Implement tests for new utility methods in sequence objects #491

lafita · lafita · commit c8b1d07ef730 · 2016-06-24T16:21:50.000+02:00
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleAlignedSequenceTest.java
@@ -141,6 +141,20 @@ public void testGetNumGaps() {
 		assertEquals(local.getNumGaps(), 2);
 		assertEquals(local2.getNumGaps(), 0);
 	}
+	
+	@Test
+	public void testGetNumGapPositions() {
+		assertEquals(global.getNumGapPositions(), 3);
+		assertEquals(local.getNumGapPositions(), 3);
+		assertEquals(local2.getNumGapPositions(), 0);
+	}
+	
+	@Test
+	public void testGetCoverage() {
+		assertEquals(global.getCoverage(), 1.0, 0.01);
+		assertEquals(local.getCoverage(), 0.556, 0.01);
+		assertEquals(local2.getCoverage(), 0.75, 0.01);
+	}
 
 	@Test
 	public void testGetOriginalSequence() {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/SimpleSequencePairTest.java
@@ -247,6 +247,12 @@ public void testGetNumIdenticals() {
 		assertEquals(global.getNumIdenticals(), 2);
 		assertEquals(local.getNumIdenticals(), 2);
 	}
+	
+	@Test
+	public void testGetPercentageOfIdentity() {
+		assertEquals(global.getPercentageOfIdentity(), 0.4, 0.01);
+		assertEquals(local.getPercentageOfIdentity(), 0.66, 0.01);
+	}
 
 	@Test
 	public void testGetNumSimilars() {
