reorganized code into separate files

@miSim/updateAdjacency.m

@@ -0,0 +1,32 @@
+function obj = updateAdjacency(obj)
+    arguments (Input)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+    end
+    arguments (Output)
+        obj (1, 1) {mustBeA(obj, 'miSim')};
+    end
+
+    % Initialize assuming only self-connections
+    A = logical(eye(size(obj.agents, 1)));
+
+    % Check lower triangle off-diagonal connections
+    for ii = 2:size(A, 1)
+        for jj = 1:(ii - 1)
+            if norm(obj.agents{ii}.pos - obj.agents{jj}.pos) <= min([obj.agents{ii}.comRange, obj.agents{jj}.comRange])
+                % Make sure that obstacles don't obstruct the line
+                % of sight, breaking the connection
+                for kk = 1:size(obj.obstacles, 1)
+                    if ~obj.obstacles{kk}.containsLine(obj.agents{ii}.pos, obj.agents{jj}.pos)
+                        A(ii, jj) = true;
+                    end
+                end
+                % need extra handling for cases with no obstacles
+                if isempty(obj.obstacles)
+                    A(ii, jj) = true;
+                end
+            end
+        end
+    end
+
+    obj.adjacency = A | A';
+end