sync with beast2 exception overhaul

src/beast/evolution/likelihood/MixtureTreeLikelihood.java

@@ -30,17 +30,17 @@ public class MixtureTreeLikelihood extends TreeLikelihood {
 
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
         // sanity check: alignment should have same #taxa as tree
         if (dataInput.get().getNrTaxa() != treeInput.get().getLeafNodeCount()) {
-            throw new Exception("The number of nodes in the tree does not match the number of sequences");
+            throw new IllegalArgumentException("The number of nodes in the tree does not match the number of sequences");
         }
         // No Beagle instance was found, so we use the good old java likelihood core
         beagle = null;
 
         int nodeCount = treeInput.get().getNodeCount();
         if (!(siteModelInput.get() instanceof SiteModel.Base)) {
-        	throw new Exception ("siteModel input should be of type SiteModel.Base");
+        	throw new IllegalArgumentException ("siteModel input should be of type SiteModel.Base");
         }
         m_siteModel = (SiteModel.Base) siteModelInput.get();
         m_siteModel.setDataType(dataInput.get().getDataType());
@@ -92,7 +92,7 @@ public void initAndValidate() throws Exception {
 
     /* Assumes there IS a branch rate model as opposed to traverse() */
 	@Override
-    int traverse(final Node node) throws Exception {
+    int traverse(final Node node) {
 
         int update = (node.isDirty() | hasDirt);
 
@@ -139,7 +139,7 @@ int traverse(final Node node) throws Exception {
                 if (siteModel.integrateAcrossCategories()) {
                 	mixtureLikelihoodCore.calculatePartials(childNum1, childNum2, iNode, classes);
                 } else {
-                    throw new Exception("Error TreeLikelihood 201: Site categories not supported");
+                    throw new IllegalArgumentException("Error TreeLikelihood 201: Site categories not supported");
                     //m_pLikelihoodCore->calculatePartials(childNum1, childNum2, nodeNum, siteCategories);
                 }
 

src/beast/evolution/likelihood/PartitionPositionLogger.java

@@ -18,7 +18,7 @@ public class PartitionPositionLogger extends BEASTObject implements Loggable {
     IntegerParameter partitionLengths;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	partitionLengths = partitionLengthsInput.get();
     }
 

src/beast/evolution/likelihood/PartitionProvider.java

@@ -51,7 +51,7 @@ public class PartitionProvider extends CalculationNode implements StateNodeIniti
 	boolean needsInitilising = false;
 
     @Override
-    public void initAndValidate() throws Exception {    	
+    public void initAndValidate() {    	
     	if (numPartitions.get() > 0) {
     	    /** we have to wait to initialise till everything is parsed, 
     	     * so that the outputs of all plug-ins are properly set up */
@@ -203,7 +203,7 @@ public boolean delayInitialisation() {
      * The StateNodeInitialiser interface can be abused for this purpose
      */
 	@Override
-	public void initStateNodes() throws Exception {
+	public void initStateNodes() {
     	System.err.println(Randomizer.getSeed());
 		PartitionedTreeLikelihood likelihood = null;
 		for (BEASTInterface plugin : getOutputs()) {
@@ -212,7 +212,7 @@ public void initStateNodes() throws Exception {
 			}
 		}
 		if (likelihood == null) {
-			throw new Exception("PartitionProvider must have PartitionedTreeLikelihood as output");
+			throw new IllegalArgumentException("PartitionProvider must have PartitionedTreeLikelihood as output");
 		}
 		SiteModel.Base siteModel = (SiteModel.Base) likelihood.siteModelInput.get();
 
@@ -255,7 +255,7 @@ public void initStateNodes() throws Exception {
 		initAndValidate();
 
 		Set<BEASTInterface> plugins = new HashSet<BEASTInterface>();
-		for (BEASTInterface plugin : mcmc.listActivePlugins()) {
+		for (BEASTInterface plugin : mcmc.listActiveBEASTObjects()) {
 			reinitialise(plugin, plugins);
 		}
 //		
@@ -267,8 +267,8 @@ public void initStateNodes() throws Exception {
 //		}
 	}
 
-	private void reinitialise(BEASTInterface plugin, Set<BEASTInterface> plugins) throws Exception {
-		for (BEASTInterface plugin2 : plugin.listActivePlugins()) {
+	private void reinitialise(BEASTInterface plugin, Set<BEASTInterface> plugins) {
+		for (BEASTInterface plugin2 : plugin.listActiveBEASTObjects()) {
 			if (!plugins.contains(plugin2)) {
 				plugins.add(plugin2);
 				reinitialise(plugin2, plugins);

src/beast/evolution/likelihood/PartitionProviderByCodon.java

@@ -10,10 +10,10 @@
 public class PartitionProviderByCodon extends PartitionProvider {
 
