jebl.evolution.align
public class SmithWatermanLinearSpace extends Align
Constructor and Description |
---|
SmithWatermanLinearSpace(Scores sub,
float d) |
Modifier and Type | Method and Description |
---|---|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2)
Performs the alignment.
|
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 |
traceback(TracebackPlotter plotter) |
doMatch, doMatch, formatScore, setGapOpen, setScores
public SmithWatermanLinearSpace(Scores sub, float d)
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
sq1
- sq2
- 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.http://code.google.com/p/jebl2/