Create a Test for the distance tree evaluation

lafita · lafita · commit 85578ccdf27b · 2015-11-17T17:22:20.000+01:00
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
@@ -0,0 +1,51 @@
+package org.biojava.nbio.phylo;
+
+import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.phylogeny.Phylogeny;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+/**
+ * Test for the evaluation of distance trees.
+ * 
+ * @author Aleix Lafita
+ *
+ */
+public class TestDistanceTreeEvaluator {
+
+	@Test
+	public void testErrorFree() throws Exception {
+
+		// Create a perfect additive distance matrix
+		BasicSymmetricalDistanceMatrix DM = new BasicSymmetricalDistanceMatrix(3);
+		
+		// dAB = 0.8, dBC = 0.4, dAC = 0.8
+		for (int i = 0; i < 3; i++){
+			char id = (char) ('A' + i);
+			DM.setIdentifier(i, id + "");
+			for (int j = i; j < 3; j++){
+				if (i == j){
+					DM.setValue(i, j, 0.0);
+				}
+				else if (i == 0) {
+					DM.setValue(i, j, 0.8);
+					DM.setValue(j, i, 0.8);
+				} else {
+					DM.setValue(i, j, 0.4);
+					DM.setValue(j, i, 0.4);
+				}
+			}
+		}
+		
+		BasicSymmetricalDistanceMatrix cloneDM = ForesterWrapper.cloneDM(DM);
+		
+		//Calculate error free tree and get the cv
+		Phylogeny tree = TreeConstructor.distanceTree(cloneDM, TreeConstructorType.NJ);
+		double cv = DistanceTreeEvaluator.evaluate(tree, DM);
+
+		// Assert error free
+		assertEquals(0.0, cv, 0.001);
+
+	}
+}
