change realparameter to function in betarange distribtuin

src/beastlabs/math/distributions/BetaRange.java

@@ -6,6 +6,7 @@
 import org.apache.commons.math.distribution.BetaDistributionImpl;
 
 import beast.base.core.Description;
+import beast.base.core.Function;
 import beast.base.inference.Distribution;
 import beast.base.core.Input;
 import beast.base.inference.State;
@@ -18,10 +19,10 @@
 public class BetaRange extends Distribution  {
 
 	final public Input<RealParameter> parameterInput = new Input<>("x", "the parameter at which the density is calculated", Input.Validate.REQUIRED);
-	final public Input<RealParameter> alphaInput = new Input<>("alpha", "first shape parameter (default 1)");
-	final public Input<RealParameter> betaInput = new Input<>("beta", "the other shape parameter (default 1)");
-    final public Input<RealParameter> lowerInput = new Input<>("lower", "lower limit of the parameter (default 0)");
-    final public Input<RealParameter> upperInput = new Input<>("upper", "upper limit of the parameter (default 1)");
+	final public Input<Function> alphaInput = new Input<>("alpha", "first shape parameter (default 1)");
+	final public Input<Function> betaInput = new Input<>("beta", "the other shape parameter (default 1)");
+    final public Input<Function> lowerInput = new Input<>("lower", "lower limit of the parameter (default 0)");
+    final public Input<Function> upperInput = new Input<>("upper", "upper limit of the parameter (default 1)");
 
 
 
@@ -30,7 +31,7 @@ public class BetaRange extends Distribution  {
 	@Override
     public void initAndValidate() {
 
-		System.out.println("BETARANGE");
+		//System.out.println("BETARANGE");
 
     }
 
@@ -41,21 +42,24 @@ public void initAndValidate() {
 	@Override
 	public double calculateLogP() {
 
-		System.out.println("BETARANGE");
+		//System.out.println("BETARANGE");
 
 		logP = 0;
 
 		RealParameter param = parameterInput.get();
 		for (int i = 0; i < param.getDimension(); i ++) {
 
-			System.out.println("BETARANGE " + i + ": " + logP);
+			//System.out.println("BETARANGE " + i + ": " + logP);
 
 			double val = param.getValue(i);
 			double alpha = getValOrDefault(alphaInput.get(), i, 1);
 			double beta = getValOrDefault(betaInput.get(), i, 1);
 			double lower = getValOrDefault(lowerInput.get(), i, 0);
 			double upper = getValOrDefault(upperInput.get(), i, 1);
 
+
+			//System.out.println("BETARANGE " + lower + ": " + upper);
+
 			// Range check
 			if (alpha <= 0 || beta <= 0) continue;
 			if (val <= lower || val >= upper) {
@@ -86,16 +90,16 @@ public double calculateLogP() {
 	 * @param defaultVal
 	 * @return
 	 */
-	private double getValOrDefault(RealParameter param, int index, double defaultVal) {
+	private double getValOrDefault(Function param, int index, double defaultVal) {
 
 		// If the parameter is null, use the default value
 		if (param == null) return defaultVal;
 
 		// If the parameter has 1 dimension get the 1st value
-		if (param.getDimension() == 1) return param.getValue();
+		if (param.getDimension() == 1) return param.getArrayValue();
 
 		// Multiple dimensions -> return the value at 'index'
-		return param.getValue(index);
+		return param.getArrayValue(index);
 
 	}