public class NonOverlapMultipleLocalAffine extends Align
Constructor | Description |
---|---|
NonOverlapMultipleLocalAffine(Scores sub,
float d,
float e,
int T) |
Modifier and Type | Method | Description |
---|---|---|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2) |
Performs the alignment.
|
java.lang.String[][] |
getAlignments() |
The indices for these correspond to those for the getScoreMatrix() matrix.
|
java.lang.String[] |
getMatch() |
|
java.lang.String |
getMatchScores(int width) |
|
float |
getScore() |
|
float[] |
getScores() |
The indices for these correspond to those for the getAlignments() matrix.
|
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 |
recurseAlignment(java.lang.String sq1,
int leftIndex) |
|
void |
setGapExtend(float e) |
|
void |
setThreshold(int T) |
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
public NonOverlapMultipleLocalAffine(Scores sub, float d, float e, int T)
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
sq1
- sq2
- public void recurseAlignment(java.lang.String sq1, int leftIndex)
public java.lang.String[] getMatch()
public java.lang.String getMatchScores(int width)
width
- length to trim lines to. -1 = infinite width.public float getScore()
public float[] getScores()
public java.lang.String[][] getAlignments()
public void printf(Output out)
out
- Output to print to.public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Align
public void setGapExtend(float e)
public Traceback next(Traceback tb)
tb
- current Tracebackpublic void setThreshold(int T)
http://code.google.com/p/jebl2/