[Biojava-l] anger error

Schreiber, Mark mark.schreiber at agresearch.co.nz
Tue Nov 25 16:32:14 EST 2003

Hi Ben -

If your Sequence contains any ambiguous Symbols (eg for DNA n,y,r,w etc), they will not be AtomicSymbols they will be BasisSymbols. BasisSymbols are made up of one or more AtomicSymbols.

If this is the case you need to use Solution 2 from the same page (http://www.biojava.org/docs/bj_in_anger/CountResidues.htm). Actually Solution 2 is the better of the two as it is more flexible.

If this still doesn't work send me the sequence and I'll take a look.

- Mark

> -----Original Message-----
> From: Ben Good [mailto:ben at schoolid.com] 
> Sent: Tuesday, 25 November 2003 9:43 p.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] anger error
> Hi,
>   Trying to implement this bit from biojava in anger ("How do 
> count the 
> residues in a sequence").
> Count counts = new IndexedCount ((FiniteAlphabet)seq.getAlphabet());
> 					//iterate through the 
> Symbols in seq
> 						for (Iterator i 
> = seq.iterator(); i.hasNext();){
> 						AtomicSymbol 
> sym = (AtomicSymbol)i.next();
> counts.increaseCount (sym,1.0);
> 						}
> It compiles but gives a class cast exception when I try to run it.  
> Won't accept (AtomicSymbol)i.next();
> It seems that seq.iterator() returns an iterator over Symbols and not 
> AtomicSymbols?
> any ideas?
> thanks
> -Ben
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