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

Class BlockImpl

java.lang.Object
org.biojava.nbio.structure.align.multiple.AbstractScoresCache
org.biojava.nbio.structure.align.multiple.BlockImpl
All Implemented Interfaces:
Serializable, Cloneable, Block, ScoresCache
public class BlockImpl extends AbstractScoresCache implements Serializable, Block, Cloneable
General implementation of a Block that supports any type of sequential alignment with gaps.
Since:
4.1.0
Author:
Aleix Lafita
See Also:

  • Constructor Details

    • BlockImpl

      public BlockImpl(BlockSet blockSet)
      Constructor. Links also the parent to this instance, by adding the Block to the parent's list.
      Parameters:
      blockSet - the parent BlockSet of the BlockImpl instance.

    • BlockImpl

      public BlockImpl(BlockImpl b)
      Copy constructor.
      Parameters:
      b - BlockImpl object to be copied.

  • Method Details

    • clone

      public Block clone()
      Description copied from interface: Block
      Creates and returns an identical copy of this block.
      Specified by:
      clone in interface Block
      Overrides:
      clone in class Object
      Returns:
      Block identical copy of this object.

    • 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 Block
      Overrides:
      clear in class AbstractScoresCache

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • setBlockSet

      public void setBlockSet(BlockSet parent)
      Description copied from interface: Block
      Set the back-reference to its parent BlockSet.
      Specified by:
      setBlockSet in interface Block
      Parameters:
      parent - the parent BlockSet.
      See Also:

    • getBlockSet

      public BlockSet getBlockSet()
      Description copied from interface: Block
      Returns the parent BlockSet of the Block. Returns null if there is no referenced object.
      Specified by:
      getBlockSet in interface Block
      Returns:
      BlockSet the parent BlockSet of the Block, or null.
      See Also:

    • getAlignRes

      public List<List<Integer>> getAlignRes()
      Description copied from interface: Block
      Returns the double List containing the aligned residues for each structure.

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

      Specified by:
      getAlignRes in interface Block
      Returns:
      List a double List of aligned residues for each structure.
      See Also:
      • #setAlignRes()

    • setAlignRes

      public void setAlignRes(List<List<Integer>> alignRes)
      Description copied from interface: Block
      Set the double List containing the aligned residues for each structure.
      Specified by:
      setAlignRes in interface Block
      Parameters:
      alignRes - a double List of Integers with the aligned residues.
      See Also:

    • length

      public int length()
      Description copied from interface: Block
      Returns the total number of aligned positions (columns) in the Block.
      Specified by:
      length in interface Block
      Returns:
      int number of aligned residues.
      See Also:

    • size

      public int size()
      Description copied from interface: Block
      Returns the number of aligned structures (rows) in the Block.
      Specified by:
      size in interface Block
      Returns:
      int number of aligned structures.
      See Also:

    • getCoreLength

      public int getCoreLength()
      Description copied from interface: Block
      Returns the number of aligned positions (columns) without gaps in the Block.
      Specified by:
      getCoreLength in interface Block
      Returns:
      int number of aligned residues.
      See Also:

    • updateCoreLength

      protected void updateCoreLength()

    • getStartIndex

      public int getStartIndex(int str)
      Description copied from interface: Block
      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.
      Specified by:
      getStartIndex in interface Block
      Parameters:
      str - structure index
      Returns:
      the first non null aligned position of the structure

    • getStartResidue

      public int getStartResidue(int str)
      Description copied from interface: Block
      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.
      Specified by:
      getStartResidue in interface Block
      Parameters:
      str - structure index
      Returns:
      the first non null aligned residue of the structure

    • getFinalIndex

      public int getFinalIndex(int str)
      Description copied from interface: Block
      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.
      Specified by:
      getFinalIndex in interface Block
      Parameters:
      str - structure index
      Returns:
      the last non null aligned position of the structure

    • getFinalResidue

      public int getFinalResidue(int str)
      Description copied from interface: Block
      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.
      Specified by:
      getFinalResidue in interface Block
      Parameters:
      str - structure index
      Returns:
      the last non null aligned residue of the structure

    • getAlignResCounts

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