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

Interface BlockSet

All Superinterfaces:
ScoresCache
All Known Implementing Classes:
BlockSetImpl
public interface BlockSet extends ScoresCache
A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment. It is described by a collection of Blocks and a transformation matrix for every structure.

It allows the description of non-topological and circularly permutated flexible parts, thus being as general as possible, thanks to the multiple Block format.

Every BlockSet has a unique transformation 4D matrix for every structure, which describes the 3D superimposition of the structures in this particular part of the alignment.

A collection of BlockSets, in a MultipleAlignment, allows the description of alignments with several flexible parts. Every BlockSet object is part of a MultipleAlignment instance, its parent.

Since:
4.1.0
Author:
Aleix Lafita, Spencer Bliven

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    clear()
    Clear scores and other properties which depend on the specific alignment.
    BlockSet
    clone()
    Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
    List<Integer>
    getAlignResCounts()
    Returns the number of non null positions (residues) of each structure in the alignment Block Set.
    List<Block>
    getBlocks()
    Returns the List of alignment Blocks of the BlockSet.
    int
    getCoreLength()
    Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
    MultipleAlignment
    getMultipleAlignment()
    Returns the parent MultipleAlignment of the BlockSet.
    List<javax.vecmath.Matrix4d>
    getTransformations()
    Returns a transformation 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 alignment: the sum of all Block lengths.
    void
    setBlocks(List<Block> blocks)
    Set the List of alignment Blocks of the BlockSet.
    void
    setMultipleAlignment(MultipleAlignment parent)
    Set the back-reference to its parent MultipleAlignment.
    void
    setTransformations(List<javax.vecmath.Matrix4d> transformations)
    Set a new superposition for the structures.
    int
    size()
    Returns the number of aligned structures in the BlockSet.

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

    getScore, getScores, putScore

  • Method Details

    • clone

      BlockSet clone()
      Creates and returns an identical copy of this blockset, including a deep copy of all constituent Blocks.
      Returns:
      BlockSet identical copy of this object.

    • getMultipleAlignment

      MultipleAlignment getMultipleAlignment()
      Returns the parent MultipleAlignment of the BlockSet. Returns null if there is no referenced object.
      Returns:
      MultipleAlignment the parent MultipleAlignment of the BlockSet, or null.
      See Also:

    • setMultipleAlignment

      void setMultipleAlignment(MultipleAlignment parent)
      Set the back-reference to its parent MultipleAlignment.

      Neither removes this BlockSet from its previous alignment, 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 MultipleAlignment.
      See Also:

    • getBlocks

      List<Block> getBlocks()
      Returns the List of alignment Blocks of the BlockSet. It initializes a new List of Blocks if it is null.
      Returns:
      List of alignment Blocks.
      See Also:

    • setBlocks

      void setBlocks(List<Block> blocks)
      Set the List of alignment Blocks of the BlockSet.

      Also calls Block.setBlockSet(BlockSet) for each argument

      Parameters:
      blocks - List of alignment Blocks.
      See Also:

    • getTransformations

      List<javax.vecmath.Matrix4d> getTransformations()
      Returns a transformation matrix for each structure giving the 3D superimposition information of the multiple structure alignment.
      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.
      Parameters:
      matrices -

    • length

      int length()
      Returns the total number of aligned residues (columns) in the alignment: the sum of all Block lengths.
      Returns:
      int the total number of aligned residues.
      See Also:

    • getCoreLength

      int getCoreLength()
      Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all Block core lengths.
      Returns:
      int the total number of aligned residues.
      See Also:

    • getAlignResCounts

      List<Integer> getAlignResCounts()
      Returns the number of non null positions (residues) of each structure in the alignment Block Set. The values can be used to compute the coverages.
      Returns:
      List of residue counts for each structure

    • size

      int size()
      Returns the number of aligned structures in the BlockSet.
      Returns:
      int number of aligned structures
      See Also:

    • clear

      void clear()
      Clear scores and other properties which depend on the specific alignment. This frees memory and ensures consistency of the cached variables.

      Recursively clears the memeber Blocks.