Adding GraphML output to options menu

src/main/java/BiGpairSEQ.java

@@ -1,6 +1,6 @@
 import java.util.Random;
 
-//main class. For choosing interface type and caching file data
+//main class. For choosing interface type and holding settings
 public class BiGpairSEQ {
 
     private static final Random rand = new Random();
@@ -14,6 +14,8 @@ public class BiGpairSEQ {
     private static boolean cachePlate = false;
     private static boolean cacheGraph = false;
     private static String priorityQueueHeapType = "FIBONACCI";
+    private static boolean outputBinary = true;
+    private static boolean outputGraphML = false;
 
     public static void main(String[] args) {
         if (args.length == 0) {
@@ -164,4 +166,11 @@ public class BiGpairSEQ {
     public static void setFibonacciHeap() {
         priorityQueueHeapType = "FIBONACCI";
     }
+
+    public static boolean outputBinary() {return outputBinary;}
+    public static void setOutputBinary(boolean b) {outputBinary = b;}
+
+    public static boolean outputGraphML() {return outputGraphML;}
+    public static void setOutputGraphML(boolean b) {outputGraphML = b;}
+
 }

src/main/java/InteractiveInterface.java

@@ -252,7 +252,6 @@ public class InteractiveInterface {
         String filename = null;
         String cellFile = null;
         String plateFile = null;
-
         try {
             String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
             str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -310,9 +309,16 @@ public class InteractiveInterface {
             List<Integer[]> cells = cellSample.getCells();
             GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
             assert filename != null;
-            GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
+            if(BiGpairSEQ.outputBinary()) {
-            dataWriter.writeDataToFile();
+                GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
-            System.out.println("Graph and Data file written to: " + filename);
+                dataWriter.writeDataToFile();
+                System.out.println("Serialized binary graph/data file written to: " + filename);
+            }
+            if(BiGpairSEQ.outputGraphML()) {
+                GraphMLFileWriter graphMLWriter = new GraphMLFileWriter(filename, data.getGraph());
+                graphMLWriter.writeGraphToFile();
+                System.out.println("GraphML file written to: " + filename);
+            }
             if(BiGpairSEQ.cacheGraph()) {
                 BiGpairSEQ.setGraphInMemory(data, filename);
 
@@ -500,7 +506,9 @@ public class InteractiveInterface {
             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("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
+            System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output");
+            System.out.println("6) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {
                 input = sc.nextInt();
@@ -508,7 +516,9 @@ public class InteractiveInterface {
                     case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
                     case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
                     case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
-                    case 4 -> algorithmOptions();
+                    case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
+                    case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
+                    case 6 -> algorithmOptions();
                     case 0 -> backToMain = true;
                     default -> System.out.println("Invalid input");
                 }

src/main/java/Simulator.java

@@ -668,7 +668,7 @@ public class Simulator implements GraphModificationFunctions {
 
     private static Map<Integer, Integer> makeVertexToSequenceMap(Map<Integer, Integer> sequences, Integer startValue) {
         Map<Integer, Integer> map = new LinkedHashMap<>(); //LinkedHashMap to preserve order of entry
-        Integer index = startValue;
+        Integer index = startValue; //is this necessary? I don't think I use this.
         for (Integer k: sequences.keySet()) {
             map.put(index, k);
             index++;