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

      All Methods Instance Methods Abstract Methods 
      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.

    • Method Detail

      • 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()

      • 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:
        setBlockSet(BlockSet)

      • 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:
        getAlignRes()

      • length

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

      • size

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

      • getCoreLength

        int getCoreLength()
        Returns the number of aligned positions (columns) without gaps in the Block.
        Returns:
        int number of aligned residues.
        See Also:
        #updateCoreLength(), length(), size()

      • 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.