This week has been the most productive so far and I was able to start coding on schedule.
Last week, I had some trouble generating APIs from 3 schemas (CellDesigner.xsd, sbml-level2-v4.xsd, and sbmlCellDesignerExtension_v4_2.xsd) with JAXB. By removing the annotation definition in sbml-level2-v4.xsd and changing the element in CellDesigner.xsd, my mentor and I have succeeded generating the APIs from schemas. It still needs testing but I was able to obtain the CellDesigner extension from species. Below are all the classes that have been generated.
For the generated APIs, I have been creating some utility classes for easier use. Since CellDesigner annotates model, compartment, species, reaction, speciesReference, and modifiedSpeciesReference, I have created wrapper classes to easily access the extended attributes for all of them. And also for speciesAlias.
For next week, I will do mainly two things. First is to test the generated APIs for the CellDesigner extended attributes. Second thing is to create classes that clones from unmarshalled data structure to the wrapper classes. Once I have checked that all datas are stored properly, I will start implementing the actual converter.