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Hi Allyson,

Pass the two files on to Morgan. libAnnotationSBML has a "format"
method that (amongst other things) reads the contents of annotations
then writes them out again. When they're written out, they'll be
written out in some reasonably consistent order. You should be able to
"diff" 'em and they should then be the same.

org.mcisb.sbml.SbmlUtils is the class. format( File in, File out ) is
the method.

Cheers,

Neil.

Neil Swainston
Experimental Officer

Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
England

On 10 Sep 2009, at 15:32, Allyson Lister wrote:

> Hi all,
>
> I realize that there is no inherent order of the various MIRIAM
> annotations
> in an <annotation> element, and I certainly don't think there should
> be any
> such thing.
>
> However, saying that, I'm trying to do a diff between two SBML
> files, and
> I'm running into trouble when comparing the MIRIAM annotations.
> Essentially,
> the ordering in the file as downloaded from BioModels seems to be
> different
> than the ordering of the messed-with version of the SBML file that I
> created
> and am trying to compare against.
>
> I know that if I just run libsbml's Reader and Writer over the
> BioModels
> file, the outputted file is identical to the one coming in.
> Therefore it
> must be my "messing" that is changing the order of the MIRIAM
> annotations.
>
> I guess all I'd like to ask at this stage is:
>
>
> 1. Does the order with which the CVTerms are added make a
> difference to
> the ultimate outcome of the way the MIRIAM annotations are written
> out? (I'm
> guessing yes from my experience)
> 2. Is there any helper method to ensure that the ordering of new
> CVTerms
> would be identical to the "biomodels/sbml approved" ordering?
>
> This #2 part would make my "diff" life much, much easier.
>
> Thanks very much,
> Allyson
>
> --
> Allyson Lister
> http://themindwobbles.wordpress.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University
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