 
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
     	partitionLengths = partitionLengthsInput.get();
     	if (partitionLengths.getDimension() * 3 != m_pSiteModel.get().size()) {
-    		throw new Exception("nr of site models must be 3 times nr of partitions defined trough partitionLengths");
+    		throw new IllegalArgumentException("nr of site models must be 3 times nr of partitions defined trough partitionLengths");
     	}
 
     	siteCount = alignment.get().getSiteCount();
@@ -34,7 +34,7 @@ public void initAndValidate() throws Exception {
     		sum += partitionLengths.getValue(i);
     	}
     	if (sum * 3 != siteCount + (siteCount % 3 == 0? 0 : 3-siteCount % 3)) {
-    		throw new Exception("nr of sites does not match partitions lengths (sum=" + sum + "*3 != siteCount=" + siteCount+")");
+    		throw new IllegalArgumentException("nr of sites does not match partitions lengths (sum=" + sum + "*3 != siteCount=" + siteCount+")");
     	}
 
 //    	weights = new int[patternIndicators.length][patternCount];

src/beast/evolution/likelihood/PartitionedTreeLikelihood.java

@@ -131,10 +131,10 @@ public PartitionedTreeLikelihood() {
 
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
         // sanity check: alignment should have same #taxa as tree
         if (dataInput.get().getNrTaxa() != treeInput.get().getLeafNodeCount()) {
-            throw new Exception("The number of nodes in the tree does not match the number of sequences");
+            throw new IllegalArgumentException("The number of nodes in the tree does not match the number of sequences");
         }
         m_beagle = null;
 //        m_beagle = new BeagleTreeLikelihood();
@@ -293,7 +293,7 @@ void setPartials(int partition, Node node, int patternCount) {
     int X = 100;
 
     @Override
-    public double calculateLogP() throws Exception {
+    public double calculateLogP() {
         if (m_beagle != null) {
             logP = m_beagle.calculateLogP();
             return logP;
@@ -342,7 +342,7 @@ public double calculateLogP() throws Exception {
         return logP;
     }
 
-    void calcLogP() throws Exception {
+    void calcLogP() {
         logP = 0.0;
         if (m_bAscertainedSitePatterns) {
         	for (int k = 0; k < partitionCount; k++) {
@@ -391,7 +391,7 @@ public void run() {
 
 	CountDownLatch m_nCountDown;
 
-	void threadedTraverse(Node root) throws Exception {
+	void threadedTraverse(Node root) {
 		try {
 			int nPatterns = m_fPatternLogLikelihoods.length;
 			if (partitionCount >= 1) {
@@ -407,7 +407,7 @@ void threadedTraverse(Node root) throws Exception {
 		    		traverse(iThread, partitionProvider.getPatternIndicators(iThread), root);
 		    	}
 			}
-		} catch (RejectedExecutionException e) {
+		} catch (RejectedExecutionException | InterruptedException e) {
 			System.err.println("Reducing nr of threads to 1 because " + e.getMessage());
 			// refresh thread pool
 	    	for (int iThread = 0; iThread < partitionCount; iThread++) {
@@ -418,7 +418,7 @@ void threadedTraverse(Node root) throws Exception {
 
 
     /* Assumes there IS a branch rate model as opposed to traverse() */
-    int traverse(int partition, List<Integer> patternIndicator, Node node) throws Exception {
+    int traverse(int partition, List<Integer> patternIndicator, Node node) {
 
         int update = (node.isDirty() | m_nHasDirt);
 
@@ -467,7 +467,7 @@ int traverse(int partition, List<Integer> patternIndicator, Node node) throws Ex
                 if (m_siteModel[partition].integrateAcrossCategories()) {
                     m_likelihoodCore[partition].calculatePartials(childNum1, childNum2, iNode, patternIndicator);
                 } else {
-                    throw new Exception("Error TreeLikelihood 201: Site categories not supported");
+                    throw new IllegalArgumentException("Error TreeLikelihood 201: Site categories not supported");
                     //m_pLikelihoodCore->calculatePartials(childNum1, childNum2, nodeNum, siteCategories);
                 }
 

src/beast/evolution/operators/FreeRateOperator.java

@@ -17,7 +17,7 @@ public class FreeRateOperator extends Operator {
 
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 	}
 
 	@Override

src/beast/evolution/operators/RBOperator.java

@@ -31,7 +31,7 @@ public class RBOperator extends Operator {
 	ParametricDistribution distr;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		rates = rateInput.get();
 		distr = new Exponential();
 		for (Object plugin : rates.getOutputs()) {

src/beast/evolution/operators/RBScaleOperator.java

@@ -17,10 +17,10 @@ public class RBScaleOperator extends ScaleOperator {
 	Parameter count;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		count = countInput.get();
 		if (treeInput.get() != null) {
-			throw new Exception("A parameter (not a tree) should not be specified");
+			throw new IllegalArgumentException("A parameter (not a tree) should not be specified");
 		}
 		super.initAndValidate();
 	}

