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package com.wcohen.ss;
import com.wcohen.ss.api.*;
/**
* Affine-gap string distance, following Durban et al.
* Sec 2.3.
*/
public class AffineGap extends AbstractStringDistance
{
private CharMatchScore charMatchScore;
private double openGapScore;
private double extendGapScore;
private double lowerBound;
public AffineGap() {
this(CharMatchScore.DIST_21, 2, 1, -Double.MAX_VALUE );
}
public AffineGap(CharMatchScore charMatchScore,double openGapScore, double extendGapScore, double lowerBound) {
this.charMatchScore = charMatchScore;
this.openGapScore = openGapScore;
this.extendGapScore = extendGapScore;
this.lowerBound = lowerBound;
}
public double score(StringWrapper s,StringWrapper t) {
MatrixTrio mat = new MatrixTrio( s, t );
return score(s,t,mat);
}
private double score(StringWrapper s,StringWrapper t,MatrixTrio 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) {
MatrixTrio mat = new MatrixTrio( s, t );
double d = score(s,t,mat);
return mat.toString() + "\nScore = "+d;
}
// a set of three linked distance matrices
protected class MatrixTrio extends MemoMatrix
{
protected MemoMatrix m;
protected InsertSMatrix is;
protected InsertTMatrix it;
public MatrixTrio(StringWrapper s,StringWrapper t) {
super(s,t);
is = new InsertSMatrix(s,t);
it = new InsertTMatrix(s,t);
m = this;
}
public double compute(int i,int j) {
if (i==0 || j==0) return 0;
double matchScore = charMatchScore.matchScore( sAt(i), tAt(j) );
return max4( lowerBound,
m.get(i-1,j-1) + matchScore,
is.get(i-1,j-1) + matchScore,
it.get(i=1,j-1) + matchScore );
}
protected class InsertSMatrix extends MemoMatrix {
public InsertSMatrix(StringWrapper s,StringWrapper t) { super(s,t); }
public double compute(int i,int j) {
if (i==0 || j==0) return 0;
return max3( lowerBound,
m.get(i-1,j) + openGapScore,
is.get(i-1,j) + extendGapScore );
}
}
protected class InsertTMatrix extends MemoMatrix {
public InsertTMatrix(StringWrapper s,StringWrapper t) { super(s,t); }
public double compute(int i,int j) {
if (i==0 || j==0) return 0;
return max3( lowerBound,
m.get(i,j-1) + openGapScore,
it.get(i,j-1) + extendGapScore );
}
}
}
static public void main(String[] argv) {
doMain(new AffineGap(), argv);
}
}
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