An optimization to calculate the intersection between 2 sequences using java Sets

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

@@ -24,6 +24,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
@@ -481,28 +482,12 @@ public List<String> getCommonElementsDistinct(List<String> seqColAFields, List<S
 
     /**
      * Return the number of common elements between listA and listB
-     * Note: Time complexity for this method is about O(n²)*/
+     * */
     public Integer getCommonElementsCount(List<?> listA, List<?> listB) {
-        List<?> listALocal = new ArrayList<>(listA); // we shouldn't be making changes on the actual lists
-        List<?> listBLocal = new ArrayList<>(listB);
-        int count = 0;
-        // Looping over the smallest list will sometimes be time saver
-        if (listALocal.size() < listBLocal.size()) {
-            for (Object element : listALocal) {
-                if (listBLocal.contains(element)) {
-                    count ++;
-                    listBLocal.remove(element);
-                }
-            }
-        } else {
-            for (Object element : listBLocal) {
-                if (listALocal.contains(element)) {
-                    count++;
-                    listALocal.remove(element);
-                }
-            }
-        }
-        return count;
+        Set<?> listALocal = new HashSet<>(listA); // we shouldn't be making changes on the actual lists
+        Set<?> listBLocal = new HashSet<>(listB);
+        listALocal.retainAll(listBLocal);
+        return listALocal.size();
     }
 
     /**

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

@@ -113,4 +113,12 @@ void A_And_B_Same_OrderTest() {
         assertFalse(seqColService.check_A_And_B_Same_Order(listA5, listB5));
     }
 
+    @Test
+    void commonElementsCountTest() {
+        List<String> listA1 = new ArrayList<>(Arrays.asList("chr1", "chr2", "chr3", "A"));
+        List<String> listA2 = new ArrayList<>(Arrays.asList("chr1", "chr5", "chr3", "M", "A"));
+
+        assertEquals(3, seqColService.getCommonElementsCount(listA1, listA2));
+    }
+
 }