Package jebl.evolution.align
Class SmithWatermanLinearSpace
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.SmithWatermanLinearSpace
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public class SmithWatermanLinearSpace extends Align
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Constructor Summary
Constructors Constructor Description SmithWatermanLinearSpace(Scores sub, float d)
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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.java.lang.String[]
getMatch()
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
traceback(TracebackPlotter plotter)
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Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores
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Constructor Detail
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SmithWatermanLinearSpace
public SmithWatermanLinearSpace(Scores sub, float d)
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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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getScore
public float getScore()
- Returns:
- the score of the best alignment
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getMatch
public java.lang.String[] getMatch()
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traceback
public void traceback(TracebackPlotter plotter)
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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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