Unskip phylo tests

lafita · lafita · commit a3d594dfdfcb · 2016-01-15T09:55:17.000+01:00
diff --git a/biojava-phylo/src/main/java/demo/DemoDistanceTree.java b/biojava-phylo/src/main/java/demo/DemoDistanceTree.java
@@ -69,7 +69,7 @@ public static void main(String[] args) throws Exception {
 				(BasicSymmetricalDistanceMatrix) DM, TreeConstructorType.NJ);
 
 		long treeT = System.currentTimeMillis();
-		String newick = ForesterWrapper.getNewickString(phylo, true, true);
+		String newick = ForesterWrapper.getNewickString(phylo, true);
 		System.out.println(newick);
 		System.out.println("Tree Construction: " + (treeT - readT) + " ms.");
 
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
@@ -65,18 +65,16 @@ public String getHeader(C sequence) {
 	 * 
 	 * @param phylo
 	 *            Phylogeny phylogenetic tree
-	 * @param simpleNewick
 	 * @param writeDistances
 	 *            write the branch lengths if true
 	 * @return
 	 * @throws Exception
 	 */
-	public static String getNewickString(Phylogeny phylo, boolean simpleNewick,
+	public static String getNewickString(Phylogeny phylo,
 			boolean writeDistances) throws Exception {
 
 		PhylogenyWriter w = new PhylogenyWriter();
-		StringBuffer newickString = w.toNewHampshire(phylo, simpleNewick,
-				writeDistances);
+		StringBuffer newickString = w.toNewHampshire(phylo, writeDistances);
 		return newickString.toString();
 	}
 
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
@@ -2,7 +2,6 @@
 
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import static org.junit.Assert.*;
@@ -16,7 +15,6 @@
 public class TestDistanceTreeEvaluator {
 
 	@Test
-	@Ignore
 	public void testErrorFree() throws Exception {
 
 		// Create a perfect additive distance matrix
@@ -48,7 +46,6 @@ public void testErrorFree() throws Exception {
 	}
 
 	@Test
-	@Ignore
 	public void testErrorEstimation() throws Exception {
 
 		// Matrix taken from forester test
@@ -57,18 +54,18 @@ public void testErrorEstimation() throws Exception {
 		m.setIdentifier(1, "B");
 		m.setIdentifier(2, "C");
 		m.setIdentifier(3, "D");
-		m.setRow("0.00 0.95 0.17 0.98", 0);
-		m.setRow("0.95 0.00 1.02 1.83", 1);
-		m.setRow("0.17 1.02 0.00 1.01", 2);
-		m.setRow("0.98 1.83 1.01 0.00", 3);
+		m.setRow("0 1 0 1", 0);
+		m.setRow("1 0 0 1", 1);
+		m.setRow("0 0 0 1", 2);
+		m.setRow("1 1 1 0", 3);
 
 		// Calculate error free tree and get the cv
 		Phylogeny tree = TreeConstructor.distanceTree(
 				ForesterWrapper.cloneDM(m), TreeConstructorType.NJ);
 		double cv = DistanceTreeEvaluator.evaluate(tree, m);
 
-		// Assert error is only 5%
-		assertEquals(0.05, cv, 0.1);
+		// Assert error is about 30%
+		assertEquals(0.3, cv, 0.05);
 
 	}
 }
