Runs on command line user input

Equations.txt

@@ -0,0 +1,50 @@
+ *** Equations for an SIR model on a Toast Graph ***
+
+0: 0 1 1 1 
+1: 1 0 1 0 
+2: 1 1 0 1 
+3: 1 0 1 0 
+Numbers of equations of each size: [8, 10, 16, 8]
+
+[〈S3〉] = - β〈S3 I0〉- β〈S3 I2〉
+[〈S2〉] = - β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈S1〉] = - β〈S1 I0〉- β〈S1 I2〉
+[〈S0〉] = - β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I3〉] = γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉
+[〈I2〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉
+[〈I1〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉
+[〈I0〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉
+[〈I3〉, 〈S2〉] = γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I3〉, 〈S0〉] = γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I2〉, 〈S3〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I2〉, 〈S1〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S1 I0〉- β〈S1 I2〉
+[〈I2〉, 〈S0〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I1〉, 〈S2〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I1〉, 〈S0〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I0〉, 〈S3〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I0〉, 〈S2〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I0〉, 〈S1〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉- β〈S1 I0〉- β〈S1 I2〉
+[〈I3〉, 〈S0〉, 〈S2〉] = γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I3〉, 〈S0〉, 〈S1〉] = γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S1 I0〉- β〈S1 I2〉
+[〈I2〉, 〈S0〉, 〈S3〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I2〉, 〈S0〉, 〈S1〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S1 I0〉- β〈S1 I2〉
+[〈I2〉, 〈I3〉, 〈S0〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉+ γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I1〉, 〈S2〉, 〈S3〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I1〉, 〈S0〉, 〈S3〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I1〉, 〈S0〉, 〈S2〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I1〉, 〈I2〉, 〈S3〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I1〉, 〈I2〉, 〈S0〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I0〉, 〈S2〉, 〈S3〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I0〉, 〈S1〉, 〈S2〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉- β〈S1 I0〉- β〈S1 I2〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I0〉, 〈I3〉, 〈S2〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉+ γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I0〉, 〈I2〉, 〈S3〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I0〉, 〈I2〉, 〈S1〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S1 I0〉- β〈S1 I2〉
+[〈I0〉, 〈I1〉, 〈S2〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉+ γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I3〉, 〈S0〉, 〈S1〉, 〈S2〉] = γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S1 I0〉- β〈S1 I2〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉
+[〈I2〉, 〈I3〉, 〈S0〉, 〈S1〉] = γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉+ γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S1 I0〉- β〈S1 I2〉
+[〈I1〉, 〈S0〉, 〈S2〉, 〈S3〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I1〉, 〈I2〉, 〈S0〉, 〈S3〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I1〉, 〈I2〉, 〈I3〉, 〈S0〉] = γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉+ γ〈S3 I0〉+ γ〈S3 I2〉- γ〈I3〉- β〈S0 I1〉- β〈S0 I2〉- β〈S0 I3〉
+[〈I0〉, 〈S1〉, 〈S2〉, 〈S3〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉- β〈S1 I0〉- β〈S1 I2〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I0〉, 〈I1〉, 〈S2〉, 〈S3〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉+ γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉- β〈S2 I0〉- β〈S2 I1〉- β〈S2 I3〉- β〈S3 I0〉- β〈S3 I2〉
+[〈I0〉, 〈I1〉, 〈I2〉, 〈S3〉] = γ〈S0 I1〉+ γ〈S0 I2〉+ γ〈S0 I3〉- γ〈I0〉+ γ〈S1 I0〉+ γ〈S1 I2〉- γ〈I1〉+ γ〈S2 I0〉+ γ〈S2 I1〉+ γ〈S2 I3〉- γ〈I2〉- β〈S3 I0〉- β〈S3 I2〉

src/META-INF/MANIFEST.MF

@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Main-Class: io.github.ethankelly.Main
+

