public class NeedlemanWunschAffine extends Align
Constructor | Description |
---|---|
NeedlemanWunschAffine(Scores sub,
float d,
float e) |
Modifier and Type | Method | Description |
---|---|---|
void |
allocateMatrices(int n,
int m) |
|
void |
appendMatch(jebl.evolution.align.AlignmentResult result1,
jebl.evolution.align.AlignmentResult result2) |
|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2) |
Performs the alignment.
|
void |
doAlignment(java.lang.String sequence1,
java.lang.String sequence2,
int startType,
int endType) |
|
void |
doAlignment(jebl.evolution.align.Profile sequence1,
jebl.evolution.align.Profile sequence2,
int offset1,
int offset2,
int n,
int m,
int startType,
int endType) |
|
void |
doAlignment(jebl.evolution.align.Profile sequence1,
jebl.evolution.align.Profile sequence2,
int offset1,
int offset2,
int n,
int m,
int startType,
int endType,
boolean freeStartGap,
boolean freeEndGap) |
|
java.lang.String[] |
getMatch() |
|
java.lang.String[] |
getMatch(char[] sq1,
char[] sq2) |
|
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) |
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
public NeedlemanWunschAffine(Scores sub, float d, float e)
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
sq1
- sq2
- public void allocateMatrices(int n, int m)
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Align
public void doAlignment(java.lang.String sequence1, java.lang.String sequence2, int startType, int endType)
public void doAlignment(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType)
public void doAlignment(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType, boolean freeStartGap, boolean freeEndGap)
public void appendMatch(jebl.evolution.align.AlignmentResult result1, jebl.evolution.align.AlignmentResult result2)
public java.lang.String[] getMatch()
public java.lang.String[] getMatch(char[] sq1, char[] sq2)
public float getScore()
public void setGapExtend(float e)
http://code.google.com/p/jebl2/