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

Interface Block

All Superinterfaces:
ScoresCache
All Known Implementing Classes:
BlockImpl
public interface Block extends ScoresCache
A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a sequential order.

A collection of Blocks, named BlockSet, allows the description of circular permutations (CP) and non-topological alignments.

Every Block object is part of a BlockSet instance, its parent, which has in turn a MultipleAlignment instance as 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.
    Block
    clone()
    Creates and returns an identical copy of this block.
    List<List<Integer>>
    getAlignRes()
    Returns the double List containing the aligned residues for each structure.
    List<Integer>
    getAlignResCounts()
    Returns the number of non null positions (residues) of each structure in the alignment Block.
    BlockSet
    getBlockSet()
    Returns the parent BlockSet of the Block.
    int
    getCoreLength()
    Returns the number of aligned positions (columns) without gaps in the Block.
    int
    getFinalIndex(int str)
    Calculates and returns the last position of the specified structure in the alignment that is not null.
    int
    getFinalResidue(int str)
    Calculates and returns the last residue of the specified structure in the alignment that is not null.
    int
    getStartIndex(int str)
    Calculates and returns the first position of the specified structure in the alignment that is not null.
    int
    getStartResidue(int str)
    Calculates and returns the first residue of the specified structure in the alignment that is not null.
    int
    length()
    Returns the total number of aligned positions (columns) in the Block.
    void
    setAlignRes(List<List<Integer>> alignRes)
    Set the double List containing the aligned residues for each structure.
    void
    setBlockSet(BlockSet parent)
    Set the back-reference to its parent BlockSet.
    int
    size()
    Returns the number of aligned structures (rows) in the Block.

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

    getScore, getScores, putScore

  • Method Details

    • clone

      Block clone()
      Creates and returns an identical copy of this block.
      Returns:
      Block identical copy of this object.

    • setBlockSet

      void setBlockSet(BlockSet parent)
      Set the back-reference to its parent BlockSet.
      Parameters:
      parent - the parent BlockSet.
      See Also:

    • getBlockSet

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

    • getAlignRes

      List<List<Integer>> getAlignRes()
      Returns the double List containing the aligned residues for each structure.

      alignRes.get(structure).get(residue) = alignRes.get(size).get(length).

      Returns:
      List a double List of aligned residues for each structure.
      See Also:
      • #setAlignRes()

    • setAlignRes

      void setAlignRes(List<List<Integer>> alignRes)
      Set the double List containing the aligned residues for each structure.
      Parameters:
      alignRes - a double List of Integers with the aligned residues.
      See Also:

    • length

      int length()
      Returns the total number of aligned positions (columns) in the Block.
      Returns:
      int number of aligned residues.
      See Also:

    • size

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

    • getCoreLength

      int getCoreLength()
      Returns the number of aligned positions (columns) without gaps in the Block.
      Returns:
      int 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. The values can be used to compute the coverages.
      Returns:
      List of residue counts for each structure

    • getStartIndex

      int getStartIndex(int str)
      Calculates and returns the first position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.
      Parameters:
      str - structure index
      Returns:
      the first non null aligned position of the structure

    • getStartResidue

      int getStartResidue(int str)
      Calculates and returns the first residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.
      Parameters:
      str - structure index
      Returns:
      the first non null aligned residue of the structure

    • getFinalIndex

      int getFinalIndex(int str)
      Calculates and returns the last position of the specified structure in the alignment that is not null. This will return the aligment index, not the reisude aligned in that position.
      Parameters:
      str - structure index
      Returns:
      the last non null aligned position of the structure

    • getFinalResidue

      int getFinalResidue(int str)
      Calculates and returns the last residue of the specified structure in the alignment that is not null. This will return the aligned residue, not the alignment index.
      Parameters:
      str - structure index
      Returns:
      the last non null aligned residue of the structure

    • clear

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