[Biojava-l] Translations

[Cox, Greg]

I'm not sure if I understand you correctly.  There's some confusion with
"symbol": in the BioJava sense this isn't neccessarily atomic.  To check if
one is, call getMatches() and see if that returns an alphabet of size 1 or
not.  

The other half is in TranslationTables.xml.  There are translations of most
encodings already there, they can be retrieved via
RNATools.getGeneticCode(name of translation).  If you have problems
translating ambiguous codons correctly, that's a know bug and is being fixed
now.

These comments apply to biojava-live.  The release version has symbols but
only the universal translation table.

If this isn't what you're looking for, let me know and I'll take another
stab at it.  As soon as you tell me what "wobbled" is.

Greg

> -----Original Message-----
> From: Armin Groll [mailto:ArminG9@compuserve.de]
> Sent: Monday, October 15, 2001 3:26 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Translations
> 
> 
> 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
> 
> 
> 
> 
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