Make calculation of p-values optional, defaulting to off

src/main/java/BiGpairSEQ.java

@@ -16,6 +16,7 @@ public class BiGpairSEQ {
     private static HeapType priorityQueueHeapType = HeapType.FIBONACCI;
     private static boolean outputBinary = true;
     private static boolean outputGraphML = false;
+    private static boolean calculatePValue = false;
     private static final String version = "version 4.1";
 
     public static void main(String[] args) {
@@ -173,5 +174,9 @@ public class BiGpairSEQ {
 
     public static boolean outputGraphML() {return outputGraphML;}
     public static void setOutputGraphML(boolean b) {outputGraphML = b;}
+
+    public static boolean calculatePValue() {return calculatePValue; }
+    public static void setCalculatePValue(boolean b) {calculatePValue = b; }
+
     public static String getVersion() { return version; }
 }

src/main/java/CommandLineInterface.java

@@ -202,9 +202,12 @@ public class CommandLineInterface {
                 else {
                     maxOccupancyDiff = Integer.MAX_VALUE;
                 }
+                if (line.hasOption("pv")) {
+                    BiGpairSEQ.setCalculatePValue(true);
+                }
                 GraphWithMapData graph = getGraph(graphFilename);
                 MatchingResult result = Simulator.matchCDR3s(graph, graphFilename, minThreshold, maxThreshold,
-                        maxOccupancyDiff, minOverlapPct, false);
+                        maxOccupancyDiff, minOverlapPct, false, BiGpairSEQ.calculatePValue());
                 if(outputFilename != null){
                     MatchingFileWriter writer = new MatchingFileWriter(outputFilename, result);
                     writer.writeResultsToFile();
@@ -479,12 +482,17 @@ public class CommandLineInterface {
                 .argName("filename")
                 .desc("(Optional) Name of output the output file. If not present, no file will be written.")
                 .build();
+        Option pValue = Option.builder("pv") //can't call the method this time, because this one's optional
+                .longOpt("p-value")
+                .desc("(Optional) Calculate p-values for sequence pairs.")
+                .build();
         matchCDR3options.addOption(graphFilename)
                 .addOption(minOccupancyOverlap)
                 .addOption(maxOccupancyOverlap)
                 .addOption(minOverlapPercent)
                 .addOption(maxOccupancyDifference)
-                .addOption(outputFile);
+                .addOption(outputFile)
+                .addOption(pValue);
 
         //options for output to System.out
         Option printAlphaCount = Option.builder().longOpt("print-alphas")

src/main/java/InteractiveInterface.java

@@ -422,7 +422,7 @@ public class InteractiveInterface {
         }
         //simulate matching
         MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
-                minOverlapPercent, true);
+                minOverlapPercent, true, BiGpairSEQ.calculatePValue());
         //write results to file
         assert filename != null;
         MatchingFileWriter writer = new MatchingFileWriter(filename, results);
@@ -544,7 +544,8 @@ public class InteractiveInterface {
             System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
             System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
             System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
-            System.out.println("6) Maximum weight matching algorithm options");
+            System.out.println("6) Turn " + getOnOff(!BiGpairSEQ.calculatePValue()) + " calculation of p-values");
+            System.out.println("7) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {
                 input = sc.nextInt();
@@ -554,7 +555,8 @@ public class InteractiveInterface {
                     case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
                     case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
                     case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
-                    case 6 -> algorithmOptions();
+                    case 6 -> BiGpairSEQ.setCalculatePValue(!BiGpairSEQ.calculatePValue());
+                    case 7 -> algorithmOptions();
                     case 0 -> backToMain = true;
                     default -> System.out.println("Invalid input");
                 }

src/main/java/Simulator.java

@@ -150,7 +150,7 @@ public class Simulator implements GraphModificationFunctions {
     //match CDR3s.
     public static MatchingResult matchCDR3s(GraphWithMapData data, String dataFilename, Integer lowThreshold,
                                             Integer highThreshold, Integer maxOccupancyDifference,
-                                            Integer minOverlapPercent, boolean verbose) {
+                                            Integer minOverlapPercent, boolean verbose, boolean calculatePValue) {
         Instant start = Instant.now();
         SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph = data.getGraph();
         Map<Vertex[], Integer> removedEdges = new HashMap<>();
@@ -228,7 +228,7 @@ public class Simulator implements GraphModificationFunctions {
         header.add("Beta well count");
         header.add("Overlap well count");
         header.add("Matched correctly?");
-        header.add("P-value");
+        if(calculatePValue) { header.add("P-value"); }
 
         //Results for csv file
         List<List<String>> allResults = new ArrayList<>();
@@ -265,10 +265,12 @@ public class Simulator implements GraphModificationFunctions {
             //overlap count
             result.add(Double.toString(graph.getEdgeWeight(e)));
             result.add(Boolean.toString(check));
-            double pValue = Equations.pValue(numWells, source.getOccupancy(),
+            if (calculatePValue) {
+                double pValue = Equations.pValue(numWells, source.getOccupancy(),
                     target.getOccupancy(), graph.getEdgeWeight(e));
-            BigDecimal pValueTrunc = new BigDecimal(pValue, mc);
+                BigDecimal pValueTrunc = new BigDecimal(pValue, mc);
-            result.add(pValueTrunc.toString());
+                result.add(pValueTrunc.toString());
+            }
             allResults.add(result);
         }