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.biojavax.ga.impl;
023import org.biojava.bio.symbol.SimpleSymbolList;
024import org.biojava.bio.symbol.SymbolList;
025import org.biojava.utils.ChangeVetoException;
026import org.biojavax.ga.Organism;
027
028/**
029 * A Simple Haploid Organism implementation
030 *
031 * @author Mark Schreiber
032 * @version 1.0
033 * @since 1.5
034 */
035
036public class SimpleOrganism extends AbstractOrganism {
037
038        public SimpleOrganism(){
039    super();
040  }
041  public SimpleOrganism(String name){
042    super();
043    try {
044      setName(name);
045    }
046    catch (ChangeVetoException ex) {
047      //can't happen till after the organism has been made
048    }
049  }
050
051  public SimpleOrganism(Organism org, String name){
052    super(org, name);
053  }
054
055  protected void setChromImpl(SymbolList[] chromosomes) {
056    this.chromosomes = chromosomes;
057  }
058
059  /**
060   * Simple Organisms are Halpoid
061   * @return true
062   */
063  public boolean isHaploid() {
064    return true;
065  }
066
067  public Organism replicate(String name){
068    SimpleOrganism o = new SimpleOrganism(name);
069    SymbolList[] symls = new SymbolList[this.getChromosomes().length];
070    for (int i = 0; i < symls.length; i++) {
071      symls[i] = new SimpleSymbolList(this.getChromosomes()[i]);
072    }
073
074    o.setChromImpl(symls);
075    return o;
076  }
077
078}