sbmlteam/jsbml: JSBML 0.8-β1

This the first beta release of JSBML 0.8, JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.

For more details, please visit http://sbml.org/Software/JSBML

• [Tracker issue #3137967] Namespaces in the sbml element were incorrectly parsed, some known namespaces like html were not kept for examples. This is fixed, thanks to Paulo Maia for reporting this.

• problem of output indentation for notes, when there is several top level elements.
• the method SBMLDocument.checkConsistency() is not working. There is a problem in the parsing of the XML return by the sbml.org validator.
• dependency on the sbml.org validator which might not be robust enough (you cannot submit a file bigger 15MB for example). It would be better to be able to install your own localy or at least have several mirrors. We will have to see how it performs.
• in a mathML block, if one 'ci'element is suppose to represent a functionDefinition but the id is not a valid id, the type of the ASTNode is not set properly, so there are some errors when trying to use the corresponding ASTNode tree. (cf model generated by COBRA)