[Biojava-dev] DNATools.forSymbol

[Schreiber, Mark]

I have changed the forSymbol methods of DNA and RNATools to use the
SymbolTokenizers for their alphabet I have also added all IUB ambiguity
codes to RNA in the AlphabetManager.xml. All ambiguity codes are now
available to both alphabets and to the forSymbol() methods.

Tests seem to pass.

- Mark

> -----Original Message-----
> From: Rhett Sutphin [mailto:rhett-sutphin at uiowa.edu] 
> Sent: Friday, 14 March 2003 11:40 a.m.
> To: Schreiber, Mark
> Cc: biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] DNATools.forSymbol
> 
> 
> Hi Mark,
> 
> Is there any reason not to use the existing converters to do 
> this?  For 
> instance
> 
> return DNATools.createDNA(String.valueOf(token)).symbolAt(1)
> 
> could be the entire method body.  That could be a little slower.  But 
> on the other hand, it uses the AlphabetManager alphabet 
> definitions so 
> it would enhance maintainability.
> 
> Rhett
> 
> On Thursday, March 13, 2003, at 04:22  PM, 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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