001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021
022package org.biojava.bio.program.homologene;
023
024
025import org.biojava.utils.ChangeVetoException;
026
027/**
028 * An abstract implementation of the OrthoPairCollection
029 * interface.  Its primary role is to implement the
030 * filter() method.i
031 *
032 * @author David Huen
033 */
034public abstract class AbstractOrthoPairCollection
035    implements OrthoPairCollection
036{
037
038    public abstract void add(OrthoPairSet group);
039
040    public abstract boolean contains(OrthoPairSet group);
041
042    public abstract boolean isEmpty();
043
044    public abstract OrthoPairCollection.Iterator iterator();
045
046    public OrthoPairCollection filter(OrthoPairSetFilter filters)
047    {
048        OrthoPairCollection results = new SimpleOrthoPairCollection();
049
050        for (Iterator pairSetsI = iterator();
051               pairSetsI.hasNext(); )
052        {
053            OrthoPairSet pairSet = pairSetsI.nextSet();
054
055            if (filters.accept(pairSet)) {
056                try {
057                    results.add(pairSet);
058                }
059                catch (ChangeVetoException cve) {
060                    // should be impossible as this group was created by me
061                }
062            }
063        }
064        return results;
065    }
066}
067