Package jebl.evolution.align
Class MaximalSegmentPair
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.MaximalSegmentPair
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public class MaximalSegmentPair extends Align
- Version:
- $Id: MaximalSegmentPair.java 185 2006-01-23 23:03:18Z rambaut $
- Author:
- Alexei Drummond
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Constructor Summary
Constructors Constructor Description MaximalSegmentPair(Scores sub)
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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.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.-
Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, getMatch, setGapOpen, setScores, traceback
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Constructor Detail
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MaximalSegmentPair
public MaximalSegmentPair(Scores sub)
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Method Detail
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doAlignment
public final void doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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next
public final Traceback next(Traceback tb)
Get the next state in the traceback- Parameters:
tb
- current Traceback- Returns:
- next Traceback
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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.- Specified by:
prepareAlignment
in classAlign
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getScore
public float getScore()
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