java.lang.Object

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

org.biojava.nbio.structure.align.multiple.MultipleAlignmentImpl

All Implemented Interfaces:: Serializable, Cloneable, MultipleAlignment, ScoresCache

public class MultipleAlignmentImpl extends AbstractScoresCache implements Serializable, MultipleAlignment, Cloneable

A general implementation of a MultipleAlignment.

Since:

4.1.0

Author:

Aleix Lafita

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor

Description

MultipleAlignmentImpl()

Default Constructor.

MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble)

Constructor linking to an existing ensemble.

MultipleAlignmentImpl(MultipleAlignmentImpl ma)

Copy constructor.
Method Summary

Modifier and Type

Method

Description

void

clear()

Clear the cached scores.

MultipleAlignmentImpl

clone()

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

List<Integer>

getAlignResCounts()

Returns the number of non null positions (residues) of each structure in the alignment.

List<Atom[]>

getAtomArrays()

Returns the array of Atoms for each structure from its parent Ensemble.

Block

getBlock(int index)

Returns the Block with the specified index of the MultipleAlignment.

List<Block>

getBlocks()

Convenience method to get a List of all Blocks from all BlockSets.

BlockSet

getBlockSet(int index)

Returns the BlockSet with the specified index of the MultipleAlignment.

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.

List<Double>

getCoverages()

Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.

MultipleAlignmentEnsemble

getEnsemble()

Returns the parent Ensemble of the MultipleAlignment.

StructureIdentifier

getStructureIdentifier(int index)

Returns the StructureIdentifier associated with the structure index from its parent Ensemble.

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.

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.

protected void

updateCache()

Updates all cached properties

protected void

updateCoreLength()

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

protected void

updateLength()

Force recalculation of the length (aligned columns) based on the BlockSet 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 Details
- MultipleAlignmentImpl
  
  public MultipleAlignmentImpl()
  
  Default Constructor. Empty alignment. No structures assigned.
- 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. Recursively copies member BlockSets.
  
  Parameters:
  
  ma - MultipleAlignmentImpl to copy.
Method Details
- 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 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 copy of all constituent BlockSets.
  
  Specified by:
  
  clone in interface MultipleAlignment
  
  Overrides:
  
  clone in class Object
  
  Returns:
  
  MultipleAlignment identical copy of this object.
- toString
  
  public String toString()
  
  Description copied from interface: MultipleAlignment
  
  Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores. Can be used as a header for the differnt display options.
  
  Specified by:
  
  toString in interface MultipleAlignment
  
  Overrides:
  
  toString in class Object
  
  Returns:
  
  String header summary of the MultipleAlignment
- getBlockSets
  
  public 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:
  
  MultipleAlignment.getBlocks()
  
  MultipleAlignment.setBlockSets(List)
- getBlocks
  
  public List<Block> getBlocks()
  
  Description copied from interface: MultipleAlignment
  
  Convenience method to get a List of all Blocks from all BlockSets. Modifications of this List will not alter the MultipleAlignment, but modifications to the Blocks will.
  Specified by:
  
  getBlocks in interface MultipleAlignment
  
  Returns:
  
  List of Blocks
  
  See Also:
  
  MultipleAlignment.getBlockSets()
- setBlockSets
  
  public void setBlockSets(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()
- getBlockSet
  
  public BlockSet getBlockSet(int index)
  
  Description copied from interface: MultipleAlignment
  
  Returns the BlockSet with the specified index of the MultipleAlignment. Throws an Exception if the index is out of bounds, like accessing a normal List.
  Specified by:
  
  getBlockSet in interface MultipleAlignment
  
  Parameters:
  
  index - of the BlockSet
  
  Returns:
  
  BlockSets at the specified index
  
  See Also:
  
  MultipleAlignment.getBlocks()
  
  MultipleAlignment.getBlockSets()
- getBlock
  
  public Block getBlock(int index)
  
  Description copied from interface: MultipleAlignment
  
  Returns the Block with the specified index of the MultipleAlignment. Throws an Exception if the index is out of bounds, like accessing a normal List.
  Specified by:
  
  getBlock in interface MultipleAlignment
  
  Parameters:
  
  index - of the BlockSet
  
  Returns:
  
  Block at the specified index
  
  See Also:
  
  MultipleAlignment.getBlocks()
  
  MultipleAlignment.getBlockSets()
- getAtomArrays
  
  public List<Atom[]> getAtomArrays()
  
  Description copied from interface: MultipleAlignment
  
  Returns the array of Atoms for each structure from its parent Ensemble. Throws an Exception if the parent ensemble is null or the Atom variables are not previously set.
  Specified by:
  
  getAtomArrays in interface MultipleAlignment
  
  Returns:
  
  List of Atom arrays
  
  See Also:
  
  MultipleAlignment.getEnsemble()
- getStructureIdentifier
  
  public StructureIdentifier getStructureIdentifier(int index)
  
  Description copied from interface: MultipleAlignment
  
  Returns the StructureIdentifier associated with the structure index from its parent Ensemble. Throws an Exception if the parent ensemble is null or the StructureIdentifiers are not previously set.
  Specified by:
  
  getStructureIdentifier in interface MultipleAlignment
  
  Returns:
  
  StructureIdentifier
  
  See Also:
  
  MultipleAlignment.getEnsemble()
- 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()
- 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:
  
  MultipleAlignment.getCoreLength()
  
  MultipleAlignment.size()
- 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:
  
  MultipleAlignment.length()
  
  MultipleAlignment.size()
- updateLength
  
  protected void updateLength()
  
  Force recalculation of the length (aligned columns) based on the BlockSet lengths.
- updateCoreLength
  
  protected void updateCoreLength()
  
  Force recalculation of the core length (ungapped columns) based on the BlockSet 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:
  
  MultipleAlignment.setEnsemble(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()
- getAlignResCounts
  
  public List<Integer> getAlignResCounts()
  
  Description copied from interface: MultipleAlignment
  
  Returns the number of non null positions (residues) of each structure in the alignment. The values can be used to compute the coverages.
  
  Specified by:
  
  getAlignResCounts in interface MultipleAlignment
  
  Returns:
  
  List of residue counts for each structure
- getCoverages
  
  public List<Double> getCoverages()
  
  Description copied from interface: MultipleAlignment
  
  Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.
  
  Specified by:
  
  getCoverages in interface MultipleAlignment
  
  Returns:
  
  List coverage for each structure

Class MultipleAlignmentImpl

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

MultipleAlignmentImpl

MultipleAlignmentImpl

MultipleAlignmentImpl

Method Details

clear

clone

toString

getBlockSets

getBlocks

setBlockSets

getBlockSet

getBlock

getAtomArrays

getStructureIdentifier

size

length

getCoreLength

updateLength

updateCoreLength

updateCache

getEnsemble

setEnsemble

getAlignResCounts

getCoverages