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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