reorganized code into separate files

@miSim/initialize.m

@@ -0,0 +1,42 @@
+function [obj, f] = initialize(obj, domain, objective, agents, timestep, partitoningFreq, maxIter, obstacles)
+    arguments (Input)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        domain (1, 1) {mustBeGeometry};
+        objective (1, 1) {mustBeA(objective, 'sensingObjective')};
+        agents (:, 1) cell;
+        timestep (:, 1) double = 0.05;
+        partitoningFreq (:, 1) double = 0.25
+        maxIter (:, 1) double = 1000;
+        obstacles (:, 1) cell {mustBeGeometry} = cell(0, 1);
+    end
+    arguments (Output)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        f (1, 1) {mustBeA(f, 'matlab.ui.Figure')};
+    end
+
+    % Define simulation time parameters
+    obj.timestep = timestep;
+    obj.maxIter = maxIter;
+
+    % Define domain
+    obj.domain = domain;
+    obj.partitioningFreq = partitoningFreq;
+
+    % Add geometries representing obstacles within the domain
+    obj.obstacles = obstacles;
+
+    % Define objective
+    obj.objective = objective;
+
+    % Define agents
+    obj.agents = agents;
+
+    % Compute adjacency matrix
+    obj = obj.updateAdjacency();
+
+    % Create initial partitioning
+    obj = obj.partition();
+
+    % Set up plots showing initialized state
+    [obj, f] = obj.plot();
+end