[Biojava-dev] [Bug 2402] Parsed genbank file lacks some annotations from original record

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2402


holland at ebi.ac.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |INVALID




------- Comment #2 from holland at ebi.ac.uk  2007-11-16 09:22 EST -------
Thanks for taking the time to report this. What you have observed is definitely
the intended behaviour.

The db_xref has gone into the CrossRef part of the object model for the parsed
sequence, and the organism has gone into the taxonomy part. If you explore the
object model of the RichSequence you'll discover the information. The reason
for this is that RichSequence is loosely based on the BioSQL schema, and if it
can assign a piece of information it finds in the annotations to a good 1:1
match with a BioSQL concept, then it will do so.

If you write the sequence back out, you'll see the annotations reappear, as the
format is clever enough to gather back together the reorganised information
from the various parts of the RichSequence object model and write it out in the
manner defined by the GenBank format.


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