[Biojava-dev] PhredTools.getPhredSymbol(dna,int) with ambiguity symbol

[Schreiber, Mark]

My mistake for relying on SymbolTokenization, not a good solution in
this case :(

> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Thursday, 14 November 2002 8:47 a.m.
> To: Jim Johnson
> Cc: Schreiber, Mark; biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] PhredTools.getPhredSymbol(dna,int) 
> with ambiguity symbol
> 
> 
> Hi Jim,
> 
> I've fixed this in the version in CVS. There is now a JUnit 
> test-case to 
> catch this in the future. There was some rather baroque code 
> in there to 
> work arround an API deficiency in Alphabet manager that was not 
> handeling ambiguities gracefully. Sory about that.
> 
> Matthew
> 
> Jim Johnson wrote:
> > Mark,
> 
> > However, I'm getting exceptions from
> > PhredTools.getPhredSymbol(Symbol dna, Symbol integer)
> > when I encountered an ambiguity symbol, e.g. 'n'.  
> > 
> > Do you have any advice as to using PhredTools with regards
> > to ambiguity symbols?
> > 
> > Thanks,
> > 
> > JJ
> > 
> 
> 
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> BioJava Consulting LTD - Support and training for BioJava 
> http://www.biojava.co.uk
> 
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