Package jebl.evolution.align
Class SmithWatermanLinearSpaceAffine
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.SmithWatermanLinearSpaceAffine
- Version:
- $Id: SmithWatermanLinearSpaceAffine.java 384 2006-07-17 07:17:39Z pepster $
- Author:
- Alexei Drummond
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
doAlignment
(String sequence1, String sequence2) Performs the alignment.void
doAlignment
(String sq1, String sq2, ProgressListener progress) 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
setGapExtend
(float e) 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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SmithWatermanLinearSpaceAffine
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Method Details
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doAlignment
- Parameters:
sq1
-sq2
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doAlignment
Performs the alignment. Abstract.- Parameters:
sequence1
-sequence2
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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.- Parameters:
sq1
-sq2
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printf
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
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setGapExtend
public void setGapExtend(float e) -
next
Get the next state in the traceback
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