sync with beast2 exception overhaul

BEAST2-Dev · Feb 22, 2016 · 04c0e63 · 04c0e63
1 parent 15b467e
commit 04c0e63
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Showing 33 changed files with 77 additions and 57 deletions.
diff --git a/src/beast/app/beauti/BeautiDiscreteTraitProvider.java b/src/beast/app/beauti/BeautiDiscreteTraitProvider.java
@@ -34,7 +34,7 @@
 public class BeautiDiscreteTraitProvider extends BeautiAlignmentProvider {
 
 	@Override
-	List<BEASTInterface> getAlignments(BeautiDoc doc) {
+	protected List<BEASTInterface> getAlignments(BeautiDoc doc) {
 		try {
             List<String> trees = new ArrayList<String>();
             doc.scrubAll(true, false);

diff --git a/src/beast/app/beauti/BeautiLocationTraitProvider.java b/src/beast/app/beauti/BeautiLocationTraitProvider.java
@@ -23,7 +23,7 @@
 public class BeautiLocationTraitProvider extends BeautiAlignmentProvider {
 
 	@Override
-	List<BEASTInterface> getAlignments(BeautiDoc doc) {
+	protected List<BEASTInterface> getAlignments(BeautiDoc doc) {
 		try {
             List<String> trees = new ArrayList<String>();
             doc.scrubAll(true, false);

diff --git a/src/beast/continuous/AbstractMultivariateTraitLikelihood.java b/src/beast/continuous/AbstractMultivariateTraitLikelihood.java
@@ -76,7 +76,7 @@ public abstract class AbstractMultivariateTraitLikelihood extends GenericTreeLik
     protected double[] m_StoredBranchLengths;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
         //super.initAndValidate();
         m_branchLengths = new double[0];
         m_StoredBranchLengths = new double[0];
@@ -125,7 +125,7 @@ public void initAndValidate() throws Exception {
         if (dataInput.get() instanceof AlignmentFromTraitMap) {
         	traitMap = ((AlignmentFromTraitMap) dataInput.get()).getTraitMap();
         } else {
-        	throw new Exception ("Expected that data input is AlignmentFromTraitMap");
+        	throw new IllegalArgumentException ("Expected that data input is AlignmentFromTraitMap");
         }
         recalculateTreeLength();                           
 //        printInformtion();
@@ -492,7 +492,7 @@ public final double getLogLikelihood() {
     }
 
     @Override
-    public double calculateLogP() throws Exception {
+    public double calculateLogP() {
     	logP = getLogLikelihood();
     	return logP;
     }

diff --git a/src/beast/continuous/IntegratedMultivariateTraitLikelihood.java b/src/beast/continuous/IntegratedMultivariateTraitLikelihood.java
@@ -113,7 +113,7 @@ public abstract class IntegratedMultivariateTraitLikelihood extends AbstractMult
 //        super(traitName, treeModel, diffusionModel, traitParameter, deltaParameter, missingIndices, cacheBranches, scaleByTime,
 //                useTreeLength, rateModel, driftModels, samplingDensity, reportAsMultivariate, reciprocalRates);
 
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	super.initAndValidate();
 
         // Delegate caches to helper

diff --git a/src/beast/continuous/MultivariateDiffusionModel.java b/src/beast/continuous/MultivariateDiffusionModel.java
@@ -26,12 +26,12 @@ public class MultivariateDiffusionModel extends ContinuousSubstitutionModel {
     int dimension;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	//diffusionPrecisionMatrix = 
         this.diffusionPrecisionMatrixParameter = diffusionPrecisionMatrixInput.get();
         dimension = (int) Math.sqrt(diffusionPrecisionMatrixParameter.getDimension());
         if (dimension * dimension != diffusionPrecisionMatrixParameter.getDimension()) {
-        	throw new Exception ("Dimension of diffusion matrix should be a square");
+        	throw new IllegalArgumentException ("Dimension of diffusion matrix should be a square");
         }
         calculatePrecisionInfo();
     }

diff --git a/src/beast/continuous/SampledMultivariateTraitLikelihood.java b/src/beast/continuous/SampledMultivariateTraitLikelihood.java
@@ -44,7 +44,7 @@ public class SampledMultivariateTraitLikelihood extends AbstractMultivariateTrai
 	public Input<Boolean> initFromTree = new Input<Boolean>("initFromTree","initiliase initial state from tree", false);
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		super.initAndValidate();
 		if (initFromTree.get()) {
 			Node [] nodes = treeModel.getNodesAsArray();

diff --git a/src/beast/evolution/alignment/AlignmentFromTrait.java b/src/beast/evolution/alignment/AlignmentFromTrait.java
@@ -26,7 +26,7 @@ public AlignmentFromTrait() {
 	    }
 
