public class SmithWaterman extends Align
Constructor | Description |
---|---|
SmithWaterman(Scores sub,
float d) |
Modifier and Type | Method | Description |
---|---|---|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2) |
Performs the alignment.
|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress) |
|
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.
|
doMatch, doMatch, formatScore, getMatch, setGapOpen, setScores, traceback
public SmithWaterman(Scores sub, float d)
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
sq1
- sq2
- progress
- public void doAlignment(java.lang.String sq1, java.lang.String sq2)
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Align
prepareAlignment
in class Align
public float getScore()
http://code.google.com/p/jebl2/