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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]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? > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
