[Biojava-l] problems with SubIntegerAlphabet

[mark.schreiber at novartis.com]

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" <heatkent at gmail.com>
Sent by: biojava-l-bounces at portal.open-bio.org
03/02/2006 05:15 AM

 
        To:     biojava-l at 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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