[Biojava-dev] Pairwise Alignment methods

[Mark Schreiber]

Hi Felipe -

Thanks for the input on this. As a general rule the GC should never be
called from code. Generally this degrades performance of the JVM.
Unless there is a very good reason I will remove this. Probably you
are right a method parameter may work better.

- Mark

On Jan 24, 2008 1:47 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> 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
> > >
> >
>
>