smile.taxonomy.TaxonomicDistance Maven / Gradle / Ivy
/*
* Copyright (c) 2010-2021 Haifeng Li. All rights reserved.
*
* Smile is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Smile is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Smile. If not, see .
*/
package smile.taxonomy;
import java.util.Iterator;
import java.util.List;
import smile.math.distance.Distance;
/**
* The distance between concepts in a taxonomy.
* The distance between two concepts a and b is defined by the length of the
* path from a to their lowest common ancestor and then to b.
*
* @author Haifeng Li
*/
public class TaxonomicDistance implements Distance {
/**
* The taxonomy basis to calculate the distance.
*/
private final Taxonomy taxonomy;
/**
* Constructor.
*
* @param taxonomy the taxonomy that this distance is associated with.
*/
public TaxonomicDistance(Taxonomy taxonomy) {
this.taxonomy = taxonomy;
}
@Override
public String toString() {
return String.format("Taxonomic distance on %s", taxonomy);
}
/**
* Computes the distance between two concepts in a taxonomy.
* @param x a concept.
* @param y the other concept.
* @return the distance.
*/
public double d(String x, String y) {
return d(taxonomy.getConcept(x), taxonomy.getConcept(y));
}
/**
* Computes the distance between two concepts in a taxonomy.
*/
@Override
public double d(Concept x, Concept y) {
if (x.taxonomy != y.taxonomy) {
throw new IllegalArgumentException("Concepts are not from the same taxonomy.");
}
List xPath = x.getPathFromRoot();
List yPath = y.getPathFromRoot();
Iterator xIter = xPath.iterator();
Iterator yIter = yPath.iterator();
int depth = 0;
while (xIter.hasNext() && yIter.hasNext()) {
if (xIter.next() != yIter.next()) {
break;
}
depth++;
}
return xPath.size() - depth + yPath.size() - depth;
}
}