Package jebl.evolution.align
Class SmithWatermanLinearSpace
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.SmithWatermanLinearSpace
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
doAlignment
(String sq1, String sq2) Performs the alignment.String[]
getMatch()
float
getScore()
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
traceback
(TracebackPlotter plotter) Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores
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Constructor Details
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SmithWatermanLinearSpace
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Method Details
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doAlignment
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
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traceback
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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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next
Get the next state in the traceback
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