Field Summary

• Fields inherited from interface org.biojava.bio.symbol.TranslationTable

  ALT_YEAST_NUC, ASCID_MITO, BACTERIAL, BLEPH_MNUC, CHLORO_MITO, CILIATE_NUC, ECHIN_MITO, EUPL_NUC, FWORM_MITO, INVERT_MITO, MOLD_MITO, SCENE_MITO, TREMA_MITO, UNIVERSAL, VERT_MITO, YEAST_MITO

Constructor Summary

Method Summary

• Methods inherited from class org.biojava.bio.symbol.AbstractManyToOneTranslationTable

  untranslate

• Methods inherited from class java.lang.Object

  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

• Methods inherited from interface org.biojava.bio.symbol.TranslationTable

  translate

Constructor Detail

• SimpleManyToOneTranslationTable

  public SimpleManyToOneTranslationTable​(FiniteAlphabet source,
                                         FiniteAlphabet target)

  Construct a new translation table.

  Parameters:

  source - the source FiniteAlphabet

  target - the target FiniteAlphabet

Method Detail

• getSourceAlphabet

  public Alphabet getSourceAlphabet()

  The alphabet of Symbols that can be translated.

  Specified by:

  getSourceAlphabet in interface TranslationTable

  Specified by:

  getSourceAlphabet in class AbstractManyToOneTranslationTable

  Returns:

  the source Alphabet

• getTargetAlphabet

  public Alphabet getTargetAlphabet()

  The alphabet of Symbols that will be produced.

  Specified by:

  getTargetAlphabet in interface TranslationTable

  Specified by:

  getTargetAlphabet in class AbstractManyToOneTranslationTable

  Returns:

  the target Alphabet

• doTranslate

  protected 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.

• doUntranslate

  protected Set doUntranslate​(Symbol sym)

  this method is expected to reverse-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.

  Specified by:

  doUntranslate in class AbstractManyToOneTranslationTable

• setTranslation

  public void setTranslation​(AtomicSymbol from,
                             AtomicSymbol to)
                      throws IllegalSymbolException

  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

  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