org.jscience.biology.alignment
Class LocalAlignmentBlock

java.lang.Object
  extended by org.jscience.biology.alignment.AlignmentBlock
      extended by org.jscience.biology.alignment.LocalAlignmentBlock

public class LocalAlignmentBlock
extends AlignmentBlock

This class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block. All fields are public (but final) in order to simplify the access to the data.

For more information on how this class is used, please refer to the specification of the CrochemoreLandauZivUkelsonLocalAlignment class.

See Also:
CrochemoreLandauZivUkelsonLocalAlignment

Field Summary
 int C
          The value of the highest scoring path contained in this block, called C-path.
 LocalAlignmentBlock[] E_path_ancestor
          An array of pointers to blocks that are source of E-paths.
 int[] E_path_ancestor_index
          Indexes of of the entry in the ancestor block that is the source of the E-path.
 int[] E_path_score
          The value of the highest scoring path which starts at the input border of this block and ends inside it, called E-path.
 byte[] path_type
          The type of the highest scoring path ending at a given position of the output border of a block.
 byte S_direction
          The direction to the source of the S-path of the new vertex of this block.
 int[] S_path_score
          The value of the highest scoring path which starts inside the block and ends at its output border.
 
Fields inherited from class org.jscience.biology.alignment.AlignmentBlock
ancestor, direction, dist_column, factor1, factor2, output_border, source_path
 
Method Summary
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

E_path_score

public int[] E_path_score
The value of the highest scoring path which starts at the input border of this block and ends inside it, called E-path.


E_path_ancestor

public LocalAlignmentBlock[] E_path_ancestor
An array of pointers to blocks that are source of E-paths.


E_path_ancestor_index

public int[] E_path_ancestor_index
Indexes of of the entry in the ancestor block that is the source of the E-path.


S_path_score

public int[] S_path_score
The value of the highest scoring path which starts inside the block and ends at its output border.


path_type

public byte[] path_type
The type of the highest scoring path ending at a given position of the output border of a block.


S_direction

public byte S_direction
The direction to the source of the S-path of the new vertex of this block.


C

public int C
The value of the highest scoring path contained in this block, called C-path.