src/beast/evolution/sitemodel/FreeRateModel.java

@@ -25,7 +25,7 @@ public class FreeRateModel extends SiteModel.Base {
     RealParameter invarParameter;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
         muParameter = muParameterInput.get();
         if (muParameter == null) {
             muParameter = new RealParameter("1.0");
@@ -62,7 +62,7 @@ public void initAndValidate() throws Exception {
 
 
         if (/*invarParameter != null && */(invarParameter.getValue() < 0 || invarParameter.getValue() > 1)) {
-            throw new Exception("proportion invariant should be between 0 and 1");
+            throw new IllegalArgumentException("proportion invariant should be between 0 and 1");
         }
         refresh();
 

src/beast/evolution/sitemodel/MixtureSiteModel.java

@@ -25,7 +25,7 @@ public class MixtureSiteModel extends DefaultMixtureSiteModel {
 	boolean [] isDirtySiteModel;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		components = componentInput.get();
 		weights = new double[components.size()];
 		updateWeights = true;

src/beast/evolution/sitemodel/MixtureSubstModel.java

@@ -20,7 +20,7 @@ public class MixtureSubstModel extends CalculationNode {
 	SubstitutionModel.Base substitutionModel;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		weight = weightInput.get();
 		rate = rateInput.get();
 		substitutionModel = substModelInput.get();

src/beast/evolution/substitutionmodel/RB.java

@@ -1,6 +1,7 @@
 package beast.evolution.substitutionmodel;
 
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.Arrays;
 
 import beast.core.Citation;
@@ -25,21 +26,26 @@ public class RB extends GeneralSubstitutionModel {
 	IntegerParameter m_count;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		m_count = m_countInput.get();
 		m_rate = ratesInput.get();
 		if (m_rate.getDimension() != 5) {
-			throw new Exception("rate input must have dimension 5");
+			throw new IllegalArgumentException("rate input must have dimension 5");
 		}
 
     	frequencies = frequenciesInput.get();
         updateMatrix = true;
         nrOfStates = frequencies.getFreqs().length;
     	if (nrOfStates != 4) {
-    		throw new Exception("Frequencies has wrong size. Expected 4, but got " + nrOfStates);
+    		throw new IllegalArgumentException("Frequencies has wrong size. Expected 4, but got " + nrOfStates);
     	}
 
-        eigenSystem = createEigenSystem();
+        try {
+			eigenSystem = createEigenSystem();
+		} catch (SecurityException | ClassNotFoundException | InstantiationException | IllegalAccessException | IllegalArgumentException
+				| InvocationTargetException e) {
+			throw new IllegalArgumentException(e);
+		}
         rateMatrix = new double[nrOfStates][nrOfStates];
         relativeRates = new double[nrOfStates * (nrOfStates - 1)];
         storedRelativeRates = new double[nrOfStates * (nrOfStates - 1)];

src/beast/evolution/substitutionmodel/VS.java

@@ -1,5 +1,6 @@
 package beast.evolution.substitutionmodel;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.Arrays;
 
 import beast.core.Citation;
@@ -21,21 +22,26 @@ public class VS extends GeneralSubstitutionModel {
 	IntegerParameter count;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		count = countInput.get();
 		rate = ratesInput.get();
 		if (rate.getDimension() != 5) {
-			throw new Exception("rate input must have dimension 5");
+			throw new IllegalArgumentException("rate input must have dimension 5");
 		}
 
     	frequencies = frequenciesInput.get();
         updateMatrix = true;
         nrOfStates = frequencies.getFreqs().length;
     	if (nrOfStates != 4) {
-    		throw new Exception("Frequencies has wrong size. Expected 4, but got " + nrOfStates);
+    		throw new IllegalArgumentException("Frequencies has wrong size. Expected 4, but got " + nrOfStates);
     	}
 
-        eigenSystem = createEigenSystem();
+        try {
+			eigenSystem = createEigenSystem();
+		} catch (SecurityException | ClassNotFoundException | InstantiationException | IllegalAccessException | IllegalArgumentException
+				| InvocationTargetException e) {
+			throw new IllegalArgumentException(e);
+		}
         rateMatrix = new double[nrOfStates][nrOfStates];
         relativeRates = new double[nrOfStates * (nrOfStates - 1)];
         storedRelativeRates = new double[nrOfStates * (nrOfStates - 1)];

src/beast/math/distributions/RBPrior.java

@@ -15,13 +15,13 @@ public class RBPrior extends Prior {
 	private Parameter counts;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		counts = countInput.get();
 		super.initAndValidate();
 	}
 
 	@Override
-	public double calculateLogP() throws Exception {
+	public double calculateLogP() {
 		Function x = m_x.get();
 		int dim = (int) counts.getArrayValue();
 		double fOffset = dist.offsetInput.get();