[Biococoa-dev] Nomenclature

[John Timmer]

> 
> Could we agree on the following names? If anyone prefers another one, let it
> know, but it would be nice if we can decide what to take (saves a lot of
> typing ;-) 
> 
> BCSymbol (instead of BCSequenceUnit)
> | 
> | 
> ------------ BCNucleotide (instead of BCBase)
> | 
> | 
> ------------ BCAminoAcid
> | 
> | 
> ------------ etc (think BCSaccharide and alikes)
> 
> I think BCFunctionalGroup should be a feature (like phosphates) and not a
> symbol, but perhaps I am wrong here.
> 
> For sequences I would propose to take the names Koen already mentioned:
> 
> BCSequence 
> | 
> | 
> ----------------BCSequenceDNA
> | 
> | 
> ----------------BCSequenceProtein
> 
Okay, the BCSequenceDNA was just a first stab at thinking of the methods
we¹d want.  Once I filled them in, I¹d think about which ones would work
generally across all sequences, and move them to the superclass, which I
haven¹t defined yet.  What you saw was the twistings of my mind in action ;)

That said, mentally I was reserving BCSequence as the wrapper for a type of
sequence and all the additions ­ features, format conversion, etc.  I was
thinking more along the lines of:

                       BCSequenceGeneric
                        |
BCSequence      | 
Contains an       |
Instance of ->   ----------------BCSequenceDNA
                        |
                        |
                        ----------------BCSequenceProtein
> 
That said, it would violate the naming conventions I¹d argued for, so I
hereby reject my own thinking.  Given that, what do we call the wrapper
object on the left then?
> 
> 
> I think this all makes life a bit simpler to implement John. I like the
> addition of the proposed equality testing methods you mention:
> - (BOOL) complementsNucleotide: (BCNucleotide *)entry; (would be BCNucleotide
> specific) 
> - (BOOL) representsSymbol: (BCSymbol *) entry; (do you mean here to test
> whether this base belongs to an ambiguous group?)
> And would like to add:
> - (BOOL) isEqualToSymbol: (BCSymbol *) entry;
> 
Wouldn¹t NSObject¹s ³isEqual² method work just as well here?

And the second method (which I wrote this morning) looks like:
- (BOOL) representsBase: (BCSequenceDNABase *) entry {
    if ( [[self matches] containsObject: entry] )
        return YES;
    return NO;    
}
> 
It works if you have an ambiguous base as self, and get handed another base.

JT

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