/* * 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.util.HashSet; import java.util.Iterator; import java.util.Set; /** * an abstract class implementing basic functionality * of a translation table that translates Symbols from * one Alphabet to another. * * @author Matthew Pocock * @author Keith James (docs) * @author Thomas Down * @author Greg Cox * @author Mark Schreiber * @author David Huen (refactoring) */ public abstract class AbstractReversibleTranslationTable extends AbstractTranslationTable implements ReversibleTranslationTable { public abstract Alphabet getSourceAlphabet(); public abstract Alphabet getTargetAlphabet(); /** * this method is expected to reverse-translate any symbol * in the source alphabet. Failure can be indicated * by returning a null if, for example, your method * only handles AtomicSymbols and you want BasisSymbols * to be taken apart. If you are sure the symbol is * illegal, you can throw the IllegalSymbolException * immediately to bypass further processing. *
* As an optimisation, if your method is capable of * immediately translating an ambiguity Symbol, just * return it and the alternate route of establishing * the translation through doing an ambiguity * lookup will be avoided. */ protected abstract Symbol doUntranslate(Symbol sym) throws IllegalSymbolException; public Symbol untranslate(final Symbol sym) throws IllegalSymbolException { // make an attempt to translate immediately Symbol s = doUntranslate(sym); // translation failed, validate and try an ambiguity lookup if(s == null) { if(sym instanceof AtomicSymbol) { //changed this from s to sym, since we already checked and s is null getSourceAlphabet().validate(sym); // the symbol was valid and still we can't handle it, bail out! throw new IllegalSymbolException("Unable to map " + sym.getName()); } else { if(sym == null) { throw new NullPointerException("Can't translate null"); } Set syms = new HashSet(); for (Iterator i = ((FiniteAlphabet) sym.getMatches()).iterator(); i.hasNext(); ) { Symbol is = (Symbol) i.next(); syms.add(this.untranslate(is)); } s = getTargetAlphabet().getAmbiguity(syms); } } return s; } }