|
NeoBio API | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--neobio.alignment.AlignmentBlock | +--neobio.alignment.LocalAlignmentBlock
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.
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 neobio.alignment.AlignmentBlock |
ancestor, direction, dist_column, factor1, factor2, output_border, source_path |
Constructor Summary | |
(package private) |
LocalAlignmentBlock(Factor factor1,
Factor factor2)
Creates a new root block. |
(package private) |
LocalAlignmentBlock(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 |
public int[] E_path_score
public LocalAlignmentBlock[] E_path_ancestor
public int[] E_path_ancestor_index
public int[] S_path_score
public byte[] path_type
public byte S_direction
public int C
Constructor Detail |
LocalAlignmentBlock(Factor factor1, Factor factor2)
factor1
- factor of the first sequence being alignedfactor2
- factor of the second sequence being alignedLocalAlignmentBlock(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
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |