Hi -
The actual code in seqString() method gets the "default" tokenizer from
the parent Alphabet (SubInteger in this case) and asks it to tokenize the
SymbolList. It is a bug that SubIntegerAlphabet doesn't have a "default",
however, if you use the code from SimpleSymbolList's .seqString() method
as an example you can do the equivalent operation "manually" as a work
around using "token" instead of default.
Let me know if you have problems...
I will also fix this bug in CVS shortly.
- Mark
"Heather Kent" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
03/02/2006 05:15 AM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] problems with SubIntegerAlphabet
Hi,
i'm currently having a problem with the
IntegerAlphabet.SubIntegerAlphabetclass. When i make a call to the
seqstring() method from
AbstractSymbolList i get an error, No such element Exception "parser not
supported by Integer Alphabet yet" in the getTokenization method of my
SubIntegerAlphabet class
the call from seqstring to getTokenization sends "default" as the string
name .....the getTokenization method for the IntegerAlphabet class accepts
both "token" or "default" but the SubIntegerAlphabet class only accepts
only
"token"
can anyone help me find a way around this when i'm working with
SubIntegerAlphabets??
thanx
Heather
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