[Biococoa-dev] BCPairwiseAlignment & BCScoreMatrix

Koen van der Drift kvddrift at earthlink.net
Fri Mar 11 19:46:12 EST 2005

Another ignorant question:

what's the difference between alignment and pairwise alignment? 
Regarding their place in BioCocoa, should BCPairwiseAlignment be a 
subclass of BCAlignment? Right now it isn't, although I would expect 
that based on their names.

- Koen.

On Mar 11, 2005, at 4:31 PM, Alexander Griekspoor wrote:

> On 11-mrt-05, at 17:47, Philipp Seibel wrote:
>> 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.
> Absolutely no problem!
> Just to make things clear for everyone, with alignments we're talking 
> about two kinds of matrices. The one with the scores one which are 
> also known as substitution matrices,  although you can implement them 
> as arrays as well like phil demonstrated before.
> These are different  from the matrices used during the actual 
> alignments (with the 3 phases as you might remember). For the first we 
> create the scoring matrix objects, the second are probably only used 
> internally in the algorithm implementation.
> So Koen, in this light your remark:
>> 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?
> The actual matrix used for calculation is the second one. But keeping 
> the matrix only saves you the memory allocation, but different 
> alignments fill the matrix differently so there's no use in keeping it 
> around as it has to be refilled again with scores based on algorithm, 
> penalty scores, gap costs etc. As most time goes into filling the 
> matrix and tracing it back after the fill, you can't reuse it. Also, 
> most algorithms that are subquadratic for memory requirements, chop up 
> the matrix and use a divide-and-conquer approach because it's the 
> storage of a complete-sized matrix that forms the memory problem.
> Does this make any sense?
> Alex
>> @Charles: Perhaps we could discuss your symbol to int mapping in more 
>> detail, i didn't get the idea. ;-)
>> Phil
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>                     ** Alexander Griekspoor **
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