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
022
023package org.biojava.bio.dp;
024
025import java.io.Serializable;
026import java.util.HashSet;
027import java.util.Iterator;
028import java.util.Set;
029
030import org.biojava.bio.BioError;
031import org.biojava.bio.dist.Distribution;
032import org.biojava.bio.dist.SimpleDistributionTrainerContext;
033import org.biojava.bio.symbol.IllegalSymbolException;
034
035/**
036 * @author Matthew Pocock
037 * @author Thomas Down
038 */
039public class SimpleModelTrainer
040extends SimpleDistributionTrainerContext
041implements ModelTrainer, Serializable {
042  private Set models = new HashSet();
043
044  public void registerModel(MarkovModel model) {
045    if(!models.contains(model)) {
046      for(Iterator i = model.stateAlphabet().iterator(); i.hasNext(); ) {
047        State s = (State) i.next();
048        try {
049          Distribution dist = model.getWeights(s);
050          registerDistribution(dist);
051        } catch (IllegalSymbolException ise) {
052          throw new BioError("Couldn't register states from model", ise);
053        }
054        if(s instanceof EmissionState) {
055          Distribution dist = ((EmissionState) s).getDistribution();
056          registerDistribution(dist);
057        }
058      }
059    }
060  }
061}