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package com.wcohen.ss;
import com.wcohen.ss.api.*;
/**
* Smith-Waterman string distance, following Durban et al.
* Sec 2.3.
*/
public class SmithWaterman extends AbstractStringDistance
{
private CharMatchScore charMatchScore;
private double gapCost;
public SmithWaterman() {
this(CharMatchScore.DIST_21, 1.0 );
}
public SmithWaterman(CharMatchScore charMatchScore,double gapCost) {
this.charMatchScore = charMatchScore;
this.gapCost = gapCost;
}
public double score(StringWrapper s,StringWrapper t) {
MyMatrix mat = new MyMatrix( s, t );
return score(s,t,mat);
}
private double score(StringWrapper s,StringWrapper t,MyMatrix mat) {
double best = -Double.MAX_VALUE;
for (int i=0; i<=s.length(); i++) {
for (int j=0; j<=t.length(); j++) {
best = Math.max( best, mat.get(i,j) );
}
}
return best;
}
public String explainScore(StringWrapper s,StringWrapper t) {
MyMatrix mat = new MyMatrix( s, t );
double d = score(s,t,mat);
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 0;
if (j==0) return 0;
return max4( 0,
get(i-1,j-1) + charMatchScore.matchScore( sAt(i), tAt(j) ),
get(i-1, j) - gapCost,
get(i, j-1) - gapCost);
}
}
public String toString() { return "[SmithWaterman]"; }
static public void main(String[] argv) {
doMain(new SmithWaterman(), argv);
}
}
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