Bioperl: Re: FTHelper changes

[hilmar.lapp@pharma.Novartis.com]

"(23.45)..102" is spat out, but "23.45" is eaten
and becomes "23..45" in the output file.

     It is good that you look at the generated output, because I haven't so far,
     nor do I understand the printing code. I agree that for the release the
     output should be equivalent to the input, although I think SwissProt can be
     a (documented!) exception here because otherwise you do not have any
     SwissProt parser at all.

     For the main trunk (in the notion of "unstable" development release), I
     don't care so much, although such inconsistencies should again be
     documented, so that people know of their risk. GenBank parsing and soon
     SwissProt parsing is something we for instance need, and this is for input
     only. So, I don't care that the feature wouldn't print out correctly, as
     long as I have it available for doing something with it (for the example
     mentioned, there ought to be a 'zero_width_feature' or a similar tag, but
     I'm not sure).

     This leads me to following concern:
     Do we want to support the notion of uncertain locations of features in
     BioPerl or would I have to support these by my own classes.

     If we want to, this involves extending the current capabilities of feature
     objects in BioPerl. Does anyone already have an idea in mind of how to
     achieve this in the best way? I must admit that so far I have rather
     limited insight into BioPerl's object hierarchy and the ideas behind it.

     Thanks for your comments.


     Cheers,

          Hilmar




=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================