[Biojava-l] Translations

[Armin Groll]

Hi out there,

I have some issues regarding interface org.biojava.symbol.Translation.
I am missing something. Exactly that:
- we have TranslationTable, that is a one way function.
- we have ReversibleTranslationTable, that is a two way function.
- I'd need some ambiguity possibility. What I mean is, let there exist
translations from one symbol of alphabet A to a choice of symbols of
alphabet B. And reverse.
Something like this:

package org.biojava.bio.symbol;

interface AmbiguousTranslationTable{
  public Alphabet getSource();
  public Alphabet getTarget();
  /** @return a set of Symbols, each of them one possible translation of
'toTranslate'
  public java.util.Set getTranslation(Symbol toTranslate);
}

Hold on, I need something more liberal:

interface AmbiguousSequenceTranslationTable{
  public Alphabet getSource();
  public Alphabet getTarget();
  /**
  * @return a set of org.biojava.bio.symbol.SymbolLists, each SymbolList a
possible translation for the symbol
  * of source into the target alphabet.
  */
  public java.util.Set getTranslation(Symbol toTranslate);
}

Yes, and then, one can get all the wobbled codons of an amino acid through
the amino acid's Symbol-instance.
This sounds poor, but please get exotic: For some organisms, we have
different translations there.
And, as I am working on cytogenetics, I can translate different
loci-alphabets into each other.

Would this be possible (and feasible)?

Armin