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java.lang.Object | +--neobio.alignment.AlignmentBlock
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.
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. |
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| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
public final Factor factor1
public final Factor factor2
public final int[] dist_column
public final AlignmentBlock[] ancestor
public final int[] output_border
public final int[] source_path
public final byte[] direction
CrochemoreLandauZivUkelson.STOP_DIRECTION,
CrochemoreLandauZivUkelson.LEFT_DIRECTION,
CrochemoreLandauZivUkelson.DIAGONAL_DIRECTION,
CrochemoreLandauZivUkelson.TOP_DIRECTION| Constructor Detail |
public AlignmentBlock(Factor factor1,
Factor factor2)
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.
factor1 - factor of the first sequence being alignedfactor2 - factor of the second sequence being aligned
public AlignmentBlock(Factor factor1,
Factor factor2,
int size)
factor1 - factor of the first sequence being alignedfactor2 - factor of the second sequence being alignedsize - size of the arrays to be created
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