[Biococoa-dev] functional groups

[Koen van der Drift]

On Mar 5, 2005, at 6:44 PM, Alexander Griekspoor wrote:

> Ideally, say a phosphorylation ADDs something to a symbol, it changes  
> it properties, its mass etc but it does STAY for instance a tyrosine.  
> That's why I came up with the idea of i.e. symbol features (now this  
> is impossible because the symbols are singletons now that I think of  
> it) but than perhaps the other way around, we should add  
> symbolFeatures (single symbol features) that have additional effects  
> than the general features in that they're taken along in  
> calculations).
> What I try to say is that I see a problem when you decide to say  
> incorporate a phosphorylated-tyrosine instead of a standard tyrosine  
> symbol because suddenly part of my BCSequence doesn't respond to  
> representedBy: for instance. Or a methylated guanine does not respond  
> to complement (which is still something to debate whether to return a  
> methylated cytosine then or a non-methylated one but let's leave that  
> for a while).

You are absolutely right. What we need is an extension of the BCSymbol  
class - without changing its basic properties. So forget about the  
BCFunctionalGroup class :) I need to think what would be a proper  
solution for this. In Design Patterns lingo it would probably be the  
Decorator, see eg  
http://www.javaworld.com/javaworld/jw-12-2001/jw-1214- 
designpatterns.html. I will see how that can be applied to ObjC.

Having fun with the snow ?


- Koen.