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