[Biococoa-dev] BCPairwiseAlignment & BCScoreMatrix

[Philipp Seibel]

Hi everybody,

i just made some modifications to the Alignment stuff. I followed Alex' 
advice and made the Scoring Matrix char based. every symbol is casted 
to a char and used as a number key for the matrix. With this approach 
we have some memory overhead, but we're much faster, because we need 
not to ask the NSArray for the Symbol index everytime.

I also copied some of alex' code ( sorry for that alex ;-) ) to provide 
a short overview over the global alignment.

@Charles: Perhaps we could discuss your symbol to int mapping in more 
detail, i didn't get the idea. ;-)

Phil