Package jebl.evolution.align
Class MaximalSegmentPair
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.MaximalSegmentPair
- Version:
- $Id: MaximalSegmentPair.java 185 2006-01-23 23:03:18Z rambaut $
- Author:
- Alexei Drummond
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfinal void
doAlignment
(String sq1, String sq2) Performs the alignment.float
getScore()
final Traceback
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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MaximalSegmentPair
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Method Details
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doAlignment
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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next
Get the next state in the traceback- Parameters:
tb
- current Traceback- Returns:
- next Traceback
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prepareAlignment
Description copied from class:Align
Initialises the matrices for the alignment.- Specified by:
prepareAlignment
in classAlign
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getScore
public float getScore() -
printf
Print matrix used to calculate this alignment.
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