Refactoring and Testing

src/io/github/ethankelly/ODESystem.java

@@ -4,6 +4,7 @@
 import io.github.ethankelly.graph.GraphGenerator;
 import io.github.ethankelly.graph.Vertex;
 import io.github.ethankelly.symbols.Greek;
+import io.github.ethankelly.symbols.Maths;
 import org.apache.commons.math3.exception.DimensionMismatchException;
 import org.apache.commons.math3.exception.MaxCountExceededException;
 import org.apache.commons.math3.ode.FirstOrderDifferentialEquations;
@@ -71,24 +72,29 @@ public static void main(String[] args) {
 
 		// Print the initial state
 		System.out.println("Initial state:\n" + Arrays.toString(y0));
+		// Specify the initial condition used in this test
+		System.out.println("I.e. " + Maths.L_ANGLE.uni() + "S0_I1_S2" + Maths.R_ANGLE.uni());
+		// Print relevant system information
+		System.out.println(triangle);
+		// Empty array to contain derivative values
 		double[] yDot = Arrays.copyOf(y0, y0.length);
-		integrator.integrate(triangle, 0, y0, 2, yDot);
-
+		// Integrate up to specified t value
+		integrator.integrate(triangle, 0, y0, 10, yDot);
+		// Compute derivatives based on equations generation
 		triangle.computeDerivatives(0, y0, yDot);
 
+		// Print found values to 2 d.p. for clarity of system output
 		DecimalFormat df = new DecimalFormat();
 		df.setMaximumFractionDigits(2);
 
-		System.out.println("Final state:\n");
+		System.out.println("Final state at t=10:\n");
 		for (Tuple t : triangle.requiredTuples.getTuples()) {
-			System.out.print(t + " = ");
-			double result = yDot[triangle.getIndicesMapping().get(t)];
-			if (result > 1) System.out.print("1.00");
-			else if (result > 0) System.out.print(df.format(result));
-			else if (result <= 0) System.out.print("0.00");
+			System.out.print(t + Maths.PRIME.uni() + " = ");
+			double resultPrime = yDot[triangle.getIndicesMapping().get(t)];
+			System.out.print(df.format(resultPrime));
 			System.out.println();
 		}
-		System.out.println(triangle);
+
 	}
 
 	/**

src/io/github/ethankelly/RequiredTuples.java

@@ -41,13 +41,57 @@ public RequiredTuples(Graph graph, char[] states, boolean closures) {
 	 * @param args command-line arguments (ignored).
 	 */
 	public static void main(String[] args) {
-		RequiredTuples t1 = new RequiredTuples(GraphGenerator.getTriangle(), new char[] {'S', 'I', 'R'}, false);
-		System.out.println(t1.findSingles());
-		System.out.println(t1.getTuples() + "\nSize: " + t1.getTuples().size());
+//		RequiredTuples t1 = new RequiredTuples(GraphGenerator.getTriangle(), new char[] {'S', 'I', 'R'}, false);
+//		System.out.println(t1.findSingles());
+//		System.out.println(t1.getTuples() + "\nSize: " + t1.getTuples().size());
+//
+//		RequiredTuples t2 = new RequiredTuples(GraphGenerator.getTriangle(), new char[] {'S', 'I', 'R'}, true);
+//		System.out.println(t2.findSingles());
+//		System.out.println(t2.getTuples() + "\nSize: " + t2.getTuples().size());
+
+		RequiredTuples complete5 = new RequiredTuples(GraphGenerator.complete(5), new char[]{'S', 'I', 'R'}, false);
+		RequiredTuples cycle5 = new RequiredTuples(GraphGenerator.cycle(5), new char[]{'S', 'I', 'R'}, false);
+		RequiredTuples complete3 = new RequiredTuples(GraphGenerator.complete(3), new char[]{'S', 'I', 'R'}, false);
+		RequiredTuples cycle3 = new RequiredTuples(GraphGenerator.cycle(3), new char[]{'S', 'I', 'R'}, false);
+		RequiredTuples complete4 = new RequiredTuples(GraphGenerator.complete(4), new char[]{'S', 'I', 'R'}, false);
+		RequiredTuples cycle4 = new RequiredTuples(GraphGenerator.cycle(4), new char[]{'S', 'I', 'R'}, false);
+
+		System.out.println("CYCLE 3");
+//		System.out.println(cycle3.findSingles());
+		System.out.println(
+//				cycle3.getTuples() +
+				"Size: " + cycle3.getTuples().size());
+
+		System.out.println("\nCOMPLETE 3");
+//		System.out.println(complete3.findSingles());
+		System.out.println(
+//				complete3.getTuples() +
+				"Size: " +  complete3.getTuples().size());
+
+		System.out.println("\nCYCLE 4");
+//		System.out.println(cycle4.findSingles());
+		System.out.println(
+				cycle4.getTuples() +
+				"Size: " + cycle4.getTuples().size());
+
+		System.out.println("\nCOMPLETE 4");
+//		System.out.println(complete4.findSingles());
+		System.out.println(
+//				complete4.getTuples() +
+				"Size: " +  complete4.getTuples().size());
+
+		System.out.println("\nCYCLE 5");
+//		System.out.println(cycle5.findSingles());
+		System.out.println(
+				cycle5.getTuples() +
+				"Size: " + cycle5.getTuples().size());
+
+		System.out.println("\nCOMPLETE 5");
+//		System.out.println(complete5.findSingles());
+		System.out.println(
+//				complete5.getTuples() +
+				"Size: " +  complete5.getTuples().size());
 
