Fix Covariate constructor and GLM intervalNr calculation

src/main/java/mascot/dynamics/GLM.java

@@ -117,7 +117,7 @@ public boolean intervalIsDirty(int i){
     public double[] getCoalescentRate(int i){
 		int intervalNr;
     	if (i >= rateShiftsInput.get().getDimension()-firstlargerzero-1)
-    		intervalNr = rateShiftsInput.get().getDimension()-2;
+    		intervalNr = rateShiftsInput.get().getDimension()-firstlargerzero-1;
     	else
     		intervalNr = i + firstlargerzero;
 
@@ -212,7 +212,7 @@ public void close(PrintStream out) {
     public double getNe(int state, int i){
 		int intervalNr;
     	if (i >= rateShiftsInput.get().getDimension()-firstlargerzero-1)
-    		intervalNr = rateShiftsInput.get().getDimension()-2;
+    		intervalNr = rateShiftsInput.get().getDimension()-firstlargerzero-1;
     	else
     		intervalNr = i + firstlargerzero;
 
@@ -224,7 +224,7 @@ public double getNe(int state, int i){
     public double getMig(int source, int sink, int i){
 		int intervalNr;
     	if (i >= rateShiftsInput.get().getDimension()-firstlargerzero-1)
-    		intervalNr = rateShiftsInput.get().getDimension()-2;
+    		intervalNr = rateShiftsInput.get().getDimension()-firstlargerzero-1;
     	else
     		intervalNr = i + firstlargerzero;
 

src/main/java/mascot/glmmodel/Covariate.java

@@ -28,6 +28,10 @@ public Covariate(Double[] values, String id) {
 		this.values = new Double[values.length];
 		System.arraycopy(values, 0, this.values, 0, values.length);
 		this.ID = id;
+		// Also populate valuesInput so initAndValidate() and XML serialization work correctly
+		for (Double v : values) {
+			valuesInput.get().add(v);
+		}
 	}
 
 	public Covariate(List<String> rawValues, String id) {

src/test/java/mascot/dynamics/GLMTest.java

@@ -0,0 +1,90 @@
+package mascot.dynamics;
+
+import beast.base.spec.domain.Real;
+import beast.base.spec.inference.parameter.BoolVectorParam;
+import beast.base.spec.inference.parameter.RealScalarParam;
+import beast.base.spec.inference.parameter.RealVectorParam;
+import mascot.glmmodel.Covariate;
+import mascot.glmmodel.CovariateList;
+import mascot.glmmodel.LogLinear;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class GLMTest {
+
+    /**
+     * Regression for the single-epoch GLM intervalNr bug.
+     * <p>
+     * In a single-epoch model (rateShifts = [Infinity]), firstlargerzero == 0
+     * and dimension == 1, so the boundary branch in getCoalescentRate / getNe /
+     * getMig is always taken for any i. The old hardcoded fallback
+     * intervalNr = dim - 2 evaluated to -1 for dim=1, causing
+     * ArrayIndexOutOfBoundsException when rates were looked up. The fix
+     * uses dim - firstlargerzero - 1, which is the correct last valid
+     * interval index for any rateShifts configuration.
+     */
+    @Test
+    public void testSingleEpochGLMRatesDoNotThrow() {
+        int dim = 2;
+
+        // single-epoch rate shifts: dim = 1 with the only value > 0, so firstlargerzero = 0
+        RateShifts rateShifts = new RateShifts();
+        rateShifts.initByName("value", "1.0");
+
+        GLM glm = buildGLM(dim, rateShifts);
+
+        double[] coalRate = glm.getCoalescentRate(0);
+        assertEquals(dim, coalRate.length);
+        for (double v : coalRate)
+            assertTrue(Double.isFinite(v), "coalescent rate must be finite, got " + v);
+
+        for (int s = 0; s < dim; s++) {
+            double ne = glm.getNe(s, 0);
+            assertTrue(Double.isFinite(ne), "Ne must be finite, got " + ne);
+        }
+
+        double mig = glm.getMig(0, 1, 0);
+        assertTrue(Double.isFinite(mig), "migration rate must be finite, got " + mig);
+    }
+
+    private GLM buildGLM(int dim, RateShifts rateShifts) {
+        LogLinear migGLM = buildLogLinear(dim * (dim - 1));
+        LogLinear neGLM = buildLogLinear(dim);
+
+        GLM glm = new GLM();
+        glm.initByName(
+                "dimension", dim,
+                "rateShifts", rateShifts,
+                "migrationGLM", migGLM,
+                "NeGLM", neGLM,
+                "types", "a b");
+        return glm;
+    }
+
+    private LogLinear buildLogLinear(int covariateDim) {
+        Double[] vals = new Double[covariateDim];
+        for (int i = 0; i < covariateDim; i++)
+            vals[i] = 1.0;
+
+        Covariate cov = new Covariate(vals, "cov");
+        cov.initAndValidate();
+
+        CovariateList covList = new CovariateList();
+        covList.initByName("covariates", cov);
+
+        RealVectorParam<Real> scaler = new RealVectorParam<>(new double[]{0.0}, Real.INSTANCE);
+        BoolVectorParam indicator = new BoolVectorParam(new boolean[]{true});
+        RealScalarParam<Real> clock = new RealScalarParam<>();
+        clock.initByName("value", "1.0");
+
+        LogLinear glm = new LogLinear();
+        glm.initByName(
+                "covariateList", covList,
+                "scaler", scaler,
+                "indicator", indicator,
+                "clock", clock);
+        return glm;
+    }
+}

src/test/java/mascot/glmmodel/CovariateTest.java

@@ -0,0 +1,44 @@
+package mascot.glmmodel;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class CovariateTest {
+
+    @Test
+    public void testDoubleArrayConstructorPopulatesValuesInput() {
+        Double[] vals = new Double[]{1.0, 2.0, 3.0};
+        Covariate c = new Covariate(vals, "test");
+        assertEquals(3, c.valuesInput.get().size());
+        assertEquals(1.0, c.valuesInput.get().get(0));
+        assertEquals(2.0, c.valuesInput.get().get(1));
+        assertEquals(3.0, c.valuesInput.get().get(2));
+    }
+
+    @Test
+    public void testInitAndValidateAfterDoubleArrayConstructorPreservesValues() {
+        // Regression for the bug where initAndValidate() rebuilt `values` from an
+        // empty valuesInput, clobbering the values set by the constructor.
+        Double[] vals = new Double[]{4.0, 5.0, 6.0};
+        Covariate c = new Covariate(vals, "test");
+        c.initAndValidate();
+        assertEquals(3, c.getDimension());
+        assertEquals(4.0, c.getArrayValue(0));
+        assertEquals(5.0, c.getArrayValue(1));
+        assertEquals(6.0, c.getArrayValue(2));
+    }
+
+    @Test
+    public void testInitAndValidateViaValuesInputStillWorks() {
+        // Existing code path: default constructor + valuesInput populated externally.
+        Covariate c = new Covariate();
+        c.valuesInput.get().add(7.0);
+        c.valuesInput.get().add(8.0);
+        c.setID("test");
+        c.initAndValidate();
+        assertEquals(2, c.getDimension());
+        assertEquals(7.0, c.getArrayValue(0));
+        assertEquals(8.0, c.getArrayValue(1));
+    }
+}