Unit tests for GT16 error model, binary and error model base

src/test/beast/evolution/errormodel/BinaryErrorModelTest.java

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+package test.beast.evolution.errormodel;
+
+import beast.evolution.datatype.Binary;
+import beast.evolution.errormodel.BinaryErrorModel;
+import org.junit.Test;
+
+import static junit.framework.Assert.assertEquals;
+
+public class BinaryErrorModelTest {
+
+    private static double DELTA = 1e-10;
+
+    @Test
+    public void testBinaryErrorModelSumsToOne() {
+        Binary datatype = new Binary();
+
+        BinaryErrorModel errorModel = new BinaryErrorModel();
+        errorModel.initByName(
+                "alpha", "0.1",
+                "beta", "0.2",
+                "datatype", datatype
+        );
+        errorModel.initAndValidate();
+
+        for (int i = 0; i < datatype.getStateCount(); i++) {
+            double sum = 0.0;
+            for (int j = 0; j < datatype.getStateCount(); j++) {
+                // getProbability(observed state, true state)
+                sum += errorModel.getProbability(j, i);
+            }
+            assertEquals(1.0, sum, DELTA);
+        }
+
+    }
+}

src/test/beast/evolution/errormodel/ErrorModelBaseTest.java

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+package test.beast.evolution.errormodel;
+
+import beast.evolution.datatype.Nucleotide;
+import beast.evolution.errormodel.ErrorModelBase;
+import org.junit.Test;
+
+import static junit.framework.Assert.assertEquals;
+
+public class ErrorModelBaseTest {
+
+    private static double DELTA = 1e-10;
+
+    @Test
+    public void testNucleotideErrorModelSumsToOne() {
+        Nucleotide datatype = new Nucleotide();
+
+        ErrorModelBase errorModel = new ErrorModelBase();
+        errorModel.initByName("epsilon", "0.1", "datatype", datatype);
+        errorModel.initAndValidate();
+
+        for (int i = 0; i < datatype.getStateCount(); i++) {
+            double sum = 0.0;
+            for (int j = 0; j < datatype.getStateCount(); j++) {
+                // getProbability(observed state, true state)
+                sum += errorModel.getProbability(j, i);
+            }
+            assertEquals(1.0, sum, DELTA);
+        }
+
+    }
+}
+

src/test/beast/evolution/errormodel/GT16ErrorModelTest.java

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+package test.beast.evolution.errormodel;
+
+import beast.evolution.datatype.NucleotideDiploid16;
+import beast.evolution.errormodel.GT16ErrorModel;
+import org.junit.Test;
+
+import static junit.framework.Assert.assertEquals;
+
+public class GT16ErrorModelTest {
+
+    private static double DELTA = 1e-10;
+
+    @Test
+    public void testGT16ErrorSumsToOne() {
+        NucleotideDiploid16 datatype = new NucleotideDiploid16();
+
+        GT16ErrorModel errorModel = new GT16ErrorModel();
+        errorModel.initByName(
+                "epsilon", "0.1",
+                "delta", "0.2",
+                "datatype", datatype
+        );
+        errorModel.initAndValidate();
+
+        for (int i = 0; i < datatype.getStateCount(); i++) {
+            double sum = 0.0;
+            for (int j = 0; j < datatype.getStateCount(); j++) {
+                // getProbability(observed state, true state)
+                sum += errorModel.getProbability(j, i);
+            }
+            assertEquals(1.0, sum, DELTA);
+        }
+
+    }
+}