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

      All Methods Instance Methods Abstract Methods 
      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.

    • Method Detail

      • 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.

      • 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:
        getMultipleAlignment()

      • 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(List)

      • 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(), size()

      • 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:
        length(), size()

      • 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:
        length(), getCoreLength()

      • 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.