[Biojava-dev] Pairwise Alignment methods

[Felipe Albrecht]

Hello,

I think that it can be solved by a simple way:
Implement (or just copy and cut) a pairwiseAlignment utilizing SymboList as
parameters and do no creating a alignment, just the calculating it and
returning the value.

Another thing that is a bit stange for me, is the utilization of garbage
collector direcly, that is: The field "scoreMatrix" is a class field, why at
the end of pairwiseAlignment it is set to null and the garbage collector
run? It is not better (and simpler) to use scoreMatrix as method variable?

I'm annexing the class code with my changes that is doing well the (4^8) *
(4^8) SymbolList pairwise alignments that I am needing :-)

Thank you,

Felipe Albrecht



On Jan 23, 2008 6:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> Hi Felipe -
>
> I agree this is a barrier to ease of use. Even if Sequences are
> required internally for some obscure reason there is no reason why
> dummy Sequences cannot be made inside the aligner.  These sequences
> could be given names like 'query' and 'subject' or even 'seq1' and
> 'seq2'.
>
> I will take a look at adding some methods.
>
> Best regards,
>
> - Mark
>
> On Jan 23, 2008 2:58 PM, Felipe Albrecht <felipe.albrecht at gmail.com>
> wrote:
> > Hello all,
> >
> > I have a simple question about pairwise alignment classes (SmithWaterman
> and
> > NeedlemanWunsch):
> > Why it is necessary two Sequence for alignment and not two SymbolList?
> >
> > Example, I have a SymbolList collection to align between then,
> > by this way I need to create some "dummies"  Sequence for to do the
> > alignment.
> >
> > Reading the source, I saw that the unique field that is exclusive to
> > Sequence is the name, for the alignment output,
> > but if I need only the alignment result, it is useless.
> >
> > It is not possible to override the pairwiseAlignment to accept
> SymbolList or
> > may be a new method that the parameters are 2 SymbolList and returns the
> > alignment score?
> >
> > Thank you
> >
> > Felipe Albrecht
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
>
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