T cell simulation
version 0.12
Copyright (C) 2003 Dennis L. Chao

driver/Driver.java - Main event loop for the simulation
driver/DriverEvent.java - Class to describe simulation "events", such as
seeding the random number generator and injecting antigen.  Used by the
user interface to communicate with the control loop.
driver/DriverView.java - The graphical interface for the running simulation.
driver/DriverNoView.java - The batch-mode interface for the running simulation.
driver/Inject.java - Dialog for injecting antigen into the running simulation.
driver/PopGraph.java - Plots the antigen and T cell population levels on
in a window.
driver/PopMap.java - Plots the relationships among the antigens and the
T cell clones.
driver/StartScreen.java - The dialog that prompts the user for the
initial conditions for the simulation run.

lib/KnuthRandom.java - Random number generator based on Knuth's.
lib/Map2d.java - Used by PopMap.
lib/Probability.java - Miscellaneous mathematical functions.

sim/Antigen.java - Stores virus parameters and infected cell numbers for
a single antigen.
sim/BitCompositionNode.java - Used by BitCompositionSet.
sim/BitCompositionSet.java - Used by XorMatchRule.
sim/Clockable.java - Interface class for simulation objects.
sim/Constants.java - Stores simulation constants.
sim/HammingMatchRule.java - Hamming string distance rule implementation.
sim/ManhattanMatchRule.java - Modified Manhattan string distance rule
implementation.
sim/MatchRule.java - Interface class for string distance rules.
sim/PeptideString.java - Stores an antigen's peptide and MHC strings.
sim/Population.java - Superclass for storing a population's (e.g., an 
Antigen or a TCell) basic parameters such as its name and growth rate.
sim/SelfAntigen.java - Stores a self peptide and its presenting MHC string.
sim/TCRGenerator.java - Generates a T cell repertoire based on existing 
antigens.
sim/TCRString.java - String class for peptides and MHC strings.
sim/TCell.java - The class for T cell clones.
sim/TCellCohort.java - Used by TCell.
sim/Uninfected.java - The uninfected cells (i.e., the "body").
sim/WaitingCells.java - Used by TCellCohort.
sim/XorMatchRule.java - Xor string distance rule implementation.

