reorganized code into separate files

@miSim/updatePlots.m

@@ -0,0 +1,43 @@
+function [obj, f] = updatePlots(obj, f, updatePartitions)
+    arguments (Input)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        f (1, 1) {mustBeA(f, 'matlab.ui.Figure')} = figure;
+        updatePartitions (1, 1) logical = false;
+    end
+    arguments (Output)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        f (1, 1) {mustBeA(f, 'matlab.ui.Figure')};
+    end
+
+    % Update agent positions, collision geometries
+    for ii = 1:size(obj.agents, 1)
+        obj.agents{ii}.updatePlots();
+    end
+
+    % The remaining updates might be possible to do in a clever way
+    % that moves existing lines instead of clearing and 
+    % re-plotting, which is much better for performance boost
+
+    % Update agent connections plot
+    delete(obj.connectionsPlot);
+    [obj, f] = obj.plotConnections(obj.spatialPlotIndices, f);
+
+    % Update network graph plot
+    delete(obj.graphPlot);
+    [obj, f] = obj.plotGraph(obj.networkGraphIndex, f);
+
+    % Update partitioning plot
+    if updatePartitions
+        delete(obj.partitionPlot);
+        [obj, f] = obj.plotPartitions(obj.partitionGraphIndex, f);
+    end
+
+    % reset plot limits to fit domain
+    for ii = 1:size(obj.spatialPlotIndices, 2)
+        xlim(f.Children(1).Children(obj.spatialPlotIndices(ii)), [obj.domain.minCorner(1), obj.domain.maxCorner(1)]);
+        ylim(f.Children(1).Children(obj.spatialPlotIndices(ii)), [obj.domain.minCorner(2), obj.domain.maxCorner(2)]);
+        zlim(f.Children(1).Children(obj.spatialPlotIndices(ii)), [obj.domain.minCorner(3), obj.domain.maxCorner(3)]);
+    end
+
+    drawnow;
+end