/* * 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.symbol; import java.io.Serializable; import java.util.HashMap; import java.util.Map; /** * A no-frills implementation of TranslationTable that uses a Map to map from * symbols in a finite source alphabet into a target alphabet. * * @author Matthew Pocock * @author David Huen (refactoring) */ public class SimpleTranslationTable extends AbstractTranslationTable implements Serializable { private final Map transMap; private final FiniteAlphabet source; private final Alphabet target; public Alphabet getSourceAlphabet() { return source; } public Alphabet getTargetAlphabet() { return target; } public Symbol doTranslate(Symbol sym) { return (Symbol) transMap.get(sym); } /** * Alter the translation mapping. * * @param from source AtomicSymbol * @param to target AtomicSymbol to be returned by translate(from) * @throws IllegalSymbolException if either from is not in the source * alphabet or to is not in the target alphabet */ public void setTranslation(AtomicSymbol from, AtomicSymbol to) throws IllegalSymbolException { source.validate(from); target.validate(to); transMap.put(from, to); } /** * Create a new translation table that will translate symbols from source to * target. *
* The source alphabet must be finite, as a Map object is used to associate * a source Symbol with a target Symbol. * The target alphabet need not be finite. * * @param source the FiniteAlphabet to translate from * @param target the Alphabet to translate into */ public SimpleTranslationTable(FiniteAlphabet source, Alphabet target) { this.source = source; this.target = target; this.transMap = new HashMap(); } /** * Create a new translation table that will translate symbols from source to * target. *
* The Map transMap should contain keys in the source alphabet with values in * the target alphabet. However, this is not currently checked. *
* The source alphabet must be finite, as a Map object is used to associate * a source Symbol with a target Symbol. * The target alphabet need not be finite. * * @param source the FiniteAlphabet to translate from * @param target the Alphabet to translate into */ public SimpleTranslationTable( FiniteAlphabet source, Alphabet target, Map transMap ) { this.source = source; this.target = target; this.transMap = transMap; } }