/*
* Taxa.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.util;
import dr.util.Identifiable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
/**
* Class for a list of taxa.
*
* @version $Id: Taxa.java,v 1.29 2006/09/05 13:29:34 rambaut Exp $
*
* @author Andrew Rambaut
* @author Alexei Drummond
*/
public class Taxa implements MutableTaxonList, Identifiable, Comparable<Taxa> {
private final ArrayList<MutableTaxonListListener> mutableTaxonListListeners = new ArrayList<MutableTaxonListListener>();
ArrayList<Taxon> taxa = new ArrayList<Taxon>();
private String id = null;
public Taxa() {
}
public Taxa(String id) {
this.id = id;
}
public Taxa(TaxonList list) {
addTaxa(list);
}
public Taxa(Collection<Taxon> taxa) {
addTaxa(taxa);
}
/**
* Adds the given taxon and returns its index. If the taxon is already in the list then it is not
* added but it returns its index.
*
* @param taxon the taxon to be added
*/
public int addTaxon(Taxon taxon) {
int index = getTaxonIndex(taxon);
if (index == -1) {
taxa.add(taxon);
fireTaxonAdded(taxon);
index = taxa.size() - 1;
}
return index;
}
/** Removes a taxon of the given name and returns true if successful. */
public boolean removeTaxon(Taxon taxon) {
boolean success = taxa.remove(taxon);
if (success) {
fireTaxonRemoved(taxon);
}
return success;
}
public void addTaxa(TaxonList taxa) {
for(int nt = 0; nt < taxa.getTaxonCount(); ++nt) {
addTaxon(taxa.getTaxon(nt));
}
}
public void addTaxa(Collection<Taxon> taxa) {
for(Taxon taxon : taxa) {
addTaxon(taxon);
}
}
public void removeTaxa(TaxonList taxa) {
for(int nt = 0; nt < taxa.getTaxonCount(); ++nt) {
removeTaxon(taxa.getTaxon(nt));
}
}
public void removeTaxa(Collection<Taxon> taxa) {
for(Taxon taxon : taxa) {
removeTaxon(taxon);
}
}
public void removeAllTaxa() {
taxa.clear();
fireTaxonRemoved(null);
}
/**
* @return a count of the number of taxa in the list.
*/
public int getTaxonCount() {
return taxa.size();
}
/**
* @return the ith taxon.
*/
public Taxon getTaxon(int taxonIndex) {
return taxa.get(taxonIndex);
}
/**
* @return the ID of the ith taxon.
*/
public String getTaxonId(int taxonIndex) {
return (taxa.get(taxonIndex)).getId();
}
/**
* Sets the unique identifier of the ith taxon.
*/
public void setTaxonId(int taxonIndex, String id) {
(taxa.get(taxonIndex)).setId(id);
fireTaxaChanged();
}
/**
* returns the index of the taxon with the given id.
*/
public int getTaxonIndex(String id) {
for (int i = 0; i < taxa.size(); i++) {
if (getTaxonId(i).equals(id)) return i;
}
return -1;
}
/**
* returns the index of the given taxon.
*/
public int getTaxonIndex(Taxon taxon) {
for (int i = 0; i < taxa.size(); i++) {
if (getTaxon(i) == taxon) return i;
}
return -1;
}
public List<Taxon> asList() {
return new ArrayList<Taxon>(taxa);
}
/**
* returns whether the list contains this taxon
* @param taxon
* @return true if taxon is in the list
*/
public boolean contains(Taxon taxon) {
return taxa.contains(taxon);
}
/**
* Returns true if at least 1 member of taxonList is contained in this Taxa.
* @param taxonList a TaxonList
* @return true if any of taxonList is in this Taxa
*/
public boolean containsAny(TaxonList taxonList) {
for (int i = 0; i < taxonList.getTaxonCount(); i++) {
Taxon taxon = taxonList.getTaxon(i);
if (taxa.contains(taxon)) {
return true;
}
}
return false;
}
/**
* Returns true if at least 1 member of taxonList is contained in this Taxa.
* @param taxa a collection of taxa
* @return true if any of taxa is in this Taxa
*/
public boolean containsAny(Collection<Taxon> taxa) {
for (Taxon taxon : taxa) {
if (taxa.contains(taxon)) {
return true;
}
}
return false;
}
/**
* Returns true if taxonList is a subset of the taxa in this Taxa.
* @param taxonList a TaxonList
* @return true if all of taxonList is in this Taxa
*/
public boolean containsAll(TaxonList taxonList) {
for (int i = 0; i < taxonList.getTaxonCount(); i++) {
Taxon taxon = taxonList.getTaxon(i);
if (!taxa.contains(taxon)) {
return false;
}
}
return true;
}
/**
* Returns true if taxonList is a subset of the taxa in this Taxa.
* @param taxa a collection of taxa
* @return true if all of taxa is in this Taxa
*/
public boolean containsAll(Collection<Taxon> taxa) {
for (Taxon taxon : taxa) {
if (!taxa.contains(taxon)) {
return false;
}
}
return true;
}
public String getId() { return id; }
public void setId(String id) { this.id = id; }
public int compareTo(Taxa o) {
return getId().compareTo(o.getId());
}
public String toString() { return id; }
public Iterator<Taxon> iterator() {
return taxa.iterator();
}
/**
* Sets an named attribute for a given taxon.
* @param taxonIndex the index of the taxon whose attribute is being set.
* @param name the name of the attribute.
* @param value the new value of the attribute.
*/
public void setTaxonAttribute(int taxonIndex, String name, Object value) {
Taxon taxon = getTaxon(taxonIndex);
taxon.setAttribute(name, value);
fireTaxaChanged();
}
/**
* @return an object representing the named attributed for the given taxon.
* @param taxonIndex the index of the taxon whose attribute is being fetched.
* @param name the name of the attribute of interest.
*/
public Object getTaxonAttribute(int taxonIndex, String name) {
Taxon taxon = getTaxon(taxonIndex);
return taxon.getAttribute(name);
}
public void addMutableTaxonListListener(MutableTaxonListListener listener) {
mutableTaxonListListeners.add(listener);
}
private void fireTaxonAdded(Taxon taxon) {
for (MutableTaxonListListener mutableTaxonListListener : mutableTaxonListListeners) {
mutableTaxonListListener.taxonAdded(this, taxon);
}
}
private void fireTaxonRemoved(Taxon taxon) {
for (MutableTaxonListListener mutableTaxonListListener : mutableTaxonListListeners) {
mutableTaxonListListener.taxonRemoved(this, taxon);
}
}
private void fireTaxaChanged() {
for (MutableTaxonListListener mutableTaxonListListener : mutableTaxonListListeners) {
mutableTaxonListListener.taxaChanged(this);
}
}
@Override
public boolean equals(final Object o) {
if (!(o instanceof TaxonList)) return false;
return Utils.areTaxaIdentical(this, (TaxonList)o);
}
}