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package com.wcohen.ss;
import com.wcohen.ss.api.*;
/**
* Needleman-Wunsch string distance, following Durban et al.
* Sec 2.3.
*/
public class NeedlemanWunsch extends AbstractStringDistance
{
private CharMatchScore charMatchScore;
private double gapCost;
public NeedlemanWunsch() { this(CharMatchScore.DIST_01, 1.0 ); }
public NeedlemanWunsch(CharMatchScore charMatchScore,double gapCost) {
this.charMatchScore = charMatchScore;
this.gapCost = gapCost;
}
public double score(StringWrapper s,StringWrapper t) {
MyMatrix mat = new MyMatrix( s, t );
return mat.get(s.length(), t.length() );
}
public String explainScore(StringWrapper s,StringWrapper t) {
MyMatrix mat = new MyMatrix( s, t );
double d = mat.get(s.length(), t.length() );
mat.setPrintNegativeValues(true);
return mat.toString() + "\nScore = "+d;
}
private class MyMatrix extends MemoMatrix {
public MyMatrix(StringWrapper s,StringWrapper t) {
super(s,t);
}
public double compute(int i,int j) {
if (i==0) return -j*gapCost;
if (j==0) return -i*gapCost;
return max3( get(i-1,j-1) + charMatchScore.matchScore( sAt(i), tAt(j) ),
get(i-1, j) - gapCost,
get(i, j-1) - gapCost);
}
}
static public void main(String[] argv) {
doMain(new NeedlemanWunsch(), argv);
}
}
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