[Biococoa-dev] More on BCSymbolSets

[Koen van der Drift]

On Feb 28, 2005, at 12:04 PM, John Timmer wrote:

> So, let me refine my suggestion.  We have a group of immutable sets 
> that
> represent all the commonly used symbol sets.  We initialize these out 
> of a
> plist file

I like the idea of using plists. This makes it much more flexible and 
allows users to create their own symbolsets.

> Finally, I just want to sound a couple of notes of caution:
>
> By having a specific symbol set associated with a sequence, it means 
> we have
> to do error testing whenever new symbols are added to the sequence, two
> sequences are combined, etc.

I think this one of the main reasons to use symbolsets. It allows the 
user to filter input and prevent illegal characters to be added.

>   We will ALWAYS have to make sure the symbol
> set and sequenceArrays are rationalized.  I actually like this, but got
> scolded for being excessively cautious when I implemented something 
> like
> this a while back ;).

The advantage of symbolsets is that you ony have to test once. As soon 
as a symbol is added to an array we know it belongs to taht symbolset, 
and there is no more need for testing. IIRC, you were testing each 
symbol everytime in many methods, which was thought of as being too 
careful.



- Koen.