Package jebl.evolution.align
Class NeedlemanWunschAffine
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.NeedlemanWunschAffine
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public class NeedlemanWunschAffine extends Align
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Constructor Summary
Constructors Constructor Description NeedlemanWunschAffine(Scores sub, float d, float e)
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Method Summary
All Methods Instance Methods Concrete Methods 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 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
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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NeedlemanWunschAffine
public NeedlemanWunschAffine(Scores sub, float d, float e)
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Method Detail
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doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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allocateMatrices
public void allocateMatrices(int n, int m)
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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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doAlignment
public void doAlignment(java.lang.String sequence1, java.lang.String sequence2, int startType, int endType)
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doAlignment
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)
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doAlignment
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)
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appendMatch
public void appendMatch(jebl.evolution.align.AlignmentResult result1, jebl.evolution.align.AlignmentResult result2)
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getMatch
public java.lang.String[] getMatch()
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getMatch
public java.lang.String[] getMatch(char[] sq1, char[] sq2)
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getScore
public float getScore()
- Returns:
- score for this alignment
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setGapExtend
public void setGapExtend(float e)
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