make BEAST v2.8 compatible

Author: rbouckaert

src/beastlabs/inference/HeatedMCMC.java

@@ -10,7 +10,6 @@
 
 import beast.base.core.Description;
 import beast.base.inference.Distribution;
-import beast.base.inference.Evaluator;
 import beast.base.inference.Logger;
 import beast.base.inference.MCMC;
 import beast.base.inference.Operator;
@@ -166,34 +165,7 @@ protected long runTillResample() throws Exception {
 	            final Operator operator = operatorSchedule.selectOperator();
 	            //System.out.print("\n" + sampleNr + " " + operator.getName()+ ":");
 
-	            final Distribution evaluatorDistribution = operator.getEvaluatorDistribution();
-	            Evaluator evaluator = null;
-
-	            if (evaluatorDistribution != null) {
-	                evaluator = new Evaluator() {
-	                    @Override
-	                    public double evaluate() {
-	                        double logP = 0.0;
-
-	                        state.storeCalculationNodes();
-	                        state.checkCalculationNodesDirtiness();
-
-	                        try {
-	                            logP = evaluatorDistribution.calculateLogP();
-	                        } catch (Exception e) {
-	                            e.printStackTrace();
-	                            System.exit(1);
-	                        }
-
-	                        state.restore();
-	                        state.store(currentState);
-
-	                        return logP;
-	                    }
-	                };
-	            }
-
-	            final double logHastingsRatio = operator.proposal(evaluator);
+	            final double logHastingsRatio = operator.proposal();
 
 	            if (logHastingsRatio != Double.NEGATIVE_INFINITY) {
 

src/beastlabs/prevalence/PrevalenceList.java

@@ -10,12 +10,13 @@
 import org.w3c.dom.Node;
 
 import beast.base.core.Description;
+import beast.base.inference.Scalable;
 import beast.base.inference.StateNode;
 
 
 
 @Description("Prevalence list is a linked list with times and actions")
-public class PrevalenceList extends StateNode {
+public class PrevalenceList extends StateNode implements Scalable {
 
 	@Override
 	public void initAndValidate() {
@@ -303,6 +304,13 @@ public int scale(double fScale) {
 		return nodes.size();
 	}
 
+	@Override
+	public void scaleOne(int i, double scale) {
+		int iTime = indexOfNode(i);
+		Item item = m_items.get(iTime); 
+		move(iTime, item.m_fTime * scale);
+	}
+
 	@Override
 	public void setEverythingDirty(boolean isDirty) {
     	setSomethingIsDirty(isDirty);
@@ -321,21 +329,6 @@ public void init(PrintStream out) {
 	public void log(long nSample, PrintStream out) {
 	}
 
-	/** Valuable interface methods **/
-	@Override
-	public double getArrayValue() {
-		return 0;
-	}
-
-	@Override
-	public double getArrayValue(int iDim) {
-		return 0;
-	}
-
-	@Override
-	public int getDimension() {
-		return 0;
-	}
 
 	@Override
 	public void restore() {
@@ -374,4 +367,5 @@ protected void store() {
 		}
 	}
 
+
 }

src/beastlabs/tools/TraceStateNodeSource.java

@@ -15,6 +15,7 @@
 import beast.base.inference.parameter.IntegerParameter;
 import beast.base.inference.parameter.Parameter;
 import beast.base.inference.parameter.RealParameter;
+import beast.base.spec.type.Tensor;
 import beastfx.app.tools.LogAnalyser;
 import beastfx.app.util.LogFile;
 
@@ -95,8 +96,8 @@ public void initAndValidate() {
 					}
 					if (from.equals("last label reached")) {
 						StateNode stateNode = stateInput.get().stateNodeInput.get().get(stateNodeNr);
-						if (dimension < stateNode.getDimension()) {
-							throw new IllegalArgumentException("Could not find all dimensions of " + stateNode.getID() + " in trace file: " + dimension + "!=" + stateNode.getDimension());
+						if (dimension < ((Tensor<?, ?>) stateNode).size()) {
+							throw new IllegalArgumentException("Could not find all dimensions of " + stateNode.getID() + " in trace file: " + dimension + "!=" + ((Tensor<?, ?>) stateNode).size());
 						}
 					}
 

src/test/beast/evolution/likelihood/TreeLikelihoodTest.java

@@ -8,7 +8,6 @@
 import org.junit.Test;
 
 import beast.base.evolution.alignment.Alignment;
-import beast.base.evolution.alignment.AscertainedAlignment;
 import beast.base.evolution.alignment.Sequence;
 import beast.base.evolution.sitemodel.SiteModel;
 import beast.base.evolution.substitutionmodel.Frequencies;