Tests failing until forester version updated

lafita · lafita · commit f53f123f6dad · 2015-11-18T16:27:00.000+01:00
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
@@ -384,7 +384,7 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 	 *            MultipleSequenceAlignment
 	 * @return
 	 */
-	public static <C extends Sequence<D>, D extends Compound> DistanceMatrix pamDistance(
+	public static <C extends Sequence<D>, D extends Compound> DistanceMatrix pamMLdistance(
 			MultipleSequenceAlignment<C, D> msa) {
 
 		// Need to import PAM1 matrix to biojava TODO
diff --git a/biojava-phylo/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java b/biojava-phylo/src/test/java/org/biojava/nbio/phylo/TestDistanceTreeEvaluator.java
@@ -41,8 +41,8 @@ public void testErrorFree() throws Exception {
 				ForesterWrapper.cloneDM(DM), TreeConstructorType.NJ);
 		double cv = DistanceTreeEvaluator.evaluate(tree, DM);
 
-		// Assert error free TODO now failing
-		//assertEquals(0.0, cv, 0.001);
+		// Assert error free
+		assertEquals(0.0, cv, 0.001);
 	}
 
 	@Test
@@ -65,7 +65,7 @@ public void testErrorEstimation() throws Exception {
 		double cv = DistanceTreeEvaluator.evaluate(tree, m);
 
 		// Assert error is only 5%
-		assertEquals(2.411, cv, 0.001);
+		assertEquals(0.05, cv, 0.1);
 
 	}
 }

Original file line number	Diff line number	Diff line change
`@@ -41,8 +41,8 @@ public void testErrorFree() throws Exception {`
`41`	`41`	`ForesterWrapper.cloneDM(DM), TreeConstructorType.NJ);`
`42`	`42`	`double cv = DistanceTreeEvaluator.evaluate(tree, DM);`
`43`	`43`
`44`		`- // Assert error free TODO now failing`
`45`		`- //assertEquals(0.0, cv, 0.001);`
	`44`	`+ // Assert error free`
	`45`	`+ assertEquals(0.0, cv, 0.001);`
`46`	`46`	`}`
`47`	`47`
`48`	`48`	`@Test`
`@@ -65,7 +65,7 @@ public void testErrorEstimation() throws Exception {`
`65`	`65`	`double cv = DistanceTreeEvaluator.evaluate(tree, m);`
`66`	`66`
`67`	`67`	`// Assert error is only 5%`
`68`		`- assertEquals(2.411, cv, 0.001);`
	`68`	`+ assertEquals(0.05, cv, 0.1);`
`69`	`69`
`70`	`70`	`}`
`71`	`71`	`}`