[Biococoa-dev] more ideas

[Koen van der Drift]

Hi,

Just reading through a few posts from today, and here are some misc 
comments I try to post in between the tornado warnings. I'll try to 
post a longer reply later today.

I think the structure of classes could have an additional base class 
from which noth BCSymbol as BCSequence can derive. Again, this 
simplifies things a little bit:


BCRoot
|
|
-------BCSymbol
|	|
|	|
|	------------ BCNucleotide
|	|
|	|
|	------------ BCAminoAcid
|	|
|	|
|	------------ etc (think BCSaccharide and alikes)
|
|
------- BCSequence
	|
	|
	----------------BCSequenceDNA
	|
	|
	----------------BCSequenceProtein


BCRoot:		NSString *name

BCSymbol:	NSString *symbol;
			NSDictionary *properties

BCSequence:	NSMutableArray *symbolList
			NSMutableDictionary *featuresList (key: position, value:feature)

BCSequenceDNA: 		complement, etc
BCSequenceProtein: 	MW, pI, etc


Regarding the complement discussion, wouldn't a member "complement" in 
BCNucleotide (either a char or string or pointer to object) be much 
easier? You only need to set it up once.

Also when maintaining a featuresList we have to update the keys 
indicating the position constantly when the sequence is edited. So that 
needs a little more thought.


- Koen.