[Biojava-l] Questions

[Ron Kuhn]

Is BioPerl more mature or do they have the same issues? Should I look
elsewhere or should I do my own parser?
Ron

-----Original Message-----
From: Thomas Down [mailto:td2@sanger.ac.uk]
Sent: Tuesday, October 16, 2001 10:44 AM
To: Ron Kuhn
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] Questions


On Tue, Oct 16, 2001 at 10:29:28AM -0400, Ron Kuhn wrote:
> Is there a forum related to the BIOJAVA software??? That is really where I
> should be posting this email.

Yes, this mailing list is where most discussion happens.  Please
post any questions/bug reports/suggestions/patches here.

> I am trying to use your software to parse Genbank and SwissProt flat
files.
> I made 2 fixes (1 for each) and all seems to work fine. I am successfully
> parsing the files and interpretting sequences. My only problem is that the
> information about the references to the sequences should be heirarchical
(in
> SwissProt - the RP, RX, RA, RT and RL fields relate to a specific RN) but
> the object used to hold the reference information (Annotation) is NOT (XML
> is though). If multiple RNs exist and 0 or more RTs exist per RN, then how
> are we supposed to relate the RTs to the correct RN???

BioJava's currently not very good at handling the metadata associated
with sequence files -- any improvements would be welcome.

When the Annotation objects were originally designed, there
was a general suggestion that they should be used as hierarchies
to model this kind of thing.  So you could have a structure like:


   Top-level annotation
          |
          |      references
          |----------------------> ArrayList
                                      |------->Reference annotation
                                      |           |
                                      |           +----> journal
                                      |           +----> author
                                      |           +----> title
                                      |
                                      +-------> Another reference

Actually, it might be even better to have a dedicated object
model for bibliographical references, but nobody has been particualary
enthusiastic about working on this.


     Thomas.                                       
       
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