Now unmarshals SBML documents to java using the SBML XML schema
Starting to access the juicy model details from an unmarshalled SBML document.
Stores SBML species in an array
Extracts data from SBML annotations
Fixed species list loop, SVP only is now one TU
updating gitignore, hopefully not breaking everything this time
i r bad porgamer
still bad
isolated promoter data from list of rules
.gitignore update
removing model files from repo, will put them in an examples folder eventually
Rewriting from one long main method to something nicer and more extendable
Manually written eugene file for comparative & testing purposes
SBML data now returns as an arraylist of Parts objects, representing a device. SBML data is hand-picked for now.
.gitignore update
First prototype - ONLY SVP.XML WILL WORK. SVP.xml SBML model is converted to a valid Eugene file. Output file checked by running automated.eug in Eugene and getting a Pigeon CAD visualisation back.
Mo' models, mo' .gitignore updates
Mo' outputs, mo' .gitignore updates
Wasn't working before. It now is. What have I changed? I'm don't know. I should commit just in case.
Promoter detection is now automatic. New method returns the indexes of all occurences of a given search string (e.g. mts:Promoter / mts:Shine_Dalgarno_sequence)

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