src/io/github/ethankelly/Equations.java

@@ -78,58 +78,4 @@ public static List<String> generateEquations(Tuple tuples) {
 
         return equations;
     }
-
-    public static void main(String[] args) throws FileNotFoundException {
-        PrintStream o = new PrintStream("TLTEquations.txt");
-        System.setOut(o);
-
-        char[] states = new char[]{'S', 'I', 'R', 'P'};
-        // TRIANGLE
-        Graph triangle = new Graph(3);
-        triangle.addEdge(0, 1);
-        triangle.addEdge(1, 2);
-        triangle.addEdge(2, 0);
-        Tuple triangleNE = new Tuple(triangle, states);
-
-        System.out.println(" *** TRIANGLE GRAPH ***\n\n" + triangle + "Numbers of equations of each size: "
-                + Arrays.toString(triangleNE.findNumbers(triangleNE.getTuples())) + "\n");
-        Equations.generateEquations(triangleNE).forEach(System.out::println);
-
-        // LOLLIPOP
-        Graph lollipop = new Graph(4);
-        lollipop.addEdge(0, 1);
-        lollipop.addEdge(0, 2);
-        lollipop.addEdge(0, 3);
-        lollipop.addEdge(2, 3);
-        Tuple lollipopNE = new Tuple(lollipop, states);
-
-        System.out.println("\n *** LOLLIPOP GRAPH ***\n\n" + lollipop + "Numbers of equations of each size: "
-                + Arrays.toString(lollipopNE.findNumbers(lollipopNE.getTuples())) + "\n");
-        Equations.generateEquations(lollipopNE).forEach(System.out::println);
-
-        // TOAST
-        Graph toast = new Graph(4);
-        toast.addEdge(0, 1);
-        toast.addEdge(0, 2);
-        toast.addEdge(0, 3);
-        toast.addEdge(1, 2);
-        toast.addEdge(2, 3);
-        Tuple toastNE = new Tuple(toast, states);
-
-        System.out.println("\n *** TOAST GRAPH ***\n\n" + toast + "Numbers of equations of each size: "
-                + Arrays.toString(toastNE.findNumbers(toastNE.getTuples())) + "\n");
-        Equations.generateEquations(toastNE).forEach(System.out::println);
-
-        // Creating another File object that represents the disk file and assign to output stream
-        PrintStream er = new PrintStream("ErdosRenyiTest.txt");
-        System.setOut(er);
-
-        // ERDOS-RENYI
-        Graph erdosRenyi = GraphGenerator.erdosRenyi(5, 0.5);
-        Tuple erdosRenyiNE = new Tuple(erdosRenyi, states);
-
-        System.out.println(" *** ERDOS-RENYI GRAPH ***\n\n" + erdosRenyi + "Numbers of equations of each size: "
-                + Arrays.toString(erdosRenyiNE.findNumbers(erdosRenyiNE.getTuples())) + "\n");
-        Equations.generateEquations(erdosRenyiNE).forEach(System.out::println);
-    }
 }

src/io/github/ethankelly/Graph.java

@@ -23,6 +23,8 @@
  * @author <a href="mailto:[email protected]">Ethan Kelly</a>
  */
 public class Graph {
+
+    private String name;
     private int numVertices;
     private int numEdges;
     private boolean[][] adjMatrix;
@@ -33,10 +35,11 @@ public class Graph {
      *
      * @param numVertices the number of vertices to create in the graph.
      */
-    public Graph(int numVertices) {
+    public Graph(int numVertices, String name) {
         this.numVertices = numVertices;
         this.adjMatrix = new boolean[numVertices][numVertices];
         this.transmissionMatrix = new int[numVertices][numVertices];
+        this.name = name;
     }
 
     /**
@@ -244,4 +247,13 @@ public int[][] getTransmissionMatrix() {
     public void setTransmissionMatrix(int[][] transmissionMatrix) {
         this.transmissionMatrix = transmissionMatrix;
     }
+
+    public Graph setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public String getName() {
+        return this.name;
+    }
 }