Package jebl.evolution.align
Class NeedlemanWunschLinearSpaceAffine
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
- All Implemented Interfaces:
PairwiseAligner
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Nested Class Summary
Nested classes/interfaces inherited from interface jebl.evolution.align.PairwiseAligner
PairwiseAligner.Result
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Constructor Summary
ConstructorsConstructorDescriptionNeedlemanWunschLinearSpaceAffine
(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) -
Method Summary
Modifier and TypeMethodDescriptionvoid
allocateMatrices
(int n, int m) void
doAlignment
(String sq1, String sq2) Performs the alignment.void
doAlignment
(String sq1, String sq2, ProgressListener progress) void
doAlignment
(String sq1, 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) doAlignment
(Sequence seq1, Sequence seq2, ProgressListener progress) String[]
getMatch()
static long
getMemoryRequiredForAlignment
(int maximumSequenceLength) float
getScore()
double
static void
Get the next state in the tracebackvoid
prepareAlignment
(String sq1, String sq2) Initialises the matrices for the alignment.void
Print matrix used to calculate this alignment.void
setDebug
(boolean display) void
setGapExtend
(float e) Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
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Constructor Details
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NeedlemanWunschLinearSpaceAffine
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NeedlemanWunschLinearSpaceAffine
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NeedlemanWunschLinearSpaceAffine
public NeedlemanWunschLinearSpaceAffine(Scores sub, float d, float e, boolean freeGapsAtEnds, boolean applyGapExtendCostToFirstGapResidue) - Parameters:
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
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Method Details
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allocateMatrices
public void allocateMatrices(int n, int m) -
doAlignment
Performs the alignment. Abstract. -
doAlignment
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doAlignment
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getMemoryRequiredForAlignment
public static long getMemoryRequiredForAlignment(int maximumSequenceLength) - Returns:
- the number of bytes required per residue in the longest sequence to be alignned.
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doAlignment
public jebl.evolution.align.AlignmentResult[] doAlignment(jebl.evolution.align.Profile profile1, jebl.evolution.align.Profile profile2, ProgressListener progress, boolean scoreOnly) -
getMatch
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getScore
public float getScore()- Returns:
- score for this alignment
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main
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setDebug
public void setDebug(boolean display) -
doAlignment
- Specified by:
doAlignment
in interfacePairwiseAligner
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getScore
- Specified by:
getScore
in interfacePairwiseAligner
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prepareAlignment
Description copied from class:Align
Initialises the matrices for the alignment. -
printf
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
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setGapExtend
public void setGapExtend(float e) -
next
Get the next state in the traceback
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