[Biojava-dev] Pairwise Alignment methods

[Mark Schreiber]

Hi -

I have just commited changes that let you use SymbolLists in all parts
of the NW and SW SequenceAlignment objects.

As you suggested I made the matrix a method local variable. I also
removed calls to the garbage collector.

This can be checked out from SVN.

- Mark

On Jan 24, 2008 9:05 PM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> 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
> > > > >
> > > >
> > >
> > >
> >
>
>