Merge pull request #567 from andviane/master

josemduarte · web-flow · commit 75a5f59fd630 · 2016-08-28T12:27:24.000+02:00
Proposed fix for #355
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
@@ -286,34 +286,41 @@ public Location union( Location other )
 	}
 
 	/**
-	* Return the intersection, or null if no overlap.
-	*
-	 * @param other The location to intersect.
-	 * @return The maximal location that is contained by both. Returns null if no overlap!
-	 * @throws IllegalArgumentException Locations are on opposite strands.
-	*/
-	public Location intersection( Location other )
-	{
-		if( isSameStrand( other ) )
-		{
-			int start= ( mStart > other.mStart)? mStart: other.mStart;	//pick larger
-			int end= ( mEnd < other.mEnd)? mEnd: other.mEnd;	//pick smaller
-
-			if( start <= end )
-			{
-				return new Location( start, end );
-			}
-			else
-			{
-				return null;
-			}
-		}
-		else
-		{
-			throw new IllegalArgumentException( "Locations are on opposite strands." );
-		}
+	 * Return the intersection, or null if no overlap.
+	 *
+	 * @param other
+	 *            The location to intersect.
+	 * @return The maximal location that is contained by both. Returns null if
+	 *         no overlap!
+	 * @throws IllegalArgumentException
+	 *             Locations are on opposite strands.
+	 */
+	public Location intersection(Location other) {
+		if (isSameStrand(other)) {
+			return intersect(mStart, mEnd, other.mStart, other.mEnd);
+		} else {
+			throw new IllegalArgumentException("Locations are on opposite strands.");
+		}
+	}
+	
+	private Location intersect(int a1, int a2, int b1, int b2) {
+		if (a1 > b1) {
+			return intersect(b1, b2, a1, a2);
+		}
+		// Safe to assume a1 <= b1
+		if (b1 >= a2) {
+			// b starts after a ends
+			return null;
+		} 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 (b1 >= a1 && a2 <= b2) {
+			// b starts after a but extends after the end of a
+			return new Location(b1, a2);
+		}
+		return null;
+	}	
 
-	}
 
 	/**
 	 * Get starting index (origin 0).
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestIssue355.java
@@ -0,0 +1,29 @@
+package org.biojava.nbio.genome;
+
+import static org.junit.Assert.*;
+
+import org.biojava.nbio.genome.parsers.gff.Location;
+import org.junit.Test;
+
+public class TestIssue355 {
+
+	@Test
+	public void testIssue1() {
+		Location l1 = Location.fromBio(51227320, 51227381, '+');
+		Location l2 = Location.fromBio(51227323, 51227382, '+');
+
+		Location union = l1.union(l2);
+		assertEquals(51227320,union.bioStart());
+		assertEquals(51227382,union.bioEnd());
+	}
+	
+	@Test
+	public void testIssue2() {
+		Location l1 = Location.fromBio(100, 200, '+');
+		Location l2 = Location.fromBio(1, 99, '+');
+		Location intersection = l1.intersection(l2);
+		assertNull(intersection);
+	}
+
+}
+
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 ) {