-		RequiredTuples t2 = new RequiredTuples(GraphGenerator.getTriangle(), new char[] {'S', 'I', 'R'}, true);
-		System.out.println(t2.findSingles());
-		System.out.println(t2.getTuples() + "\nSize: " + t2.getTuples().size());
 	}
 
 	/**

src/io/github/ethankelly/Tuple.java

@@ -61,7 +61,7 @@ public boolean areStatesDifferent(boolean reqClosures) {
     /**
      * Given some list of vertices (some tuple), this method checks whether the index locations of every element of the
      * tuple are all distinct. If even two of the vertices have the same location, it is not a valid tuple for our
-     * purposes and we will not hve to consider the associated equation in the final system of equations that describes
+     * purposes, and we will not have to consider the associated equation in the final system of equations that describes
      * our compartmental model.
      *
      * @return true if no index location is repeated in the vertices, false otherwise.
@@ -81,7 +81,7 @@ public boolean areLocationsDifferent() {
 
     /**
      * Given a potential tuple, this method checks that the states of each probability are not all the same, that each
-     * probability corresponds to a different vertex and that all of the vertices involved are in fact connected. If
+     * probability corresponds to a different vertex and that all the vertices involved are in fact connected. If
      * these three conditions are met, then it is a tuple that we are required to express in the total set of equations
      * describing the system dynamics.
      *

src/io/github/ethankelly/graph/GraphGenerator.java

@@ -417,7 +417,13 @@ public static Graph erdosRenyi(int numVertices, double probability) {
      * @return the complete graph on the given number of vertices.
      */
     public static Graph complete(int numVertices) {
-        return erdosRenyi(numVertices, 1.0).setName("Complete");
+        Graph complete = new Graph(numVertices, "Complete");
+        for (int i = 0; i < complete.getNumVertices(); i++) {
+            for (int j = 0; j < complete.getNumVertices(); j++) {
+                if (i != j && !complete.hasEdge(i, j)) complete.addEdge(i, j);
+            }
+        }
+        return complete;
     }
 
     /**
@@ -541,9 +547,8 @@ public static Graph binaryTree(int numVertices) {
      */
     public static Graph cycle(int numVertices) {
         Graph g = new Graph(numVertices, "Cycle");
-        // Generate an array: [0, 1, ..., numVertices] and randomly shuffle it.
+        // Generate an array: [0, 1, ..., numVertices]
         int[] vertices = IntStream.range(0, numVertices).toArray();
-        Rand.shuffle(vertices);
         // Connect vertices from 0 to 2 less than the number of vertices consecutively
         for (int i = 0; i < numVertices - 1; i++) {
             g.addEdge(vertices[i], vertices[i + 1]);

src/io/github/ethankelly/symbols/Maths.java

@@ -8,9 +8,10 @@
 public enum Maths {
 
     L_ANGLE("\u3008"),
-    R_ANGLE("\u3009");
+    R_ANGLE("\u3009"),
+    PRIME("\u2032");
 
-    private final String uni;
+	private final String uni;
 
     Maths(String uni) {
         this.uni = uni;