Added metadata to MatchingResult to enable CLI options

src/main/java/MatchingResult.java

@@ -1,18 +1,42 @@
 import java.time.Duration;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
 public class MatchingResult {
-    private String sourceFile;
-    private List<String> comments;
-    private List<String> headers;
-    private List<List<String>> allResults;
-    private Map<Integer, Integer> matchMap;
-    private Duration time;
+    private final String sourceFile;
+    private final Map<String, String> metadata;
+    private final List<String> comments;
+    private final List<String> headers;
+    private final List<List<String>> allResults;
+    private final Map<Integer, Integer> matchMap;
+    private final Duration time;
 
-    public MatchingResult(String sourceFileName, List<String> comments, List<String> headers, List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
+    public MatchingResult(String sourceFileName, Map<String, String> metadata, List<String> headers,
+                          List<List<String>> allResults, Map<Integer, Integer>matchMap, Duration time){
         this.sourceFile = sourceFileName;
-        this.comments = comments;
+        /*
+         * POSSIBLE KEYS FOR METADATA MAP ARE:
+         * sample plate filename
+         * graph filename
+         * well populations
+         * total alphas found
+         * total betas found
+         * high overlap threshold
+         * low overlap threshold
+         * maximum occupancy difference
+         * minimum overlap percent
+         * pairing attempt rate
+         * correct pairing count
+         * incorrect pairing count
+         * pairing error rate
+         * simulation time
+         */
+        this.metadata = metadata;
+        this.comments = new ArrayList<>();
+        for (String key : metadata.keySet()) {
+            comments.add(key +": " + metadata.get(key));
+        }
         this.headers = headers;
         this.allResults = allResults;
         this.matchMap = matchMap;
@@ -20,6 +44,8 @@ public class MatchingResult {
 
     }
 
+    public Map<String, String> getMetadata() {return metadata;}
+
     public List<String> getComments() {
         return comments;
     }