Forums

Hi all,

Related to this mail, recent chatter about developing a pure Java
version and - dare I say it - the speciesType discussion, could I
throw in a cheeky request for implementation of equals / hashCode
methods for SBases in libsbml?

I don't know what the equivalents are in C++, but these two methods -
if implemented correctly - are enormous time-savers, and would be
immensely useful if and when we ever get around to merging our models.

Also, if the equality comparison was made at the level of annotations,
as I suspect they should be (two "things" that share "is" annotations
are equal), then it may act as an encouragement for us all to use
annotations, rather than the id="my_thing_in_this_compartment" syntax
that we've all grown to know and love.

This may reignite the "we can't annotate everything" discussion, but
given that we don't implement any kind of equality operators at the
moment, nobody would lose anything, and it also may act as an impetus
to solve outstanding "we can't annotate everything" problems.

Cheers,

Neil.

P.S. Further reading for those with lots of time on their hands this
weekend: http://java.sun.com/developer/Books/effectivejava/Chapter3.pdf

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
>> ____________________________________________________________
>> To manage your sbml-interoperability list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
>>
>> For a web interface to the sbml-interoperability mailing list, visit
>> http://sbml.org/Forums/
>>
>> For questions or feedback about the sbml-interoperability list,
>> contact sbml-team@caltech.edu
____________________________________________________________
To manage your sbml-interoperability list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability

For a web interface to the sbml-interoperability mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-interoperability list,
contact sbml-team@caltech.edu