neobio.alignment
Class AlignmentBlock

java.lang.Object
  |
  +--neobio.alignment.AlignmentBlock

Direct Known Subclasses:

LocalAlignmentBlock

public class AlignmentBlock

extends java.lang.Object

This class is used by the CrochemoreLandauZivUkelson 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 CrochemoreLandauZivUkelson class and it subclasses.

Author:

Sergio A. de Carvalho Jr.

See Also:

CrochemoreLandauZivUkelson

Field Summary

AlignmentBlock[]	ancestor An array of pointers to prefix blocks of this block.
byte[]	direction An array of directions that must be followed to reach the source of the highest scoring path for each entry in the output border.
int[]	dist_column The DIST column of this block.
Factor	factor1 A pointer to the factor of the first sequence being aligned.
Factor	factor2 A pointer to the factor of the second sequence being aligned.
int[]	output_border This block's output border.
int[]	source_path An array of indexes to the source of the highest scoring path for each entry in the output border.

Constructor Summary

AlignmentBlock(Factor factor1, Factor factor2)
Creates a new root block.

AlignmentBlock(Factor factor1, Factor factor2, int size)
Creates a new alignment block, with all arrays created with the specified size.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

factor1

public final Factor factor1

A pointer to the factor of the first sequence being aligned.

factor2

public final Factor factor2

A pointer to the factor of the second sequence being aligned.

dist_column

public final int[] dist_column

The DIST column of this block.

ancestor

public final AlignmentBlock[] ancestor

An array of pointers to prefix blocks of this block.

output_border

public final int[] output_border

This block's output border.

source_path

public final int[] source_path

An array of indexes to the source of the highest scoring path for each entry in the output border.

direction

public final byte[] direction

An array of directions that must be followed to reach the source of the highest scoring path for each entry in the output border.

See Also:

CrochemoreLandauZivUkelson.STOP_DIRECTION, CrochemoreLandauZivUkelson.LEFT_DIRECTION, CrochemoreLandauZivUkelson.DIAGONAL_DIRECTION, CrochemoreLandauZivUkelson.TOP_DIRECTION

Constructor Detail

AlignmentBlock

public AlignmentBlock(Factor factor1,
                      Factor factor2)

Creates a new root block. A root block does not have source_path and ancestor arrays. Moreover, its dist_column and output_border arrays are set to zero, and the direction array is set to contain an STOP_DIRECTION.

Parameters:

factor1 - factor of the first sequence being aligned

factor2 - factor of the second sequence being aligned

AlignmentBlock

public AlignmentBlock(Factor factor1,
                      Factor factor2,
                      int size)

Creates a new alignment block, with all arrays created with the specified size.

Parameters:

factor1 - factor of the first sequence being aligned

factor2 - factor of the second sequence being aligned

size - size of the arrays to be created