Hi Eric -
I think the problem is caused by trying to determine the ambiguity for a
set that contains the gap symbol. In reality there is no IUPAC ambiguity
code for anything paired with a gap. An ambiguity is like saying either
this nucleotide or this one (as in an ambiguous DNA sequence read). It
can't really cover the concept of either this nucleotide or a gap
- Mark
Eric BELLARD <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/14/2004 06:40 PM
Please respond to eric
To: [EMAIL PROTECTED]
cc:
Subject: [Biojava-l] ClassCastException during ambiguity calcul
Hi,
I'm calculating ambiguity of symbol sets and i've got
a class cast exception. I've managed to isolate the
bug. The following code triggers the exception:
Set lc_set = new HashSet();
SymbolList lc_sequence =
DNATools.createDNA("AG");
Iterator lc_i = lc_sequence.iterator();
while (lc_i.hasNext()) {
lc_set.add(lc_i.next());
}
lc_set.add(DNATools.getDNA().getGapSymbol());
try {
Symbol lc_symbol =
DNATools.getDNA().getAmbiguity(lc_set);
System.out.println(lc_symbol.getName());
} catch (IllegalSymbolException e) {
throw e;
}
If I don't add the gap symbol in the set I don't have
the exception.
Even an excpetion must be thrown during this code
execution, I don't think the class cast exception is
the good one.
Does someone have a clue? Is it a bug? Do you want me
to propose a fix?
I think I got good java skills but the worst
biological skill you've ever seen :-)
Regards,
Eric
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