[Biojava-dev] Alignment algorithms

[mark.schreiber at group.novartis.com]

As a word of advice, you will find it much easier to define some 
interfaces at the start such as SubstitutionTable, DPMatrix, DPAlgorithm. 
If you do this you can swap any substitution scoring system like Pam450 
Blosum62 etc into any DPAlgorithm (NW or SW) while using any 
implementation of a DPMatrix (eg a basic one or a memory optimized sparse 
matrix).

I could hopefully commit some basic Interfaces soon which could be 
developed to.

- Mark





Rahul Karnik <rahul at genebrew.com>
10/04/2004 10:05 AM

 
        To:     Mark Schreiber/GP/Novartis at PH
        cc:     biojava-dev at biojava.org, biojava-dev-bounces at portal.open-bio.org
        Subject:        Re: [Biojava-dev] Alignment algorithms


mark.schreiber at group.novartis.com wrote:
> Nope, looks like its gone to the big Hard Drive in the Sky.
> 
> I could recode it if there is interest.

I should have something ready in a couple of weeks. It's a good way to 
get used to BioJava.

Thanks,
Rahul