[Biojava-l] Generalized HMM in biojava?

[Matthew Pocock]

On Friday 20 January 2006 22:11, wendy wong wrote:
> what I am trying to do is to develop a phylogenetic HMM. so say there
> are 3 sequences, in the alignment, that means each site consists of 3
> symbols, and if it is a generalized HMM, each state has several sites,
> say 7.

OK - so you have a single HMM that emits whole columns of an alignment? 
Usually to a lign three sequences, you would use a 3-head HMM where each head 
emits one of the sequences.

> I wrote a testing program to see if it works. when the length 
> of sites in the state = 5 it worked. (I just want to see if I can
> factorize a symbol in the state alphabet. but when number of sites in
> the state = 7, I get  java.lang.ArrayIndexOutOfBoundsException.  (code
> attached)
>
> Is it because i was not using the alphabet efficiently?

You shouldn't be getting exceptions. This is almost certainly a bug. Could you 
send the stack-trace?

Matthew

>
> again, thanks very much for helping!
>
> Wendy
>
> public static void main(String[] args) throws MarshalException,
> ValidationException, IOException {
>
> 		Alphabet sequenceAlphabet = DNATools.getDNA();
> 		Set alphabetSet = AlphabetManager.getAllSymbols((FiniteAlphabet)
> sequenceAlphabet);
>
> 	    	int no_sequences = 3;
> 		List siteAlphabetList = Collections.nCopies(no_sequences,
> sequenceAlphabet); Alphabet siteAlphabet =
> AlphabetManager.getCrossProductAlphabet(siteAlphabetList);
> 	    int length = 7;
> 	    List staeAlphabetList = Collections.nCopies(length, siteAlphabet);
> 	    Alphabet stateAlphabet =
> AlphabetManager.getCrossProductAlphabet(staeAlphabetList);
>
> 	    AlphabetIndex alphabetIndex =
> AlphabetManager.getAlphabetIndex((FiniteAlphabet) stateAlphabet);
> 	AtomicSymbol sym = (AtomicSymbol) alphabetIndex.symbolForIndex(3);
> 	    List symList = sym.getSymbols();
> 	    log.info("sym (index=3)  is " + sym);
> 	    log.info("sym is composed of:");
> 	    Iterator symIter = symList.iterator();
> 	    while (symIter.hasNext()) {
> 	    		log.info(symIter.next());
> 	    }
> }