Package jebl.evolution.align
Class OldNeedlemanWunschAffine
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.OldNeedlemanWunschAffine
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public class OldNeedlemanWunschAffine extends Align
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Constructor Summary
Constructors Constructor Description OldNeedlemanWunschAffine(Scores sub, float d, float e)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment.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, getMatch, setGapOpen, setScores, traceback
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Constructor Detail
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OldNeedlemanWunschAffine
public OldNeedlemanWunschAffine(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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prepareAlignment
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Description copied from class:Align
Initialises the matrices for the alignment.- Specified by:
prepareAlignment
in classAlign
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setGapExtend
public void setGapExtend(float e)
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getScore
public float getScore()
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