[Biojava-dev] Pairwise Alignment methods

[Mark Schreiber]

Hi Felipe -

I agree your method is more efficient but I think it violates the
SequenceAlignment interface which would cause compatibility problems.
I also wonder what should happen if a user calls the getAlignment()
method if you have only calculated a score.

instanceof is potentially expensive but it is nothing compared to
actually performing the SmithWaterman.

Biojava is somewhat memory heavy but this is largely because it is
object oriented. Certainly something in C would be lighter and faster
but the whole point in using Java is the relative benefits of object
oriented design.  While ultra optimized algorithms where once a major
feature of bioinformatics this is becoming less necessary as standard
desktops are now equivalent to the super computers of 5 years ago.

I actually find the SW and NW to be reasonably fast. This is because
all the heavy lifting is done in loops that the JVM presumably
compiles and executes natively.

- Mark


On Jan 25, 2008 3:40 AM, Felipe Albrecht <felipe.albrecht at gmail.com> wrote:
> Hello,
>
> I saw the commit and I think that this solution is not the better.
> I think it because you are creating internally two Sequence and probably the
> programmer will not use others alignment information,  he will use only the
> score.
>
> Because it, I think that if you have 2 SymbolList, just do the alignment and
> return the score, as I did.Otherwise, If the programmer want the "visual
> alignment", he should create externally the SimpleSequences, it is, not the
> method must do it.
>
> IMHO, one [serious] problem in biojava is the memory consumption, it have
> not "lightweight" classes or methods that do the things quickly. Because it,
> may be is a good choice to have a method that simply gives the alignment
> score, and not do the others things, like backtracking. Another think, the
> cost of the "instanceof" is high.
>
> Thank you,
>
> Felipe Albrecht
>
>
>
>
> On Jan 24, 2008 11:35 AM, Mark Schreiber <markjschreiber at gmail.com> wrote:
> > 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
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
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