fix common elements count algorithm - Comparison API

src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java

@@ -215,11 +215,8 @@ public SeqColComparisonResultEntity compareSeqCols(
         // "elements" attribute | "a-and-b-same-order"
         // LENGTHS
         if (lessThanTwoOverlappingElements(seqColALengths, seqColBLengths) || unbalancedDuplicatesPresent(seqColALengths, seqColBLengths)) {
-            System.out.println("More than two overlapping elements: !!!");
             comparisonResult.putIntoElements("a-and-b-same-order", "lengths", null);
         } else {
-            System.out.println("seqColALengths Size: " + seqColALengths.size() + " SECOND Element: " + seqColALengths.get(1));
-            System.out.println("seqColBLengths Size: " + seqColBLengths.size() + " SECOND Element: " + seqColBLengths.get(1));
             boolean lengthsSameOrder = seqColALengths.equals(seqColBLengths);
             comparisonResult.putIntoElements("a-and-b-same-order", "lengths", lengthsSameOrder);
         }
@@ -298,6 +295,30 @@ public List<String> getCommonFieldsDistinct(List<String> seqColAFields, List<Str
         return commonFieldsDistinct;
     }
 
+    /**
+     * Return the number of common elements between listA and listB
+     * Note: Time complexity for this method is about O(n²)*/
+    public Integer getCommonElementsCount(List<String> listA, List<String> listB) {
+        int count = 0;
+        // Looping over the smallest list will sometimes be time saver
+        if (listA.size() < listB.size()) {
+            for (String element : listA) {
+                if (listB.contains(element)) {
+                    count ++;
+                    listB.remove(element);
+                }
+            }
+        } else {
+            for (String element : listB) {
+                if (listA.contains(element)) {
+                    count++;
+                    listA.remove(element);
+                }
+            }
+        }
+        return count;
+    }
+
     /**
      * Return true if there are less than two overlapping elements
      * @see 'https://github.com/ga4gh/seqcol-spec/blob/master/docs/decision_record.md#same-order-specification'*/

src/test/java/uk/ac/ebi/eva/evaseqcol/service/SeqColServiceTest.java

@@ -19,6 +19,7 @@
 
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
@@ -89,4 +90,24 @@ void unbalancedDuplicatesPresentTest() {
         assertFalse(seqColService.unbalancedDuplicatesPresent(A2, B2));
         assertTrue(seqColService.unbalancedDuplicatesPresent(A3, B3));
     }
+
+    @Test
+    void getCommonFieldsDistinctTest() {
+        List<String> A1 = new ArrayList<>();
+        List<String> B1 = new ArrayList<>();
+        A1.add("1");A1.add("2");A1.add("1"); // A1 = ["1", "2", "1"]
+        B1.add("1");B1.add("1");B1.add("2"); // B1 = ["1", "1", "2"]
+
+        List<String> A2 = new ArrayList<>();
+        List<String> B2 = new ArrayList<>();
+        A2.add("1");A2.add("2");A2.add("1"); // A2 = ["1", "2", "1"]
+        B2.add("1"); B2.add("2");            // B2 = ["1", "2"]
+
+        Integer common1Count = seqColService.getCommonElementsCount(A1, A2);
+        Integer common2Count = seqColService.getCommonElementsCount(A2, B2);
+
+        assertEquals(3, common1Count);
+        assertEquals(2, common2Count);
+
+    }
 }