PairwiseAligner
public class NeedlemanWunschLinearSpaceAffine extends Align implements PairwiseAligner
PairwiseAligner.Result
Constructor | Description |
---|---|
NeedlemanWunschLinearSpaceAffine(Scores sub,
float openGapPenalty,
float extendGapPenalty) |
|
NeedlemanWunschLinearSpaceAffine(Scores sub,
float d,
float e,
boolean freeGapsAtEnds) |
|
NeedlemanWunschLinearSpaceAffine(Scores sub,
float d,
float e,
boolean freeGapsAtEnds,
boolean applyGapExtendCostToFirstGapResidue) |
Modifier and Type | Method | Description |
---|---|---|
void |
allocateMatrices(int n,
int m) |
|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2) |
Performs the alignment.
|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress) |
|
void |
doAlignment(java.lang.String sq1,
java.lang.String sq2,
ProgressListener progress,
boolean scoreOnly) |
|
jebl.evolution.align.AlignmentResult[] |
doAlignment(jebl.evolution.align.Profile profile1,
jebl.evolution.align.Profile profile2,
ProgressListener progress,
boolean scoreOnly) |
|
PairwiseAligner.Result |
doAlignment(Sequence seq1,
Sequence seq2,
ProgressListener progress) |
|
java.lang.String[] |
getMatch() |
|
static long |
getMemoryRequiredForAlignment(int maximumSequenceLength) |
|
float |
getScore() |
|
double |
getScore(Sequence seq1,
Sequence seq2) |
|
static void |
main(java.lang.String[] arguments) |
|
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 |
setDebug(boolean display) |
|
void |
setGapExtend(float e) |
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
public NeedlemanWunschLinearSpaceAffine(Scores sub, float openGapPenalty, float extendGapPenalty)
public NeedlemanWunschLinearSpaceAffine(Scores sub, float d, float e, boolean freeGapsAtEnds)
public NeedlemanWunschLinearSpaceAffine(Scores sub, float d, float e, boolean freeGapsAtEnds, boolean applyGapExtendCostToFirstGapResidue)
applyGapExtendCostToFirstGapResidue
- Generally there is an ambiguity in bioinformatics whether "gap opening" already includes the first gap character - in other words, whether a gap of length N has
(a) a cost of gapOpen + N * gapExtend or (b) gapOpen + (N-1) * gapExtend..
applyGapExtendCostToFirstGapResidue
should be true if using interpretation (a).sub
- d
- e
- freeGapsAtEnds
- public void allocateMatrices(int n, int m)
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress, boolean scoreOnly)
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
public static long getMemoryRequiredForAlignment(int maximumSequenceLength)
public jebl.evolution.align.AlignmentResult[] doAlignment(jebl.evolution.align.Profile profile1, jebl.evolution.align.Profile profile2, ProgressListener progress, boolean scoreOnly)
public java.lang.String[] getMatch()
public float getScore()
public static void main(java.lang.String[] arguments)
public void setDebug(boolean display)
public PairwiseAligner.Result doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)
doAlignment
in interface PairwiseAligner
public double getScore(Sequence seq1, Sequence seq2)
getScore
in interface PairwiseAligner
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/