/* * 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 org.biojava.bio.symbol.Alphabet; import org.biojava.bio.symbol.IllegalAlphabetException; import org.biojava.bio.symbol.IllegalSymbolException; import org.biojava.bio.symbol.Symbol; import org.biojava.utils.ChangeVetoException; import org.biojava.utils.Unchangeable; /** * This distribution emits gap symbols. *
* It is a useful thing to have around for pair-wise alignment, as you can * build a PairDistribution that emits gaps in one sequence and Symbols in the * other. The GapDistriution will always emit with a probability of 1, as every * symbol has a matches alphabet that contains the empty set. Or is this so? * * @author Matthew Pocock * @since 1.0 */ public class GapDistribution extends Unchangeable implements Distribution, Serializable { private final Alphabet alpha; private static final long serialVersionUID = 88622317; public double getWeight(Symbol sym) throws IllegalSymbolException { return 1.0; } public void setWeight(Symbol s, double w) throws IllegalSymbolException, UnsupportedOperationException { getAlphabet().validate(s); throw new UnsupportedOperationException( "The weights are immutable: " + s.getName() + " -> " + w ); } public Alphabet getAlphabet() { return alpha; } public Symbol sampleSymbol() { return getAlphabet().getGapSymbol(); } public Distribution getNullModel() { return this; } public void setNullModel(Distribution nullModel) throws IllegalAlphabetException, ChangeVetoException { throw new ChangeVetoException("Can't change null model for GapDistribution"); } public void registerWithTrainer(DistributionTrainerContext dtc) { dtc.registerTrainer(this, IgnoreCountsTrainer.getInstance()); } /** * Get a GapDistribution for an alphabet. * * @param alpha the Alphabet that this distribution is over */ public GapDistribution(Alphabet alpha) { this.alpha = alpha; } }