[Biococoa-dev] converting from 3-letter code to 1-letter code
Koen van der Drift
kvddrift at earthlink.net
Wed Aug 31 17:53:04 EDT 2005
[repost - I never received the first one back]
On Aug 28, 2005, at 9:00 PM, Koen van der Drift wrote:
> Hi,
>
> To enable the reading of PDB file, I added some code that converts
> the three letter code for the amino acid to a string of 1-letter
> code. Right now it is in readPDBFile in BCSequenceIO. After
> fiddling with subdictionaries and arrays, I suddenly realized it
> would be easier with using a symbolset.
>
> I will commit the code if cvs lets me, so it might take a while
> for the code is available. In the meantime, I have these questions:
>
> 1. Maybe we should move this to a separate method, in case there
> are more file formats that use the three letter code? (I guess the
> answer is yes)
>
I an attempt to make it more usuable, I moved the code to a separate
method in BCSequence, instead of BCSequenceIO. Here's some code:
// new method:
+ (BCSequence *)sequenceWithThreeLetterString:(NSString *)aString
symbolSet:(BCSymbolSet *)aSet
{
NSString *oneLetterString = [self
convertThreeLetterStringToOneLetterString: aString symbolSet: aSet];
return [[[BCSequence alloc] initWithString:oneLetterString
symbolSet:aSet] autorelease];
}
// another new method:
- (NSString *)convertThreeLetterStringToOneLetterString:(NSString *)
aString symbolSet: (BCSymbolSet *)aSet
{
....do the conversion, and return a new string
}
I have been staring at this for a while now, but the compiler says that:
'BCSequence' may not respond to
'+convertThreeLetterStringToOneLetterString:symbolSet:'
As far as I can tell (also in the .h file)
convertThreeLetterStringToOneLetterString is a regular method, not a
class method. I must be overlooking something, but I cannot see it.
Any ideas?
thanks,
- Koen.
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