/*
* DistanceMatrix.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evolution.distance;
import dr.evolution.alignment.PatternList;
import dr.evolution.datatype.DataType;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.matrix.Matrix;
import java.util.*;
/**
* storage for pairwise distance matrices.<p>
*
* @author Andrew Rambaut
* @author Alexei Drummond
* @version $Id: DistanceMatrix.java,v 1.23 2005/07/11 14:06:25 rambaut Exp $
*/
public class DistanceMatrix extends Matrix.AbstractMatrix implements TaxonList {
public static final double MAX_DISTANCE = 1000.0;
/**
* constructor
*/
public DistanceMatrix() {
super();
}
/**
* constructor taking a dimension
*/
public DistanceMatrix(TaxonList taxa) {
super();
this.taxa = taxa;
dimension = taxa.getTaxonCount();
distances = new double[dimension][dimension];
distancesKnown = true;
}
/**
* constructor taking a pattern source
*/
public DistanceMatrix(PatternList patterns) {
super();
setPatterns(patterns);
}
/**
* set the pattern source
*/
public void setPatterns(PatternList patterns) {
this.taxa = patterns;
this.patterns = patterns;
dimension = patterns.getTaxonCount();
dataType = patterns.getDataType();
distancesKnown = false;
}
/**
* @return the number of rows
*/
public int getRowCount() {
return dimension;
}
/**
* @return the number of columns
*/
public int getColumnCount() {
return dimension;
}
/**
* @return an element
*/
public double getElement(int row, int column) {
if (!distancesKnown) {
calculateDistances();
}
return distances[row][column];
}
/**
* set an element - this overwrites any existing elements
*/
public void setElement(int row, int column, double value) {
if (!distancesKnown) {
calculateDistances();
}
distances[row][column] = value;
}
/**
* Calculate the distances
*/
public void calculateDistances() {
distances = new double[dimension][dimension];
for (int i = 0; i < dimension; i++) {
for (int j = i + 1; j < dimension; j++) {
distances[i][j] = calculatePairwiseDistance(i, j);
distances[j][i] = distances[i][j];
}
distances[i][i] = 0.0;
}
distancesKnown = true;
}
/**
* Calculate a pairwise distance
*/
protected double calculatePairwiseDistance(int taxon1, int taxon2) {
int state1, state2;
int n = patterns.getPatternCount();
double weight, distance;
double sumDistance = 0.0;
double sumWeight = 0.0;
int[] pattern;
for (int i = 0; i < n; i++) {
pattern = patterns.getPattern(i);
state1 = pattern[taxon1];
state2 = pattern[taxon2];
weight = patterns.getPatternWeight(i);
// sumDistance += dataType.getObservedDistance(state1, state2) * weight;
if (!dataType.isAmbiguousState(state1) && !dataType.isAmbiguousState(state2) &&
state1 != state2) {
sumDistance += weight;
}
sumWeight += weight;
}
distance = sumDistance / sumWeight;
return distance;
}
/**
* Returns the mean pairwise distance of this matrix
*/
public double getMeanDistance() {
if (!distancesKnown) {
calculateDistances();
}
double dist = 0.0;
int count = 0;
for (int i = 0; i < dimension; i++) {
for (int j = 0; j < dimension; j++) {
if (i != j) {
dist += distances[i][j];
count += 1;
}
}
}
return dist / (double) count;
}
public String toString() {
try {
double[] dists = getUpperTriangle();
StringBuffer buffer = new StringBuffer(String.valueOf(dists[0]));
for (int i = 1; i < dists.length; i++) {
buffer.append(", ").append(String.valueOf(dists[i]));
}
return buffer.toString();
} catch (Matrix.NotSquareException e) {
return e.toString();
}
}
// **************************************************************
// TaxonList IMPLEMENTATION
// **************************************************************
/**
* @return a count of the number of taxa in the list.
*/
public int getTaxonCount() {
return taxa.getTaxonCount();
}
/**
* @return the ith taxon.
*/
public Taxon getTaxon(int taxonIndex) {
return taxa.getTaxon(taxonIndex);
}
/**
* @return the ID of the ith taxon.
*/
public String getTaxonId(int taxonIndex) {
return taxa.getTaxonId(taxonIndex);
}
/**
* returns the index of the taxon with the given id.
*/
public int getTaxonIndex(String id) {
return taxa.getTaxonIndex(id);
}
/**
* returns the index of the given taxon.
*/
public int getTaxonIndex(Taxon taxon) {
return taxa.getTaxonIndex(taxon);
}
public List<Taxon> asList() {
List<Taxon> taxa = new ArrayList<Taxon>();
for (int i = 0, n = getTaxonCount(); i < n; i++) {
taxa.add(getTaxon(i));
}
return taxa;
}
public Iterator<Taxon> iterator() {
return new Iterator<Taxon>() {
private int index = -1;
public boolean hasNext() {
return index < getTaxonCount() - 1;
}
public Taxon next() {
index ++;
return getTaxon(index);
}
public void remove() { /* do nothing */ }
};
}
/**
* @param taxonIndex the index of the taxon whose attribute is being fetched.
* @param name the name of the attribute of interest.
* @return an object representing the named attributed for the given taxon.
*/
public Object getTaxonAttribute(int taxonIndex, String name) {
return taxa.getTaxonAttribute(taxonIndex, name);
}
// **************************************************************
// Identifiable IMPLEMENTATION
// **************************************************************
protected String id = null;
/**
* @return the id.
*/
public String getId() {
return id;
}
/**
* Sets the id.
*/
public void setId(String id) {
this.id = id;
}
//
// Private stuff
//
protected DataType dataType = null;
int dimension = 0;
boolean distancesKnown;
private double[][] distances = null;
protected PatternList patterns = null;
private TaxonList taxa = null;
}