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
- 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
- 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.
  
  See Also:
  
  #updateDistanceMatrix()
- 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.
  
  See Also:
  
  #setMultipleAlignments()
- 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.
  
  See Also:
  
  #setMultipleAlignments()
- 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
- 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

Class MultipleAlignmentEnsembleImpl

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.structure.align.multiple.AbstractScoresCache

Methods inherited from class java.lang.Object

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

Constructor Details

MultipleAlignmentEnsembleImpl

MultipleAlignmentEnsembleImpl

MultipleAlignmentEnsembleImpl

MultipleAlignmentEnsembleImpl

Method Details

clone

getAlgorithmName

setAlgorithmName

getVersion

setVersion

getIoTime

setIoTime

getCalculationTime

setCalculationTime

getStructureIdentifiers

setStructureIdentifiers

getAtomArrays

setAtomArrays

updateAtomArrays

getDistanceMatrix

updateDistanceMatrix

getMultipleAlignments

getMultipleAlignment

setMultipleAlignments

addMultipleAlignment

size

clear