[Biojava-l] AGAVE usage

[Brian King]

Patrick,

Yes, I think the intention of having the FeatureSet at
the top level was to allow you to pass around
annotations without the associated sequence.  This can
be useful when you need to separate different
annotation types into different files.  If you are
validating using the XML Schema definition of AGAVE
(agave.xsd), XML Schema doesn't require a root
element, so you can have any globally scoped element
as the document root.  Most of the elements have
global scope, so a document with a single seq_feature
should be valid.  

I'm working on a version of the AGAVE IO package that
spits out AGAVE 3, so I have a chance to reduce some
of the flakiness that was mentioned.

Brian


-------------------------------------------------
Looking at the schema, I believe that you can push
around annotations
without the sequence.

The root element, sciobj, can have zero or more of any
of the 
following:
      bio_sequence
      contig
      FeatureSet
      chromosome.

So, I think what you are looking for is the
FeatureSet, which contains 
an
annotations element, distinct from the bio_sequence
elements.

Please, an Agave expert correct me if I am wrong.

-Patrick




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