[Biojava-dev] Pairwise Alignment methods

[Felipe Albrecht]

If you prefer, I can send a diff and should I do the same thing in
SequenceAlignment and NeedlemanWunsch classes?

Thank  you,

Felipe Albrecht

On Jan 24, 2008 5:50 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:

> 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
> > > >
> > >
> >
> >
>