[Biococoa-dev] starting BCAlignment

[Koen van der Drift]

On Mar 10, 2005, at 4:54 PM, Alexander Griekspoor wrote:

>>
>> Seems to grow up into an alignment battle between me and you LOL ;-).
> No, please no, that was exactly what I didn't want to do.... sorry for 
> that. The last sentence was purely informative for the others, without 
> any offensive ideas towards your plans.

I'm still reading, but I get the picture now - great expansion!


>>
>> I want to start coding with the BCNeedlemanWunsch, but i'm not sure 
>> whether i should put it into my BCAlignments folder or in the BCTools 
>> folder. I would prefer the BCAlignment folder. What do you think
> I think you're right, it would be nice to keep everything alignment in 
> the BCAlignment folder. In fact I'm not even sure if we even need a 
> tool by smart use of class methods, but time will tell...


I am thinking how this will be used. The end user probably wants to try 
out one type of alignment, see the result, then try another one, 
compare the results, etc. So if we make a BCNeedlemanWunsch, and then a 
BCSmithWaterman where is the actual matrix that is used to calculate. I 
think it is a good idea if we have just one matrix, that is used as a 
basis for each different calculation. It would be a waste if for every 
calculation the starting matrix has to be re-calculated. Or maybe 
that's where BCMatrix comes in place?

cheers,

- Koen.