Patrial FBC2 extension support #7
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Adding an 'SBMLResourceIdentifiers' class for importing references on Genes, Proteins, Metabolites, and Reactions. SBML importer can now read geneProduct FBC objects and turn them into Protein objects. Importer also reads “is” and “isEncodedBy” MIRIAM biological qualifiers and parses them into SBMLResourceIdentifiers. Correctly reading the fbc:upperFluxBound and fbc:lowerFluxBound values. Clarifying some exceptions in rangedNumber, Proteins, and Genes. Additional checking for SBML import to work nicely with versions of the library lacking FBC. Extracting chemical formula from FBC SBML attribute for metabolites. Adding code to track 'non-canonical' proteins - i.e. proteins that represent unknown connectors between genes and reactions. Untangling a series of circular import dependencies that prevented modular testing of parts of the JQMM including sbmlio.
Changes to reflect the slight change in calling convention needed by the dependency untangling.
Member
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Note: We need this to use jQMM with P. putida, as the only up-to-date models are in SBML3. |
Contributor
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ok, cool |
Contributor
Author
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If you give me a link to the model you use, I can test it... |
Member
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The putida model isn't ready yet... we have to convert the identifiers to BiGG format. Can we just test with the smbl3 version of iJR904 (http://bigg.ucsd.edu/static/models/iJR904.xml)? |
Contributor
Author
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iJR904 works fine - it's one of the models I used to test Arrowland. |
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Support for reading SBML3 files with FBC2 extension. Note that WRITING SBML3 with FBC2 is not supported in these changes. Writing SBML will still result in a non-FBC2-format file.