jebl.evolution.align
Class OverlapAlign
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.OverlapAlign
public class OverlapAlign
- extends Align
Method Summary |
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2)
Performs the alignment. |
float |
getScore()
|
Traceback |
next(Traceback tb)
Get the next state in the traceback |
void |
prepareAlignment(java.lang.String sq1,
java.lang.String sq2)
Initialises the matrices for the alignment. |
void |
printf(Output out)
Print matrix used to calculate this alignment. |
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
OverlapAlign
public OverlapAlign(Scores sub,
float d)
doAlignment
public void doAlignment(java.lang.String sq1,
java.lang.String sq2)
- Performs the alignment. Abstract.
- Parameters:
sq1
- sq2
-
prepareAlignment
public void prepareAlignment(java.lang.String sq1,
java.lang.String sq2)
- Description copied from class:
Align
- Initialises the matrices for the alignment.
- Specified by:
prepareAlignment
in class Align
next
public Traceback next(Traceback tb)
- Get the next state in the traceback
- Overrides:
next
in class Align
- Parameters:
tb
- current Traceback
- Returns:
- next Traceback
getScore
public float getScore()
- Specified by:
getScore
in class Align
- Returns:
- the score of the best alignment
printf
public void printf(Output out)
- Print matrix used to calculate this alignment.
- Specified by:
printf
in class Align
- Parameters:
out
- Output to print to.
http://code.google.com/p/jebl2/