public class SmithWatermanLinearSpaceAffine extends Align
Constructor | Description |
---|---|
SmithWatermanLinearSpaceAffine(Scores sub,
float d,
float e) |
Modifier and Type | Method | Description |
---|---|---|
void |
doAlignment(java.lang.String sequence1,
java.lang.String sequence2) |
Performs the alignment.
|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress) |
|
java.lang.String[] |
getMatch() |
|
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.
|
void |
setGapExtend(float e) |
|
void |
traceback(TracebackPlotter plotter) |
doMatch, doMatch, formatScore, setGapOpen, setScores
public SmithWatermanLinearSpaceAffine(Scores sub, float d, float e)
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
sq1
- sq2
- public void doAlignment(java.lang.String sequence1, java.lang.String sequence2)
public float getScore()
public java.lang.String[] getMatch()
public void traceback(TracebackPlotter plotter)
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Align
public void printf(Output out)
out
- Output to print to.public void setGapExtend(float e)
http://code.google.com/p/jebl2/