Package jebl.evolution.align
Class SmithWaterman
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.SmithWaterman
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
doAlignment
(String sq1, String sq2) Performs the alignment.void
doAlignment
(String sq1, String sq2, ProgressListener progress) 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.Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, getMatch, setGapOpen, setScores, traceback
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Constructor Details
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SmithWaterman
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Method Details
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doAlignment
- Parameters:
sq1
-sq2
-progress
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doAlignment
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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prepareAlignment
Description copied from class:Align
Initialises the matrices for the alignment.- Specified by:
prepareAlignment
in classAlign
- Parameters:
sq1
-sq2
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next
Get the next state in the traceback -
getScore
public float getScore() -
printf
Print matrix used to calculate this alignment.
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