public class SmithWaterman extends Align
Constructor and Description |
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SmithWaterman(Scores sub,
float d) |
Modifier and Type | Method and Description |
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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/