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

      • UNIVERSAL

        static final java.lang.String UNIVERSAL
        Translation table name for the universal genetic code.
        See Also:
        Constant Field Values
      • VERT_MITO

        static final java.lang.String VERT_MITO
        Translation table name for the vertebrate mitochondrial genetic code.
        See Also:
        Constant Field Values
      • YEAST_MITO

        static final java.lang.String YEAST_MITO
        Translation table name for the yeast mitochondrial genetic code.
        See Also:
        Constant Field Values
      • MOLD_MITO

        static final java.lang.String MOLD_MITO
        Translation table name for the mold mitochondrial genetic code.
        See Also:
        Constant Field Values
      • INVERT_MITO

        static final java.lang.String INVERT_MITO
        Translation table name for the invertebrate mitochondrial genetic code.
        See Also:
        Constant Field Values
      • CILIATE_NUC

        static final java.lang.String CILIATE_NUC
        Translation table name for the ciliate nuclear genetic code.
        See Also:
        Constant Field Values
      • ECHIN_MITO

        static final java.lang.String ECHIN_MITO
        Translation table name for the echinoderm mitochondrial genetic code.
        See Also:
        Constant Field Values
      • EUPL_NUC

        static final java.lang.String EUPL_NUC
        Translation table name for the euplotid nuclear genetic code.
        See Also:
        Constant Field Values
      • BACTERIAL

        static final java.lang.String BACTERIAL
        Translation table name for the bacterial and plant plastid genetic code.
        See Also:
        Constant Field Values
      • ALT_YEAST_NUC

        static final java.lang.String ALT_YEAST_NUC
        Translation table name for the alternative yeast nuclear genetic code.
        See Also:
        Constant Field Values
      • ASCID_MITO

        static final java.lang.String ASCID_MITO
        Translation table name for the ascidian mitochondrial genetic code.
        See Also:
        Constant Field Values
      • FWORM_MITO

        static final java.lang.String FWORM_MITO
        Translation table name for the flatworm mitochondrial genetic code.
        See Also:
        Constant Field Values
      • BLEPH_MNUC

        static final java.lang.String BLEPH_MNUC
        Translation table name for the blepharisma macronuclear genetic code.
        See Also:
        Constant Field Values
      • CHLORO_MITO

        static final java.lang.String CHLORO_MITO
        Translation table name for the chlorophycean mitochondrial genetic code.
        See Also:
        Constant Field Values
      • TREMA_MITO

        static final java.lang.String TREMA_MITO
        Translation table name for the trematode mitochondrial genetic code.
        See Also:
        Constant Field Values
      • SCENE_MITO

        static final java.lang.String SCENE_MITO
        Translation table name for the scenedesmus obliquus mitochondrial genetic code.
        See Also:
        Constant Field Values
    • Method Detail

      • getSourceAlphabet

        Alphabet getSourceAlphabet()
        The alphabet of Symbols that can be translated.
        Returns:
        the source Alphabet
      • getTargetAlphabet

        Alphabet getTargetAlphabet()
        The alphabet of Symbols that will be produced.
        Returns:
        the target Alphabet
      • translate

        Symbol translate​(Symbol sym)
                  throws IllegalSymbolException
        Translate a single symbol from source alphabet to the target alphabet.
        Parameters:
        sym - the Symbol to translate (member of source alphabet)
        Returns:
        the translated version of sym (member of target alphabet)
        Throws:
        IllegalSymbolException - if sym is not a member of the source alphabet