Added heap type selection, fixed error handling

readme.md

@@ -39,7 +39,7 @@ in practice.
 
 [Download the current version of BiGpairSEQ_Sim.](https://gitea.ejsf.synology.me/efischer/BiGpairSEQ/releases)
 
-BiGpairSEQ_Sim is an executable .jar file. Requires Java 11 or higher. [OpenJDK 17](https://jdk.java.net/17/)
+BiGpairSEQ_Sim is an executable .jar file. Requires Java 14 or higher. [OpenJDK 17](https://jdk.java.net/17/)
 recommended.
 
 Run with the command:

src/main/java/BiGpairSEQ.java

@@ -13,6 +13,7 @@ public class BiGpairSEQ {
     private static boolean cacheCells = false;
     private static boolean cachePlate = false;
     private static boolean cacheGraph = true;
+    private static String priorityQueueHeapType = "PAIRING";
 
     public static void main(String[] args) {
         if (args.length == 0) {
@@ -151,4 +152,16 @@ public class BiGpairSEQ {
         }
         BiGpairSEQ.cacheGraph = cacheGraph;
     }
+
+    public static String getPriorityQueueHeapType() {
+        return priorityQueueHeapType;
+    }
+
+    public static void setPairingHeap() {
+        priorityQueueHeapType = "PAIRING";
+    }
+
+    public static void setFibonacciHeap() {
+        priorityQueueHeapType = "FIBONACCI";
+    }
 }

src/main/java/InteractiveInterface.java

@@ -38,10 +38,10 @@ public class InteractiveInterface {
                         case 3 -> makeCDR3Graph();
                         case 4 -> matchCDR3s();
                         //case 6 -> matchCellsCDR1();
-                        case 8 -> options();
+                        case 8 -> mainOptions();
                         case 9 -> acknowledge();
                         case 0 -> quit = true;
-                        default -> throw new InputMismatchException("Invalid input.");
+                        default -> System.out.println("Invalid input.");
                     }
                 } catch (InputMismatchException | IOException ex) {
                     System.out.println(ex);
@@ -493,13 +493,14 @@ public class InteractiveInterface {
 //        }
 //    }
 
-    private static void options(){
+    private static void mainOptions(){
         boolean backToMain = false;
         while(!backToMain) {
             System.out.println("\n--------------OPTIONS---------------");
             System.out.println("1) Turn " + getOnOff(!BiGpairSEQ.cacheCells()) + " cell sample file caching");
             System.out.println("2) Turn " + getOnOff(!BiGpairSEQ.cachePlate()) + " plate file caching");
             System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
+            System.out.println("4) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {
                 input = sc.nextInt();
@@ -508,7 +509,7 @@ public class InteractiveInterface {
                     case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
                     case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
                     case 0 -> backToMain = true;
-                    default -> throw new InputMismatchException("Invalid input.");
+                    default -> System.out.println("Invalid input");
                 }
             } catch (InputMismatchException ex) {
                 System.out.println(ex);
@@ -517,11 +518,41 @@ public class InteractiveInterface {
         }
     }
 
+    /**
+     * Helper function for printing menu items in mainOptions(). Returns a string based on the value of parameter.
+     *
+     * @param b - a boolean value
+     * @return String "on" if b is true, "off" if b is false
+     */
     private static String getOnOff(boolean b) {
         if (b) { return "on";}
         else { return "off"; }
     }
 
+    private static void algorithmOptions(){
+        boolean backToOptions = false;
+        while(!backToOptions) {
+            System.out.println("\n---------ALGORITHM OPTIONS----------");
+            System.out.println("1) Use scaling algorithm by Duan and Su.");
+            System.out.println("2) Use Hungarian algorithm with Fibonacci heap priority queue");
+            System.out.println("3) Use Hungarian algorithm with pairing heap priority queue");
+            System.out.println("0) Return to Options menu");
+            try {
+                input = sc.nextInt();
+                switch (input) {
+                    case 1 -> System.out.println("This option is not yet implemented. Choose another.");
+                    case 2 -> BiGpairSEQ.setFibonacciHeap();
+                    case 3 -> BiGpairSEQ.setPairingHeap();
+                    case 0 -> backToOptions = true;
+                    default -> System.out.println("Invalid input");
+                }
+            } catch (InputMismatchException ex) {
+                System.out.println(ex);
+                sc.next();
+            }
+        }
+    }
+
     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.");

src/main/java/Simulator.java

@@ -3,6 +3,7 @@ import org.jgrapht.alg.matching.MaximumWeightBipartiteMatching;
 import org.jgrapht.generate.SimpleWeightedBipartiteGraphMatrixGenerator;
 import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
+import org.jheaps.tree.FibonacciHeap;
 import org.jheaps.tree.PairingHeap;
 
 import java.math.BigDecimal;
@@ -181,12 +182,29 @@ public class Simulator {
         //Find Maximum Weighted Matching
         //using jheaps library class PairingHeap for improved efficiency
         if(verbose){System.out.println("Finding maximum weighted matching");}
-        //Attempting to use addressable heap to improve performance
+        MaximumWeightBipartiteMatching maxWeightMatching;
-        MaximumWeightBipartiteMatching maxWeightMatching =
+        //Use correct heap type for priority queue
-                new MaximumWeightBipartiteMatching(graph,
+        String heapType = BiGpairSEQ.getPriorityQueueHeapType();
+        switch (heapType) {
+            case "PAIRING" -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
                         plateVtoAMap.keySet(),
                         plateVtoBMap.keySet(),
                         i -> new PairingHeap(Comparator.naturalOrder()));
+            }
+            case "FIBONACCI" -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
+                        plateVtoAMap.keySet(),
+                        plateVtoBMap.keySet(),
+                        i -> new FibonacciHeap(Comparator.naturalOrder()));
+            }
+            default -> {
+                maxWeightMatching = new MaximumWeightBipartiteMatching(graph,
+                        plateVtoAMap.keySet(),
+                        plateVtoBMap.keySet());
+            }
+        }
+        //get the matching
         MatchingAlgorithm.Matching<String, DefaultWeightedEdge> graphMatching = maxWeightMatching.getMatching();
         if(verbose){System.out.println("Matching completed");}
         Instant stop = Instant.now();