implement option menu for file caching

src/main/java/BiGpairSEQ.java

@@ -10,6 +10,9 @@ public class BiGpairSEQ {
     private static String plateFilename = null;
     private static GraphWithMapData graphInMemory = null;
     private static String graphFilename = null;
+    private static boolean cacheCells = false;
+    private static boolean cachePlate = false;
+    private static boolean cacheGraph = true;
 
     public static void main(String[] args) {
         if (args.length == 0) {
@@ -92,4 +95,27 @@ public class BiGpairSEQ {
         graphFilename = filename;
     }
 
+    public static boolean cacheCells() {
+        return cacheCells;
+    }
+
+    public static void setCacheCells(boolean cacheCells) {
+        BiGpairSEQ.cacheCells = cacheCells;
+    }
+
+    public static boolean cachePlate() {
+        return cachePlate;
+    }
+
+    public static void setCachePlate(boolean cachePlate) {
+        BiGpairSEQ.cachePlate = cachePlate;
+    }
+
+    public static boolean cacheGraph() {
+        return cacheGraph;
+    }
+
+    public static void setCacheGraph(boolean cacheGraph) {
+        BiGpairSEQ.cacheGraph = cacheGraph;
+    }
 }

src/main/java/InteractiveInterface.java

@@ -27,6 +27,7 @@ public class InteractiveInterface {
                 //Need to re-do the CDR3/CDR1 matching to correspond to new pattern
                 //System.out.println("5) Generate CDR3/CDR1 occupancy graph");
                 //System.out.println("6) Simulate CDR3/CDR1 T cell matching");
+                System.out.println("8) Options");
                 System.out.println("9) About/Acknowledgments");
                 System.out.println("0) Exit");
                 try {
@@ -37,6 +38,7 @@ public class InteractiveInterface {
                         case 3 -> makeCDR3Graph();
                         case 4 -> matchCDR3s();
                         //case 6 -> matchCellsCDR1();
+                        case 8 -> options();
                         case 9 -> acknowledge();
                         case 0 -> quit = true;
                         default -> throw new InputMismatchException("Invalid input.");
@@ -493,6 +495,39 @@ public class InteractiveInterface {
 //        }
 //    }
 
+    private static void options(){
+        boolean backToMain = false;
+        while(!backToMain) {
+            System.out.println("-------------OPTIONS----------------");
+            System.out.println("1) Turn cell sample file caching " + getOnOff(!BiGpairSEQ.cacheCells()));
+            System.out.println("2) Turn sample plate file caching " + getOnOff(!BiGpairSEQ.cachePlate()));
+            System.out.println("3) Turn graph/data file caching " + getOnOff(!BiGpairSEQ.cacheGraph()));
+            System.out.println("0) Return to main menu");
+            try {
+                input = sc.nextInt();
+                switch (input) {
+                    case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
+                    case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
+                    case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
+                    case 0 -> backToMain = true;
+                    default -> throw new InputMismatchException("Invalid input.");
+                }
+            } catch (InputMismatchException ex) {
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+    }
+
+    private static String getOnOff(boolean b) {
+        if (b) {
+            return "on";
+        }
+        else {
+            return "off";
+        }
+    }
+
     private static void acknowledge(){
         System.out.println("This program simulates BiGpairSEQ, a graph theory based adaptation");
         System.out.println("of the pairSEQ algorithm for pairing T cell receptor sequences.");