 	    @Override
-	    public void initAndValidate() throws Exception {
+	    public void initAndValidate() {
 	    	traitSet = traitInput.get();
 	    	patternIndex = new int[0];
 	        counts = new ArrayList<List<Integer>>();
@@ -37,12 +37,17 @@ public void initAndValidate() throws Exception {
 	            m_dataType = userDataTypeInput.get();
 	        } else {
 	            if (types.indexOf(dataTypeInput.get()) < 0) {
-	                throw new Exception("data type + '" + dataTypeInput.get() + "' cannot be found. " +
+	                throw new IllegalArgumentException("data type + '" + dataTypeInput.get() + "' cannot be found. " +
 	                        "Choose one of " + Arrays.toString(types.toArray(new String[0])));
 	            }
 	            List<String> sDataTypes = AddOnManager.find(beast.evolution.datatype.DataType.class, IMPLEMENTATION_DIR);
 	            for (String sDataType : sDataTypes) {
-	                DataType dataType = (DataType) Class.forName(sDataType).newInstance();
+	                DataType dataType = null;
+					try {
+						dataType = (DataType) Class.forName(sDataType).newInstance();
+					} catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) {
+						throw new IllegalArgumentException(e);
+					}
 	                if (dataTypeInput.get().equals(dataType.getTypeDescription())) {
 	                    m_dataType = dataType;
 	                    break;
@@ -61,7 +66,7 @@ public void initAndValidate() throws Exception {
 	        for (int i = 0; i < taxaNames.size(); i++) {
 	        	String sValue = traitSet.getStringValue(i);
 	        	if (sValue == null) {
-	        		throw new Exception("Trait not specified for " + i);
+	        		throw new IllegalArgumentException("Trait not specified for " + i);
 	        	}
 	        	List<Integer> iStates = m_dataType.string2state(sValue);
 	        	counts.add(iStates);

diff --git a/src/beast/evolution/alignment/AlignmentFromTraitMap.java b/src/beast/evolution/alignment/AlignmentFromTraitMap.java
@@ -27,7 +27,7 @@ public AlignmentFromTraitMap() {
 	}
 
 	@Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	traitMap = traitInput.get();
     	patternIndex = new int[0];
         counts = new ArrayList<List<Integer>>();
@@ -36,7 +36,7 @@ public void initAndValidate() throws Exception {
     	}
     	m_dataType = userDataTypeInput.get();
         if (!(m_dataType instanceof ContinuousDataType)) {
-        	throw new Exception("Data type must be a ContinuousDataType, not " + m_dataType.getClass().getName());
+        	throw new IllegalArgumentException("Data type must be a ContinuousDataType, not " + m_dataType.getClass().getName());
         }
 
         taxaNames = new ArrayList<String>();

diff --git a/src/beast/evolution/datatype/ContinuousDataType.java b/src/beast/evolution/datatype/ContinuousDataType.java
@@ -22,7 +22,7 @@ public int getStateCount() {
 	}
 
 	@Override
-	public List<Integer> string2state(String sSequence) throws Exception {
+	public List<Integer> string2state(String sSequence) {
 		return null;
 	}
 

diff --git a/src/beast/evolution/datatype/LocationDataType.java b/src/beast/evolution/datatype/LocationDataType.java
@@ -6,7 +6,7 @@
 public class LocationDataType extends ContinuousDataType {
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		// nothing to do
 	}
 

