Package jebl.evolution.align
Class NeedlemanWunschLinearSpace
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.NeedlemanWunschLinearSpace
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public class NeedlemanWunschLinearSpace extends Align
- Version:
- $Id: NeedlemanWunschLinearSpace.java 186 2006-01-24 00:41:22Z pepster $
- Author:
- Alexei Drummond
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Constructor Summary
Constructors Constructor Description NeedlemanWunschLinearSpace(Scores sub, float d)
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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.java.lang.String[]
getMatch()
float
getScore()
int
getV()
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.void
traceback(TracebackPlotter plotter)
void
traceback(TracebackPlotter plotter, int startx, int starty, java.lang.String sq1, java.lang.String sq2)
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Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores
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Constructor Detail
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NeedlemanWunschLinearSpace
public NeedlemanWunschLinearSpace(Scores sub, float d)
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Method Detail
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doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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getV
public int getV()
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getMatch
public java.lang.String[] getMatch()
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traceback
public void traceback(TracebackPlotter plotter)
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traceback
public void traceback(TracebackPlotter plotter, int startx, int starty, java.lang.String sq1, java.lang.String sq2)
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getScore
public float getScore()
- Returns:
- the score of the best alignment
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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.
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printf
public void printf(Output out)
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
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