[Biococoa-dev] starting BCAlignment

[Alexander Griekspoor]

>  [code snippet ]
> I think it's a quite good approach, but we have to decide wheter we 
> want to "ask" the matrix with two BCSymbols or just with chars. Take a 
> look at my recent implementation of the scoring matrix. It's perhaps 
> slower than this one, but more comfortable. I think we just have to 
> test the performance, when we've done the first algorithm.
I'm a big advocate of using our symbols and sequences natively wherever 
possible, so I'm absolutely in favor of your implementation!
>
>> Again, my experience is pretty limited, so I believe you immediately 
>> that using a simple int array is faster than a matrix, and certainly 
>> much simpler!!
>
> My experience is limited to several java alignment implementations, so 
> i've never done this with a good programming language ;-)
Oooohhh, you'd better hope no one from that camp is listening ;-) LOL
I hope you don't see my remarks as obstructions to your plans, I'm very 
much looking forward to your implementations!
Cheers,
Alex

*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut
              http://www.mekentosj.com/enzymex

*********************************************************


*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut
              http://www.mekentosj.com/enzymex

*********************************************************