diff --git a/src/beast/evolution/likelihood/AncestralStateTreeLikelihood.java b/src/beast/evolution/likelihood/AncestralStateTreeLikelihood.java
@@ -70,7 +70,7 @@ public class AncestralStateTreeLikelihood extends TreeLikelihood implements Tree
     int[][] tipStates; // used to store tip states when using beagle
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	if (dataInput.get().getSiteCount() == 0) {
     		return;
     	}
@@ -127,7 +127,7 @@ public String getTraitString(TreeInterface tree, Node node) {
 //        }
         if (beagle != null) {
             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();
         	substitutionModel = (SubstitutionModel.Base) m_siteModel.substModelInput.get();
@@ -179,7 +179,7 @@ public String getTraitString(TreeInterface tree, Node node) {
 			parameters[i] = leafTrait.parameter.get();
 			// sanity check
 			if (parameters[i].getDimension() != traitDimension) {
-				throw new Exception("Expected parameter dimension to be " + traitDimension + ", not "
+				throw new IllegalArgumentException("Expected parameter dimension to be " + traitDimension + ", not "
 						+ parameters[i].getDimension());
 			}
 			// identify node
@@ -191,7 +191,7 @@ public String getTraitString(TreeInterface tree, Node node) {
 			leafNr[i] = k;
 			// sanity check
 			if (k == taxaNames.size()) {
-				throw new Exception("Could not find taxon '" + taxon + "' in tree");
+				throw new IllegalArgumentException("Could not find taxon '" + taxon + "' in tree");
 			}
 			// initialise parameter value from states
 			Integer[] values = new Integer[tipStates[k].length];
@@ -334,7 +334,7 @@ public void redrawAncestralStates() {
 
 
     @Override
-    public double calculateLogP() throws Exception {
+    public double calculateLogP() {
         areStatesRedrawn = false;
         double marginalLogLikelihood = super.calculateLogP();
         if (returnMarginalLogLikelihood) {

diff --git a/src/beast/evolution/likelihood/LeafTrait.java b/src/beast/evolution/likelihood/LeafTrait.java
@@ -11,7 +11,7 @@ public class LeafTrait extends CalculationNode {
 	public Input<String> taxonName = new Input<String>("taxon", "taxon name identifying the leaf", Validate.REQUIRED);
 	public Input<IntegerParameter> parameter = new Input<IntegerParameter>("parameter", "parameter associated with the leaf", Validate.REQUIRED);
 
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		// nothing to do
 	};
 }
diff --git a/src/beast/evolution/operators/GMRFSkyrideBlockUpdateOperator.java b/src/beast/evolution/operators/GMRFSkyrideBlockUpdateOperator.java
@@ -48,7 +48,7 @@ public class GMRFSkyrideBlockUpdateOperator extends Operator {
     private double[] zeros;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
         gmrfField = GMRFSkyrideLikelihoodInput .get();
         popSizeParameter = gmrfField.getPopSizeParameter();
         precisionParameter = gmrfField.getPrecisionParameter();
@@ -385,7 +385,7 @@ public void optimize(double logAlpha) {
     }
 
     @Override
-    public List<StateNode> listStateNodes() throws Exception {
+    public List<StateNode> listStateNodes() {
     	List<StateNode> list = new ArrayList<StateNode>();
         list.add(precisionParameter);
         if (lambdaParameter.isEstimatedInput.get()) {

diff --git a/src/beast/evolution/operators/GeneralIntegerOperator.java b/src/beast/evolution/operators/GeneralIntegerOperator.java
@@ -28,7 +28,7 @@ public class GeneralIntegerOperator extends Operator {
 	IntegerParameter parameter;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		howMany = howManyyInput.get();
 
 		parameter = parameterInput.get();
@@ -61,7 +61,7 @@ public void initAndValidate() throws Exception {
     		RealParameter probsParam = probsInput.get();
     		IntegerParameter indexParam = indexInput.get();
     		if (probsParam.getDimension() != indexParam.getDimension()) {
-    			throw new Exception("probs and index must be of the same length");
+    			throw new IllegalArgumentException("probs and index must be of the same length");
     		}
     		Integer [] indices = indexParam.getValues();
     		int max = 0;
@@ -80,7 +80,7 @@ public void initAndValidate() throws Exception {
     		sum += f;
     	}
     	if (Math.abs(sum - 1.0) > 1e-6) {
-    		throw new Exception("Probabilities must sum to one (instead of " + sum + ")");
+    		throw new IllegalArgumentException("Probabilities must sum to one (instead of " + sum + ")");
     	}
 
