/* * 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 org.biojava.bio.BioError; /** * Provides a 'translated' view of an underlying SymbolList. *
* This class allows you to translate from one alphabet into another, so * for example, you could translate from DNA-triplets into amino-acids. You * could also translate from DNA-dinucleotide into the 'twist' structural * metric, or any other translation that takes your fancy. *
* The actual mapping from source to view Symbol is encapsulated in a * TranslationTable object. *
* The TranslatedSymbolList will be the same length as the source, and each * Symbol in the view will correspond to a single Symbol in the source. * * @author Matthew Pocock */ class TranslatedSymbolList extends AbstractSymbolList implements SymbolList { /** * The source symbol list to translate. */ private final SymbolList source; /** * The TranslationTable that will be used to translate source->view symbols */ private final TranslationTable transTable; /** *Obtain the translation table associated with this symbol list */ public TranslationTable getTranslationTable() { return transTable; } /** *Returns the symbol list associated with this translated symbol list. */ public SymbolList getSource() { return source; } public TranslatedSymbolList(SymbolList source, TranslationTable transTable) throws IllegalAlphabetException { if(transTable.getSourceAlphabet() != source.getAlphabet()) { throw new IllegalAlphabetException( "The source alphabet and translation table source alphabets don't match: " + source.getAlphabet().getName() + " and " + transTable.getSourceAlphabet().getName() ); } this.source = source; this.transTable = transTable; } public int length() { return source.length(); } public Symbol symbolAt(int indx) { try { return transTable.translate(source.symbolAt(indx)); } catch (IllegalSymbolException ire) { throw new BioError( "I thought that I had checked that the translation table was compatible with " + "my source, but apparently something has messed up.", ire ); } } public Alphabet getAlphabet() { return transTable.getTargetAlphabet(); } }