More tests for issue #355

andviane · andviane · commit b3142b9dfd6c · 2016-08-25T22:25:03.000+02:00
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -311,10 +311,10 @@ private Location intersect(int a1, int a2, int b1, int b2) {
 		if (b1 >= a2) {
 			// b starts after a ends
 			return null;
-		} else if (b1 < a2 && b2 < a2) {
-			// b starts after a and ends before a ends
+		} else if (b1 < a2 && b2 <= a2) {
+			// b starts after a starts and ends before or at where a ends
 			return new Location(b1, b2);
-		} else if (a2 < b2) {
+		} else if (b1 >= a1 && a2 <= b2) {
 			// b starts after a but extends after the end of a
 			return new Location(b1, a2);
 		}
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestLocation.java
@@ -91,6 +91,29 @@ public void testLocation() {
 		assertEquals(L(12,20), L(2,20).suffix( L(10,12)));
 
 	}
+	
+	@Test
+	public void testLocationIntersections() {
+		// One inside another
+		Location r21_25 = new Location( 21, 25 );
+		Location r1_100 = new Location(1, 100 );
+		
+		assertEquals(r21_25, r21_25.intersection( r1_100));
+		assertEquals(r21_25, r1_100.intersection( r21_25));
+		
+		// Non overlapping
+		Location r10_100 = new Location(10, 100 );
+		Location r1_9 = new Location( 1, 9 );
+		
+		assertNull(r10_100.intersection( r1_9));
+		assertNull(r1_9.intersection( new Location( 9, 10 )));
+		
+		// Partially overlappping
+		Location r1_25 = new Location( 1, 25 );
+		Location r21_100 = new Location(21, 100 );
+		assertEquals(r21_25, r1_25.intersection( r21_100));
+		assertEquals(r21_25, r21_100.intersection( r1_25));		
+	}
 
 	//shorthand for testing
 	private static Location L( int s, int e ) {
