Added timing to CDR3/CDR1 matching

src/main/java/MatchingResult.java

@@ -1,3 +1,4 @@
+import java.time.Duration;
 import java.util.List;
 import java.util.Map;
 
@@ -6,12 +7,15 @@ public class MatchingResult {
     private List<String> headers;
     private List<List<String>> allResults;
     private Map<Integer, Integer> matchMap;
+    private Duration time;
 
-    public MatchingResult(List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap){
+    public MatchingResult(List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
         this.comments = comments;
         this.headers = headers;
         this.allResults = allResults;
         this.matchMap = matchMap;
+        this.time = time;
+
     }
 
     public List<String> getComments() {
@@ -29,4 +33,8 @@ public class MatchingResult {
     public Map<Integer, Integer> getMatchMap() {
         return matchMap;
     }
+
+    public Duration getTime() {
+        return time;
+    }
 }

src/main/java/Simulator.java

@@ -283,12 +283,12 @@ public class Simulator {
         comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
         System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
 
-        return new MatchingResult(comments, header, allResults, matchMap);
+        return new MatchingResult(comments, header, allResults, matchMap, time);
     }
 
     public static MatchingResult[] matchCDR1s(List<Integer[]> distinctCells,
                                   Plate samplePlate, Integer lowThreshold,
-                                            Integer highThreshold, Map<Integer, Integer> previousMatches){
+                                            Integer highThreshold, Map<Integer, Integer> previousMatches, Duration previousTime){
         Instant start = Instant.now();
 
         int numWells = samplePlate.getSize();
@@ -548,11 +548,16 @@ public class Simulator {
         comments.add("Number of correct matches: " + trueCount);
         double correctRate = (double) trueCount / allResults.size();
         comments.add("Correct matching rate: " + correctRate);
-
+        NumberFormat nf = NumberFormat.getInstance(Locale.US);
+        Duration time = Duration.between(start, stop);
+        time.plus(previousTime);
+        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
         for(String s: comments){
             System.out.println(s);
         }
 
+
+
         List<String> headers = new ArrayList<>();
         headers.add("CDR3 alpha");
         headers.add("CDR3 beta");
@@ -560,7 +565,7 @@ public class Simulator {
         headers.add("second matched CDR1");
         headers.add("Correct match?");
 
-        MatchingResult firstTest = new MatchingResult(comments, headers, allResults, dualMatchesMap);
+        MatchingResult firstTest = new MatchingResult(comments, headers, allResults, dualMatchesMap, time);
 
         //results for dual map
         System.out.println("Results for second pass");
@@ -602,18 +607,15 @@ public class Simulator {
         comments.add("Number of correct matches: " + trueCount);
         correctRate = (double) trueCount / allResults.size();
         comments.add("Correct matching rate: " + correctRate);
-
+        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
-
 
         for(String s: comments){
             System.out.println(s);
         }
-        NumberFormat nf = NumberFormat.getInstance(Locale.US);
+
-        Duration time = Duration.between(start, stop);
-        comments.add("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
         System.out.println("Simulation time: " + nf.format(time.toSeconds()) + " seconds");
 
-        MatchingResult dualTest = new MatchingResult(comments, headers, allResults, dualMatchesMap);
+        MatchingResult dualTest = new MatchingResult(comments, headers, allResults, dualMatchesMap, time);
 
 
         MatchingResult[] output = {firstTest, dualTest};

src/main/java/UserInterface.java

@@ -256,7 +256,7 @@ public class UserInterface {
             List<Integer[]> cells = cellReader.getCells();
             MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3);
             MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
-                    highThresholdCDR1, preliminaryResults.getMatchMap());
+                    highThresholdCDR1, preliminaryResults.getMatchMap(), preliminaryResults.getTime());
 
             //result writer
             MatchingFileWriter writer = new MatchingFileWriter(filename + "First", results[0].getComments(),