Package org.biojava.bio.symbol

Interface TranslationTable

  • All Known Subinterfaces:
    ManyToOneTranslationTable, ReversibleTranslationTable
    All Known Implementing Classes:
    AbstractManyToOneTranslationTable, AbstractReversibleTranslationTable, SimpleGeneticCodeTable, SimpleManyToOneTranslationTable, SimpleReversibleTranslationTable, SimpleTranslationTable
    public interface TranslationTable

    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, Keith James

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String ALT_YEAST_NUC
      Translation table name for the alternative yeast nuclear genetic code.
      static String ASCID_MITO
      Translation table name for the ascidian mitochondrial genetic code.
      static String BACTERIAL
      Translation table name for the bacterial and plant plastid genetic code.
      static String BLEPH_MNUC
      Translation table name for the blepharisma macronuclear genetic code.
      static String CHLORO_MITO
      Translation table name for the chlorophycean mitochondrial genetic code.
      static String CILIATE_NUC
      Translation table name for the ciliate nuclear genetic code.
      static String ECHIN_MITO
      Translation table name for the echinoderm mitochondrial genetic code.
      static String EUPL_NUC
      Translation table name for the euplotid nuclear genetic code.
      static String FWORM_MITO
      Translation table name for the flatworm mitochondrial genetic code.
      static String INVERT_MITO
      Translation table name for the invertebrate mitochondrial genetic code.
      static String MOLD_MITO
      Translation table name for the mold mitochondrial genetic code.
      static String SCENE_MITO
      Translation table name for the scenedesmus obliquus mitochondrial genetic code.
      static String TREMA_MITO
      Translation table name for the trematode mitochondrial genetic code.
      static String UNIVERSAL
      Translation table name for the universal genetic code.
      static String VERT_MITO
      Translation table name for the vertebrate mitochondrial genetic code.
      static String YEAST_MITO
      Translation table name for the yeast mitochondrial genetic code.