iDynoMiCS v1.1 on 17 Jan 2013

The current state of the code. In the source code only the .java files
are included, and so the .class binaries need to be compiled (e.g.
Eclipse will do this automatically)
Minor bug fix
Minor fix: Exception output changed in XMLParser
first push with java 7 bug fix
planktonics and biofilms integrated (except desloughing). Begun work on
PlantonicMangager and implementing a planktonicTimeStep
Created PlanktonicManager.java to handle the higher-resolution
planktonic time stepping. Included logic to detect if a planktonic is
close enough to the biofilm to attach, but have not implemented
attachment yet.
simple Planktonic attachment to biofilm complete
VERY simple chemotaxis implemented. ChemotaxingPlanktonics move up,
down, left, or right depending on the concentrations of surrounding grid
cells. Responds to high concentration of MyCOD as repellent.
added print statement in idynomics.java main method
Incorporated Andrew n's AI2 production protocol adjustments. Added
capability for planktonics to become a single different species as they
join biofilm, specifying this new species in the protocol file.
Note: many parameters are still hard-coded (not read in from protocol
file) for now
Added Andrew N's AI2 protocols. Planktonic joiners now become a new
species defined in protocol file

Note: many parameters still hard-coded. Will be read in from protocol
file in future.
Merge branch 'master' of https://github.com/codicorn/iDynoMiCS.git

Conflicts:
	bin/simulator/Planktonic/PlanktonicManager.class
Added fixes for a huge bug that was occurring due to planktonics being
registered in the padded grid cells. Bacterial leaving partially
implemented. Improved randomness of Planktonic, nonchemotactic swimmers.
BactLeaver first version complete: bacteria on border leave at given ai2
concentration with given probability (reading in parameters from
protocol file not implemented).
Reads all Planktonic/ChemotaxingPlanktonic/BactLeaver/PlanktonicManager
inputs from protocol files. Bacterial Leaving, gradient chemotaxis, and
multiple planktonics implemented. Some changes to matlab routines.
Adding files that are missing from repo in last commit
git test
Re-committing changes after accidental writeover of repository