Class SimpleTranslationTable

java.lang.Object
org.biojava.bio.symbol.SimpleTranslationTable
All Implemented Interfaces:
Serializable, TranslationTable

public class SimpleTranslationTable extends Object implements Serializable
A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
Author:
Matthew Pocock, David Huen (refactoring)
See Also:
  • Constructor Details

    • SimpleTranslationTable

      Create a new translation table that will translate symbols from source to target.

      The source alphabet must be finite, as a Map object is used to associate a source Symbol with a target Symbol. The target alphabet need not be finite.

      Parameters:
      source - the FiniteAlphabet to translate from
      target - the Alphabet to translate into
    • SimpleTranslationTable

      public SimpleTranslationTable(FiniteAlphabet source, Alphabet target, Map transMap)
      Create a new translation table that will translate symbols from source to target.

      The Map transMap should contain keys in the source alphabet with values in the target alphabet. However, this is not currently checked.

      The source alphabet must be finite, as a Map object is used to associate a source Symbol with a target Symbol. The target alphabet need not be finite.

      Parameters:
      source - the FiniteAlphabet to translate from
      target - the Alphabet to translate into
  • Method Details

    • getSourceAlphabet

      Description copied from interface: TranslationTable
      The alphabet of Symbols that can be translated.
      Specified by:
      getSourceAlphabet in interface TranslationTable
      Returns:
      the source Alphabet
    • getTargetAlphabet

      Description copied from interface: TranslationTable
      The alphabet of Symbols that will be produced.
      Specified by:
      getTargetAlphabet in interface TranslationTable
      Returns:
      the target Alphabet
    • doTranslate

      public Symbol doTranslate(Symbol sym)
      this method is expected to 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.

    • setTranslation

      Alter the translation mapping.
      Parameters:
      from - source AtomicSymbol
      to - target AtomicSymbol to be returned by translate(from)
      Throws:
      IllegalSymbolException - if either from is not in the source alphabet or to is not in the target alphabet
    • translate

      public Symbol translate(Symbol sym) throws IllegalSymbolException
      Description copied from interface: TranslationTable
      Translate a single symbol from source alphabet to the target alphabet.
      Specified by:
      translate in interface TranslationTable
      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