Package jebl.evolution.align
Class NeedlemanWunschLinearSpaceAffine
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.NeedlemanWunschLinearSpaceAffine
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- All Implemented Interfaces:
PairwiseAligner
public class NeedlemanWunschLinearSpaceAffine extends Align implements PairwiseAligner
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Nested Class Summary
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Nested classes/interfaces inherited from interface jebl.evolution.align.PairwiseAligner
PairwiseAligner.Result
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Constructor Summary
Constructors 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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 tracebackvoid
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)
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Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
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Constructor Detail
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NeedlemanWunschLinearSpaceAffine
public NeedlemanWunschLinearSpaceAffine(Scores sub, float openGapPenalty, float extendGapPenalty)
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NeedlemanWunschLinearSpaceAffine
public NeedlemanWunschLinearSpaceAffine(Scores sub, float d, float e, boolean freeGapsAtEnds)
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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 Detail
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allocateMatrices
public void allocateMatrices(int n, int m)
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doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment. Abstract.
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doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress, boolean scoreOnly)
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doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
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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)
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getMatch
public java.lang.String[] getMatch()
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getScore
public float getScore()
- Returns:
- score for this alignment
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main
public static void main(java.lang.String[] arguments)
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setDebug
public void setDebug(boolean display)
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doAlignment
public PairwiseAligner.Result doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress)
- Specified by:
doAlignment
in interfacePairwiseAligner
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getScore
public double getScore(Sequence seq1, Sequence seq2)
- Specified by:
getScore
in interfacePairwiseAligner
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prepareAlignment
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Description copied from class:Align
Initialises the matrices for the alignment.
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printf
public void printf(Output out)
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
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setGapExtend
public void setGapExtend(float e)
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