/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.dist; import java.io.Serializable; import java.util.HashMap; import java.util.Iterator; import java.util.Map; import org.biojava.bio.BioError; import org.biojava.bio.symbol.Alphabet; import org.biojava.bio.symbol.AtomicSymbol; import org.biojava.bio.symbol.FiniteAlphabet; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; import org.biojava.bio.symbol.Symbol; import org.biojava.utils.ChangeVetoException; /** * A simple implemenation of a distribution trainer. *
* This requires the distribuiton being trained to have a working setWeight * method that doesn't throw an UnsupportedOperationExcepiton. *
* * @author Matthew Pocock * @deprecated Distribution impls should be providing custom trainers. */ public final class SimpleDistributionTrainer implements DistributionTrainer, Serializable { private final Distribution dis; private final Map c; { this.c = new HashMap(); } public void addCount( DistributionTrainerContext dtc, AtomicSymbol sym, double count ) throws IllegalSymbolException { Double d = (Double) c.get(sym); if (d == null) { throw new IllegalSymbolException( "Symbol " + sym.getName() + " not found in " + dis.getAlphabet().getName() ); } if(count < 0) { throw new Error( "Can't add a negative count for " + sym.getName() + " of " + count ); } c.put(sym, new Double(d.doubleValue() + count)); } public double getCount( DistributionTrainerContext dtc, AtomicSymbol sym ) throws IllegalSymbolException { Double d = (Double) c.get(sym); if (d == null) { throw new IllegalSymbolException( "Symbol " + sym.getName() + " not found in " + dis.getAlphabet().getName() ); } return ((Double) c.get(sym)).doubleValue(); } public void train(DistributionTrainerContext dtc, double weight) throws ChangeVetoException { Distribution nullModel = dis.getNullModel(); double sum = 0.0; try { for( Iterator i = ((FiniteAlphabet) dis.getAlphabet()).iterator(); i.hasNext(); ) { Symbol s = (Symbol) i.next(); Double d = (Double) c.get(s); sum += d.doubleValue() + nullModel.getWeight(s) * weight; // System.out.println(s.getName() + ": sum=" + sum); } for( Iterator i = ((FiniteAlphabet) dis.getAlphabet()).iterator(); i.hasNext(); ) { Symbol sym = (Symbol) i.next(); Double d = (Double) c.get(sym); dis.setWeight( sym, (d.doubleValue() + nullModel.getWeight(sym) * weight) / sum ); } } catch (IllegalSymbolException ise) { throw new BioError( "The alphabet for this distribution is not self-consistent" ); } } public void clearCounts(DistributionTrainerContext dtc) { for( Iterator i = ((FiniteAlphabet) dis.getAlphabet()).iterator(); i.hasNext(); ) { c.put(i.next(), new Double(0.0)); } } public SimpleDistributionTrainer(Distribution dis) throws IllegalAlphabetException { Alphabet a = dis.getAlphabet(); if(! (a instanceof FiniteAlphabet)) { throw new IllegalAlphabetException( "Can't create a SimpleDistributionTrainer for non-finite alphabet " + a.getName() + " of type " + a.getClass() ); } this.dis = dis; } }