/* * 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; /** *
Encapsulates the mapping from a source to a destination * alphabet.
* *A TranslationTable is in effect a map or function with the * source domain being getSourceAlphabet() and the target domain being * getTargetAlphabet(). The method translate() maps a single symbol * from source to target.
* *It is presumed that there will be some explicit declaration of * the mapping for attomic symbols, and that the mapping for all other * symbols will be infered from these.
* *If you wish to translate every symbol in a symbol list then use * TranslatedSymbolList to automate the job. If you want to translate * windowed regions then first construct a WindowedSymbolList from the * original sequence and then build a TranslatedSymbolList from this * windowed view.
* *There are a range of named tables available. Their names are * specified by the public static final fields in this interface. Each * table can be retrieved by calling the static method * RNATools.getGeneticCode(name) which will return the appropriate * TanslationTable instance.
* * @author Matthew Pocock * @author Keith James */ public interface TranslationTable { /** * Translation table name for the universal genetic code. */ public static final String UNIVERSAL = "UNIVERSAL"; /** * Translation table name for the vertebrate mitochondrial genetic * code. */ public static final String VERT_MITO = "VERTEBRATE_MITOCHONDRIAL"; /** * Translation table name for the yeast mitochondrial genetic * code. */ public static final String YEAST_MITO = "YEAST_MITOCHONDRIAL"; /** * Translation table name for the mold mitochondrial genetic code. */ public static final String MOLD_MITO = "MOLD_MITOCHONDRIAL"; /** * Translation table name for the invertebrate mitochondrial * genetic code. */ public static final String INVERT_MITO = "INVERTEBRATE_MITOCHONDRIAL"; /** * Translation table name for the ciliate nuclear genetic code. */ public static final String CILIATE_NUC = "CILIATE_NUCLEAR"; /** * Translation table name for the echinoderm mitochondrial genetic * code. */ public static final String ECHIN_MITO = "ECHINODERM_MITOCHONDRIAL"; /** * Translation table name for the euplotid nuclear genetic code. */ public static final String EUPL_NUC = "EUPLOTID_NUCLEAR"; /** * Translation table name for the bacterial and plant plastid genetic code. */ public static final String BACTERIAL = "BACTERIAL"; /** * Translation table name for the alternative yeast nuclear * genetic code. */ public static final String ALT_YEAST_NUC = "ALTERNATIVE_YEAST_NUCLEAR"; /** * Translation table name for the ascidian mitochondrial genetic * code. */ public static final String ASCID_MITO = "ASCIDIAN_MITOCHONDRIAL"; /** * Translation table name for the flatworm mitochondrial genetic * code. */ public static final String FWORM_MITO = "FLATWORM_MITOCHONDRIAL"; /** * Translation table name for the blepharisma macronuclear genetic * code. */ public static final String BLEPH_MNUC = "BLEPHARISMA_MACRONUCLEAR"; /** * Translation table name for the chlorophycean mitochondrial genetic * code. */ public static final String CHLORO_MITO = "CHLOROPHYCEAN_MITOCHONDRIAL"; /** * Translation table name for the trematode mitochondrial genetic * code. */ public static final String TREMA_MITO = "TREMATODE_MITOCHONDRIAL"; /** * Translation table name for the scenedesmus obliquus mitochondrial genetic * code. */ public static final String SCENE_MITO = "SCENEDESMUS_MITOCHONDRIAL"; /** * The alphabet of Symbols that can be translated. * * @return the source Alphabet */ public Alphabet getSourceAlphabet(); /** * The alphabet of Symbols that will be produced. * * @return the target Alphabet */ public Alphabet getTargetAlphabet(); /** * Translate a single symbol from source alphabet to the target alphabet. * * @param sym the Symbol to translate (member of source alphabet) * @return the translated version of sym (member of target alphabet) * @throws IllegalSymbolException if sym is not a member of the source * alphabet */ public Symbol translate(Symbol sym) throws IllegalSymbolException; }