public class NeedlemanWunschLinearSpace extends Align
Constructor | Description |
---|---|
NeedlemanWunschLinearSpace(Scores sub,
float d) |
Modifier and Type | Method | Description |
---|---|---|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2) |
Performs the alignment.
|
java.lang.String[] |
getMatch() |
|
float |
getScore() |
|
int |
getV() |
|
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) |
|
void |
traceback(TracebackPlotter plotter,
int startx,
int starty,
java.lang.String sq1,
java.lang.String sq2) |
doMatch, doMatch, formatScore, setGapOpen, setScores
public NeedlemanWunschLinearSpace(Scores sub, float d)
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
sq1
- sq2
- public int getV()
public java.lang.String[] getMatch()
public void traceback(TracebackPlotter plotter)
public void traceback(TracebackPlotter plotter, int startx, int starty, java.lang.String sq1, java.lang.String sq2)
public float getScore()
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/