SBML Level 2 Parsing Library for Java Tutorial

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SBML Level 2 Parsing Library for Java: Tutorial. Note: The software packages provided are betas, and intended to serve to further the …

Website: sbml.org | Filesize: 66kb

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SBML Level 2 Parsing Library for Java: Tutorial
Note: The software packages provided are betas, and intended to serve to further the
community’s efforts, find bugs in the software, and to clarify SBML itself through
discussion. My email is mvass@vt.edu.
Version 1 follows the latest specification of Level 2 given. It incorporates a minimal level
of error checking above that of type checking on fields where integers are called for
instead of strings. It uses SAX2 to parse the XML file itself. RDF’s are supported, but are
treated as strings and are not separately parsed. Facilities for the separate parsing of
MathML 2.0 are provided.
Vectors are used to represent the list structure for elements in the SBML document. So,
when accessing an object from the functions vector in the model it will be of type
FunctionDefinition.
SBML Reading and Writing
Reading: Package - jigcell.modelbuilder.sbml
To read in an SBML 2.0 file, use the SBMLLevel2Reader class. Simply provide the
constructor with the name of the file and a new instance of Model. Your Model instance
will now contain a representation of the SBML 2.0 file that corresponds (as close as
possible) to the data types…