[Biojava-l] Alignments

[David Waring]

Our use of the Phred package is still mostly in development, so I say change
the API sooner rather than latter.

David


> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
> Behalf Of Schreiber, Mark
> Sent: Wednesday, May 15, 2002 3:01 PM
> To: Matthew Pocock; David Waring
> Cc: biojava
> Subject: RE: [Biojava-l] Alignments
>
>
> Hi -
>
> Right off the bat I would like to say that the Phred package was poorly
> designed. I can say that cause I made it ;-)
>
> The major problem with it was that initially I couldn't think of a way
> to store the infinite integer alphabet with the DNA alphabet as a
> cross-product. This problem is actually now solved (see PhredTools). I
> have been very slowly trying to integrate this 'great leap forward' into
> the rest of the Phred package. One nice thing is that a SimpleSymbolList
> can now be constructed over the PHRED alphabet.
>
> The PhredSequence and GappedPhredSequence are actually largely
> deprecated by this improvement although I'm always reluctant to simply
> break stuff as it sounds that David is actually using this stuff a lot.
> One possibility would be to keep the API shell of PhredSequence,
> GappedPhredSequence and gut the internals so they simply become
> convinience classes, I suspect that some API breaking is required but
> keeping it to a minimum would be good.
>
> Another issue that needs solving is the tokenization -> fasta formating
> of the Phred stuff. There are methods that read and write the DNA/ Phred
> score and merge them but they where written for the old situtation where
> the DNA and Phred sequences where kept separate.
>
> Any suggestions on making all this mess look pretty and well designed
> are very welcome.
>
> - Mark
>
>
> > >> Could you explain what Qualitative means?
> > >
> > >
> > > Qualitative is defined in biojava.bio.program.phred package. In the
> > > case of PhredSequence it represents the quality score given
> > by Phred
> > > or Phrap. there is just one method qualityAt().
> >
> >
> > I will check this out. Quality scores are the sort of thing that the
> > integer alphabet is meant to be used for, so I will see how the phred
> > API shapes up to how Thomas and I had envisioned data being
> > represented.
> > It is a corner of the library that I have never visited before.
> >
> > >
> > > What methods would the gapped interface contain? I would be
> > happy to
> > > make GappedSymbolList an interface and add a
> > SimpleGappedSymbolList.
> > > Perhaps that would make people mad. The idea of
> > GappedSymbolList was
> > > that it wrapped another symbol list, adding the ability to view it
> > > with gaps. GappedSequence does the same for a Sequence
> > instance, and
> > > takes care of projecting features from un-gapped to gapped
> > > coordinates. Both classes have (or should have) methods to
> > fetch the
> > > underlying object being viewed. Perhaps the need for your gapped
> > > interface goes away if we have a generic 'View' interface, and code
> > > would walk down the decorating views untill they hit one
> > that has the
> > > funcitonality they want. Grr. Sometimes I don't like OOP.
> > >
> > >
> > > The gapped interface would contain the methods in
> > GappedSymbolList. I
> > > see that we now have GappedSequence which is what I am
> > after. But we
> > > also have GappedPhrepSequence, which with the exception of the
> > > capitolization of method names could implement the gapped
> > interface. I
> > > suspect that renaming GappedSymbolList would cause a bunch of
> > > headaches so a different name for the interface might be in order
> > >
> >
> > Again, I will take a look at GappedPhredSequence and see if
> > it can't be
> > refactored as a gapped view of a phred sequence. Do any phred
> > users have
> > views?
> >
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