[Biojava-dev] DNATools.forSymbol

[Matthew Pocock]

Hi,

I think this is a throw-back to the days before alphabet indexers and 
symbol tokenizers. Are we going to end up with two methods that do the 
same thing? Should we deprecate/remove one of them?

Matthew

Schreiber, Mark wrote:
> Hi -
> 
> This method works on a switch statement which doesn't have a case for n
> but I don't see any reason I cannot put one in. I may even put one in
> for all the IUB ambiguity codes.
> 
> - Mark
> 
> 
>>-----Original Message-----
>>From: Rhett Sutphin [mailto:rhett-sutphin at uiowa.edu] 
>>Sent: Friday, 14 March 2003 11:14 a.m.
>>To: Schreiber, Mark
>>Cc: biojava-dev at biojava.org
>>Subject: Re: [Biojava-dev] DNATools.forSymbol
>>
>>
>>Hi Mark,
>>
>>Thanks for the amazingly quick response.  (With a patch, no less.)
>>
>>But I'm still wondering why DNATools.forSymbol('n') should throw an 
>>exception while DNATools.createDNA("n") does not.  Is there a reason?
>>
>>Rhett
>>
>>On Thursday, March 13, 2003, at 03:51  PM, Schreiber, Mark wrote:
>>
>>
>>>Hi -
>>>
>>>There is no good reason other than it is a weakly observed 
>>
>>convention
>>
>>>to
>>>use lower case letters for DNA and RNA and upper case for Protein. I
>>>have changed the methods in DNA and RNA tools to be case 
>>
>>insensitive. I
>>
>>>have commited the changes to biojava-live.
>>>
>>>- Mark
>>>
>>>
>>>
>>>>-----Original Message-----
>>>>From: Rhett Sutphin [mailto:rhett-sutphin at uiowa.edu]
>>>>Sent: Friday, 14 March 2003 10:44 a.m.
>>>>To: biojava-dev at biojava.org
>>>>Subject: [Biojava-dev] DNATools.forSymbol
>>>>
>>>>
>>>>Hi,
>>>>
>>>>I have what might be a stupid question:  why isn't
>>>>DNATools.forSymbol(c) the same as
>>>>DNATools.createDNA(Character.toString(c)).symbolAt(1) for all c? 
>>>>forSymbol only works for lowercase a, c, g, and t, while createDNA 
>>>>handles uppercase and lowercase of the whole DNA alphabet, 
>>
>>plus gaps.
>>
>>>>Is there a special meaning/use of forSymbol that warrants this
>>>>difference in behavior?
>>>>
>>>>Just curious,
>>>>Rhett
>>
>>
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