlignmentEnsemble

Sets the version of the algorithm used to generate the MultipleAlignment objects.

Specified by:

setVersion in interface MultipleAlignmentEnsemble

Parameters:

version - the version of the algorithm.

See Also:

• MultipleAlignmentEnsemble.getVersion()

getIoTime

public Long getIoTime()

Description copied from interface: MultipleAlignmentEnsemble

Returns the io time for this object, in milliseconds.

Specified by:

getIoTime in interface MultipleAlignmentEnsemble

Returns:

long creation time, or null if unset

setIoTime

public void setIoTime(Long millis)

Description copied from interface: MultipleAlignmentEnsemble

Set the IO time to load this object

Specified by:

setIoTime in interface MultipleAlignmentEnsemble

Parameters:

millis -

getCalculationTime

public Long getCalculationTime()

Description copied from interface: MultipleAlignmentEnsemble

Returns the running time of the structure alignment calculation, in milliseconds.

Specified by:

getCalculationTime in interface MultipleAlignmentEnsemble

Returns:

long running time of the calculation, or null if unset

See Also:

• MultipleAlignmentEnsemble.getIoTime()

setCalculationTime

public void setCalculationTime(Long millis)

Description copied from interface: MultipleAlignmentEnsemble

Set the running time spent to calculate this alignment.

Specified by:

setCalculationTime in interface MultipleAlignmentEnsemble

Parameters:

millis -

getStructureIdentifiers

public List<StructureIdentifier> getStructureIdentifiers()

Description copied from interface: MultipleAlignmentEnsemble

Returns a List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).

The names are structure identifiers of the structures. They are in the same order as in the alignment Blocks (same index number for same structure).

Specified by:

getStructureIdentifiers in interface MultipleAlignmentEnsemble

Returns:

List of String names of the structures

See Also:

• MultipleAlignmentEnsemble.setStructureIdentifiers(List)
• MultipleAlignmentEnsemble.getAtomArrays()

setStructureIdentifiers

public void setStructureIdentifiers(List<StructureIdentifier> structureNames)

Description copied from interface: MultipleAlignmentEnsemble

Set the List containing the names of the structures aligned (i.e.: PDB code, SCOP domain, etc.).

The names are structure identifiers of the structures.

Specified by:

setStructureIdentifiers in interface MultipleAlignmentEnsemble

Parameters:

structureNames - names of the structures, structure identifiers

See Also:

• MultipleAlignmentEnsemble.getStructureIdentifiers()
• MultipleAlignmentEnsemble.setAtomArrays(List)

getAtomArrays

public List<Atom[]> getAtomArrays()

Description copied from interface: MultipleAlignmentEnsemble

Get an array of representative atoms for each structure (CA atoms for proteins).

Atoms should be unrotated. Thus, to obtain a superimposed set of structures, each atom array should be cloned and then rotated according to the transformation matrix.

If atoms have not previously been set using MultipleAlignmentEnsemble.setAtomArrays(List), attempts to load representative atoms based on MultipleAlignmentEnsemble.getStructureIdentifiers(). If it fails to load the Atoms it gives a NullPointerException before returning null.

Specified by:

getAtomArrays in interface MultipleAlignmentEnsemble

Returns:

List of Atom[].

See Also:

• MultipleAlignmentEnsemble.setAtomArrays(List)

setAtomArrays

public void setAtomArrays(List<Atom[]> atomArrays)

Description copied from interface: MultipleAlignmentEnsemble

Sets the List of Atom arrays. Every structure has an Atom array associated. Note that this should be called in conjunction with MultipleAlignmentEnsemble.setStructureIdentifiers(List).

Setting the atom arrays to null will cause them to be automatically regenerated based on MultipleAlignmentEnsemble.getStructureIdentifiers() during the next call to MultipleAlignmentEnsemble.getAtomArrays().

Specified by:

setAtomArrays in interface MultipleAlignmentEnsemble

Parameters:

atomArrays - the List of representative (C-alpha) atom arrays

See Also:

• MultipleAlignmentEnsemble.getAtomArrays()
• MultipleAlignmentEnsemble.setStructureIdentifiers(List)

updateAtomArrays

public void updateAtomArrays()
                      throws IOException,
StructureException

Force the atom arrays to regenerate based on getStructureIdentifiers().

Throws:

IOException

StructureException

getDistanceMatrix

public List<Matrix> getDistanceMatrix()

Description copied from interface: MultipleAlignmentEnsemble

Returns the List containing the interatomic distance Matrix of each structure.

Specified by:

getDistanceMatrix in interface MultipleAlignmentEnsemble

Returns:

List of Matrix interatomic distance matrices.

updateDistanceMatrix

public void updateDistanceMatrix()

Force recalculation of the distance matrices.

getMultipleAlignments

public List<MultipleAlignment> getMultipleAlignments()

Description copied from interface: MultipleAlignmentEnsemble

Returns the List of MultipleAlignments in the ensemble.

Specified by:

getMultipleAlignments in interface MultipleAlignmentEnsemble

Returns:

List of MultipleAlignment in the ensemble.

getMultipleAlignment

public MultipleAlignment getMultipleAlignment(int index)

Description copied from interface: MultipleAlignmentEnsemble

Returns the MultipleAlignments at the specified index in the ensemble. Throws an exception equivalently to accessing an index of a List

Specified by:

getMultipleAlignment in interface MultipleAlignmentEnsemble

Returns:

MultipleAlignment at the index in the ensemble.

setMultipleAlignments

public void setMultipleAlignments(List<MultipleAlignment> alignments)

Description copied from interface: MultipleAlignmentEnsemble

Set the List of MultipleAlignments in the ensemble.

Specified by:

setMultipleAlignments in interface MultipleAlignmentEnsemble

Parameters:

alignments - List of MultipleAlignments that are part of the ensemble.

See Also:

• MultipleAlignmentEnsemble.addMultipleAlignment(MultipleAlignment)

addMultipleAlignment

public void addMultipleAlignment(MultipleAlignment alignment)

Description copied from interface: MultipleAlignmentEnsemble

Add a new MultipleAlignment to the end of the ensemble and set its parent ensemble to this.

Specified by:

addMultipleAlignment in interface MultipleAlignmentEnsemble

Parameters:

alignment -

size

public int size()

Description copied from interface: MultipleAlignmentEnsemble

Returns the number of aligned structures in the MultipleAlignments.

Specified by:

size in interface MultipleAlignmentEnsemble

Returns:

int number of aligned structures.

See Also:

• MultipleAlignmentEnsemble.getStructureIdentifiers()
• MultipleAlignmentEnsemble.getAtomArrays()

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 MultipleAlignmentEnsemble

Overrides:

clear in class AbstractScoresCache