org.simmetrics.metrics.SmithWatermanGotoh Maven / Gradle / Ivy
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* Simmetrics Core
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* Copyright (C) 2014 - 2015 Simmetrics Authors
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* Licensed under the Apache License, Version 2.0 (the "License");
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* http://www.apache.org/licenses/LICENSE-2.0
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package org.simmetrics.metrics;
import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import static java.lang.Math.max;
import static java.lang.Math.min;
import static org.simmetrics.metrics.Math.max;
import org.simmetrics.StringMetric;
import org.simmetrics.metrics.functions.MatchMismatch;
import org.simmetrics.metrics.functions.Substitution;
/**
* Applies the Smith-Waterman algorithm to calculate the similarity between two
* strings. This implementation uses optimizations described in Osamu Gotoh
* (1982). "An improved algorithm for matching biological sequences". Journal of
* molecular biology 162: 705" and uses constant space and quadratic time.
*
*
* This class is immutable and thread-safe if its substitution functions are.
*
* @see NeedlemanWunch
* @see SmithWaterman
* @see Wikipedia
* - Smith-Waterman algorithm
*
*/
public final class SmithWatermanGotoh implements StringMetric {
private static final Substitution MATCH_1_MISMATCH_MINUS_2 = new MatchMismatch(
1.0f, -2.0f);
private final float gapValue;
private Substitution substitution;
/**
* Constructs a new Smith Waterman metric. Gap penalty is -0.5, mismatch
* penalty -2.0 and a matching score 1.0.
*
*/
public SmithWatermanGotoh() {
this(-0.5f, MATCH_1_MISMATCH_MINUS_2);
}
/**
* Constructs a new Smith Waterman metric.
*
* @param gapValue
* a non-positive gap penalty
* @param substitution
* a substitution function
*/
public SmithWatermanGotoh(float gapValue, Substitution substitution) {
checkArgument(gapValue <= 0.0f);
checkNotNull(substitution);
this.gapValue = gapValue;
this.substitution = substitution;
}
@Override
public float compare(final String a, final String b) {
if (a.isEmpty() && b.isEmpty()) {
return 1.0f;
}
if (a.isEmpty() || b.isEmpty()) {
return 0.0f;
}
float maxDistance = min(a.length(), b.length())
* max(substitution.max(), gapValue);
return smithWatermanGotoh(a, b) / maxDistance;
}
private float smithWatermanGotoh(final String s, final String t) {
float[] v0 = new float[t.length()];
float[] v1 = new float[t.length()];
float max = v0[0] = max(0, gapValue, substitution.compare(s, 0, t, 0));
for (int j = 1; j < v0.length; j++) {
v0[j] = max(0, v0[j - 1] + gapValue,
substitution.compare(s, 0, t, j));
max = max(max, v0[j]);
}
// Find max
for (int i = 1; i < s.length(); i++) {
v1[0] = max(0, v0[0] + gapValue, substitution.compare(s, i, t, 0));
max = max(max, v1[0]);
for (int j = 1; j < v0.length; j++) {
v1[j] = max(0, v0[j] + gapValue, v1[j - 1] + gapValue,
v0[j - 1] + substitution.compare(s, i, t, j));
max = max(max, v1[j]);
}
for (int j = 0; j < v0.length; j++) {
v0[j] = v1[j];
}
}
return max;
}
@Override
public String toString() {
return "SmithWatermanGotoh [substitution=" + substitution + ", gapValue="
+ gapValue + "]";
}
}