reorganized code into separate files

@miSim/run.m

@@ -0,0 +1,52 @@
+function [obj, f] = run(obj, f)
+    arguments (Input)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        f (1, 1) {mustBeA(f, 'matlab.ui.Figure')} = figure;
+    end
+    arguments (Output)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        f (1, 1) {mustBeA(f, 'matlab.ui.Figure')};
+    end
+
+    % Create axes if they don't already exist
+    f = firstPlotSetup(f);
+
+    % Set up times to iterate over
+    times = linspace(0, obj.timestep * obj.maxIter, obj.maxIter+1)';
+    partitioningTimes = times(obj.partitioningFreq:obj.partitioningFreq:size(times, 1));
+
+    % Start video writer
+    v = obj.setupVideoWriter();
+    v.open();
+
+    for ii = 1:size(times, 1)
+        % Display current sim time
+        t = times(ii);
+        fprintf("Sim Time: %4.2f (%d/%d)\n", t, ii, obj.maxIter)
+
+        % Check if it's time for new partitions
+        updatePartitions = false;
+        if ismember(t, partitioningTimes)
+            updatePartitions = true;
+            obj = obj.partition();
+        end
+
+        % Iterate over agents to simulate their motion
+        for jj = 1:size(obj.agents, 1)
+            obj.agents{jj} = obj.agents{jj}.run(obj.objective, obj.domain, obj.partitioning);
+        end
+
+        % Update adjacency matrix
+        obj = obj.updateAdjacency;
+
+        % Update plots
+        [obj, f] = obj.updatePlots(f, updatePartitions);
+
+        % Write frame in to video
+        I = getframe(f);
+        v.writeVideo(I);
+    end
+
+    % Close video file
+    v.close();
+end