Package jebl.evolution.align
Class SmithWatermanLinearSpaceAffine
- java.lang.Object
-
- jebl.evolution.align.Align
-
- jebl.evolution.align.SmithWatermanLinearSpaceAffine
-
public class SmithWatermanLinearSpaceAffine extends Align
- Version:
- $Id: SmithWatermanLinearSpaceAffine.java 384 2006-07-17 07:17:39Z pepster $
- Author:
- Alexei Drummond
-
-
Constructor Summary
Constructors Constructor Description SmithWatermanLinearSpaceAffine(Scores sub, float d, float e)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
doAlignment(java.lang.String sequence1, java.lang.String sequence2)
Performs the alignment.void
doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
java.lang.String[]
getMatch()
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.void
setGapExtend(float e)
void
traceback(TracebackPlotter plotter)
-
Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores
-
-
-
-
Constructor Detail
-
SmithWatermanLinearSpaceAffine
public SmithWatermanLinearSpaceAffine(Scores sub, float d, float e)
-
-
Method Detail
-
doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2, ProgressListener progress)
- Parameters:
sq1
-sq2
-
-
doAlignment
public void doAlignment(java.lang.String sequence1, java.lang.String sequence2)
Performs the alignment. Abstract.
-
getScore
public float getScore()
- Returns:
- the score of the best alignment
-
getMatch
public java.lang.String[] getMatch()
-
traceback
public void traceback(TracebackPlotter plotter)
-
prepareAlignment
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Description copied from class:Align
Initialises the matrices for the alignment.
-
printf
public void printf(Output out)
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
-
setGapExtend
public void setGapExtend(float e)
-
-