make everything use same random number generator

src/main/java/BiGpairSEQ.java

@@ -1,11 +1,13 @@
+import java.util.Random;
+
 //main class. For choosing interface type and caching file data
 public class BiGpairSEQ {
 
+    private static final Random rand = new Random();
     private static CellSample cellSampleInMemory = null;
     private static String cellFilename = null;
     private static Plate plateInMemory = null;
     private static String plateFilename = null;
-
     private static GraphWithMapData graphInMemory = null;
     private static String graphFilename = null;
 
@@ -20,6 +22,10 @@ public class BiGpairSEQ {
         }
     }
 
+    public static Random getRand() {
+        return rand;
+    }
+
     public static CellSample getCellSampleInMemory() {
         return cellSampleInMemory;
     }

src/main/java/Equations.java

@@ -4,10 +4,6 @@ import java.math.MathContext;
 
 public abstract class Equations {
 
-    public static int getRandomInt(int min, int max) {
-        return (int) ((Math.random() * (max - min)) + min);
-    }
-
     //pValue calculation as described in original pairSEQ paper.
     //Included for comparison with original results.
     //Not used by BiGpairSEQ for matching.

src/main/java/InteractiveInterface.java

@@ -1,17 +1,15 @@
 import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Scanner;
-import java.util.InputMismatchException;
+import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 //
 public class InteractiveInterface {
 
-    final static Scanner sc = new Scanner(System.in);
-    static int input;
-    static boolean quit = false;
+    private static final Random rand = BiGpairSEQ.getRand();
+    private static final Scanner sc = new Scanner(System.in);
+    private static int input;
+    private static boolean quit = false;
 
     public static void startInteractive() {
 
@@ -169,10 +167,11 @@ public class InteractiveInterface {
                 if(maxPop < minPop) {
                     throw new InputMismatchException("Max well population must be greater than min well population");
                 }
-                populations = new Integer[numSections];
-                for(int i = 0; i < numSections; i++) {
-                    populations[i] = Equations.getRandomInt(minPop, maxPop);
-                }
+                //maximum should be inclusive, so need to add one to max of randomly generated values
+                populations = (Integer[]) rand.ints(minPop, maxPop + 1)
+                        .limit(numSections)
+                        .boxed()
+                        .toArray();
                 System.out.print("Populations: ");
                 System.out.println(Arrays.toString(populations));
             }

src/main/java/Plate.java

@@ -10,7 +10,7 @@ import java.util.*;
 public class Plate {
     private String sourceFile;
     private List<List<Integer[]>> wells;
-    private Random rand = new Random();
+    private final Random rand = BiGpairSEQ.getRand();
     private int size;
     private double error;
     private Integer[] populations;