reorganized code into separate files

@miSim/plotConnections.m

@@ -0,0 +1,45 @@
+function [obj, f] = plotConnections(obj, ind, f)
+    arguments (Input)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+        ind (1, :) double = NaN;
+        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
+
+    % Iterate over lower triangle off-diagonal region of the 
+    % adjacency matrix to plot communications links between agents
+    X = []; Y = []; Z = [];
+    for ii = 2:size(obj.adjacency, 1)
+        for jj = 1:(ii - 1)
+            if obj.adjacency(ii, jj)
+                X = [X; obj.agents{ii}.pos(1), obj.agents{jj}.pos(1)];
+                Y = [Y; obj.agents{ii}.pos(2), obj.agents{jj}.pos(2)];
+                Z = [Z; obj.agents{ii}.pos(3), obj.agents{jj}.pos(3)];
+            end
+        end
+    end
+    X = X'; Y = Y'; Z = Z';
+
+    % Plot the connections
+    if isnan(ind)
+        hold(f.CurrentAxes, "on");
+        o = plot3(f.CurrentAxes, X, Y, Z, 'Color', 'g', 'LineWidth', 2, 'LineStyle', '--');
+        hold(f.CurrentAxes, "off");
+    else
+        hold(f.Children(1).Children(ind(1)), "on");
+        o = plot3(f.Children(1).Children(ind(1)), X, Y, Z, 'Color', 'g', 'LineWidth', 2, 'LineStyle', '--');
+        hold(f.Children(1).Children(ind(1)), "off");
+    end
+
+    % Copy to other plots
+    if size(ind, 2) > 1
+        for ii = 2:size(ind, 2)
+            o = [o, copyobj(o(:, 1), f.Children(1).Children(ind(ii)))];
+        end 
+    end
+
+    obj.connectionsPlot = o;
+end