New test and implementing a proper equals for Location

josemduarte · josemduarte · commit d144c9b1dfc2 · 2015-12-16T12:45:41.000-08:00
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
@@ -849,18 +849,37 @@ public String toString()
 		return new String( "[L=" + (mEnd - mStart) + "; S=" + mStart + "; E=" + mEnd +"]" );
 	}
 	
-	/**	
-	 * Compare locations for equality.
-	 *
-	 * @param other The location to compare.
-	 * @return True if locations are the same.
+	/* (non-Javadoc)
+	 * @see java.lang.Object#hashCode()
 	 */
-	public boolean equals( Location other )
-	{
-		return mStart == other.mStart && mEnd == other.mEnd;
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + mEnd;
+		result = prime * result + mStart;
+		return result;
 	}
-	
-	
+
+	/* (non-Javadoc)
+	 * @see java.lang.Object#equals(java.lang.Object)
+	 */
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		Location other = (Location) obj;
+		if (mEnd != other.mEnd)
+			return false;
+		if (mStart != other.mStart)
+			return false;
+		return true;
+	}
+
 	/**	
 	 * 
 	 */
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
@@ -0,0 +1,80 @@
+package org.biojava.nbio.genome;
+
+import static org.junit.Assert.*;
+
+import org.biojava.nbio.genome.parsers.gff.Location;
+import org.junit.Test;
+
+public class TestLocation {
+
+	@Test
+	public void testLocation() {
+		// tests taken from Location.main()
+		
+		//Location p3_7= new Location( 3, 7 );
+		Location p16_19= new Location( 16, 19 );
+		Location p15_19= new Location( 15, 19 );
+		Location p15_16= new Location( 15, 16 );
+		Location p10_17= new Location( 10, 17 );
+		Location p10_12= new Location( 10, 12 );
+		Location p14_17= new Location( 14, 17 );
+		//Location p14_14= new Location( 14, 14 );
+		
+		Location r13_17= new Location( 13, 17 );
+		Location r21_25= new Location( 21, 25 );
+		
+		Location r4_7= new Location( 4, 7 );
+		Location r2_5= new Location( 2, 5 );
+		Location r0_3= new Location( 0, 3 );
+		Location r5_8= new Location( 5, 8 );
+		
+		//distance
+		assertEquals(7, L(14,14).distance( L(3,7) ));
+		assertEquals(7, L(3,7).distance( L(14,14) ));
+		assertEquals(3, L(1,4).distance( L(7, 10) ));
+		
+		//union
+		assertEquals(p10_17, p10_12.union( p14_17 ));
+		assertEquals(p10_17, p14_17.union( p10_12 ));		
+		assertEquals(p15_19, p15_19.union( p15_16 ));
+		
+		//intersection
+		assertEquals(new Location( 21, 25 ), r13_17.union( r21_25 ).intersection( r21_25 ));
+		
+				
+		//isBefore
+		assertTrue( r2_5.isBefore( r5_8 ));		
+		assertTrue( !r2_5.isBefore( r4_7 ));
+		
+		//isAfter
+		assertTrue(r5_8.isAfter( r2_5 ));
+		assertTrue(!r5_8.isAfter( r4_7 ));
+		
+		//contains
+		assertTrue(p15_19.contains( p16_19 ));
+				
+		//overlaps		
+		assertTrue(r2_5.overlaps( r4_7 ));
+		assertTrue(r2_5.overlaps( r0_3 ));
+		assertTrue(!r5_8.overlaps( r2_5 ));
+		assertTrue(!r2_5.overlaps( r5_8 ));
+		
+		
+        //prefix
+        assertEquals(L(2,3), L(2,20).prefix(1));
+        assertEquals(L(2,19), L(2,20).prefix(-1));
+        assertEquals( L(2,10), L(2,20).prefix( L(10,12)));
+       
+        //suffix
+        assertEquals(L(3,20), L(2,20).suffix(1));
+        assertEquals(L(19,20), L(2,20).suffix(-1));
+        assertEquals(L(12,20), L(2,20).suffix( L(10,12)));
+		
+	}
+
+	//shorthand for testing
+	private static Location L( int s, int e ) {
+		return new Location( s, e );
+	}
+	
+}