     	// convert to cumulative pdf

diff --git a/src/beast/evolution/operators/PrecisionMatrixGibbsOperator.java b/src/beast/evolution/operators/PrecisionMatrixGibbsOperator.java
@@ -77,7 +77,7 @@ public class PrecisionMatrixGibbsOperator extends Operator {
     TreeTraitMap traitMap;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	traitMap = mapInput.get();
     	treeModel = treeInput.get();
     	precisionParam = precisionParamInput.get();

diff --git a/src/beast/evolution/operators/RegressionGibbsEffectOperator.java b/src/beast/evolution/operators/RegressionGibbsEffectOperator.java
@@ -39,7 +39,7 @@ public class RegressionGibbsEffectOperator extends Operator {
     private double[][] precision = null;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
         this.linearModel = linearModelInput.get();
         this.effect = effectInput.get();
         this.indicators = indicatorsInput.get();

diff --git a/src/beast/evolution/operators/RegressionGibbsPrecisionOperator.java b/src/beast/evolution/operators/RegressionGibbsPrecisionOperator.java
@@ -30,7 +30,7 @@ public class RegressionGibbsPrecisionOperator extends Operator {
     private Gamma prior;
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     //if (!(prior instanceof GammaDistribution))
         //      throw new RuntimeException("Precision prior must be Gamma");
         this.prior = priorInput.get();

diff --git a/src/beast/evolution/operators/SphereRandomWalker.java b/src/beast/evolution/operators/SphereRandomWalker.java
@@ -41,7 +41,7 @@ public class SphereRandomWalker extends Operator {
 	boolean optimise = false;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		location = locationInput.get();
 		windowSize = windowSizeInput.get();
 		range = 1 + location.getDimension()/2;

diff --git a/src/beast/evolution/operators/TraitGibbsOperator.java b/src/beast/evolution/operators/TraitGibbsOperator.java
@@ -97,7 +97,7 @@ public class TraitGibbsOperator extends Operator {
 	TreeTraitMap traitMap;
 
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
     	traitMap = mapInput.get();
 
 		this.traitModel = traitModelInput.get();

diff --git a/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java b/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java
@@ -2,6 +2,7 @@
 
 
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.Arrays;
 
 import beast.core.Function;
@@ -36,14 +37,14 @@ public class SVSGeneralSubstitutionModel extends GeneralSubstitutionModel implem
     private BooleanParameter rateIndicator;
 
     @Override
-    public void initAndValidate() throws Exception{
+    public void initAndValidate(){
 
         frequencies = frequenciesInput.get();
 
         updateMatrix = true;
         nrOfStates = frequencies.getFreqs().length;
         if (isSymmetricInput.get() && ratesInput.get().getDimension() != nrOfStates * (nrOfStates-1)/2) {
-            throw new Exception("Dimension of input 'rates' is " + ratesInput.get().getDimension() + " but a " +
+            throw new IllegalArgumentException("Dimension of input 'rates' is " + ratesInput.get().getDimension() + " but a " +
                     "rate matrix of dimension " + nrOfStates + "x" + (nrOfStates -1) + "/2" + "=" + nrOfStates * (nrOfStates -1) / 2 + " was " +
                     "expected");
         }
@@ -62,7 +63,12 @@ public void initAndValidate() throws Exception{
         	Log.warning.println("WARNING: eigenSystemClass is DefautlEigneSystem, which may cause trouble with asymtric analysis. "
         			+ "You may want to consider eigensystem='beast.evolution.substitutionmodel.RobustEigenSystem' instead.");
         }
-        eigenSystem = createEigenSystem();
+        try {
+			eigenSystem = createEigenSystem();
+		} catch (SecurityException | ClassNotFoundException | InstantiationException | IllegalAccessException | IllegalArgumentException
+				| InvocationTargetException e) {
+			throw new IllegalArgumentException(e);
+		}
 
 //        if (robust.get()){
 //            eigenSystem = new RobustEigenSystem(m_nStates);

diff --git a/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java b/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java
@@ -51,7 +51,7 @@ public class SVSGeneralSubstitutionModelLogger extends BEASTObject implements Lo
     public SVSGeneralSubstitutionModelLogger() { }
 
     @Override
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
         model = modelInput.get();
     }
 

diff --git a/src/beast/evolution/tree/RootTrait.java b/src/beast/evolution/tree/RootTrait.java
@@ -17,7 +17,7 @@ public class RootTrait extends CalculationNode implements Function, Loggable {
     RealParameter parameter;
     int dim;
 
-    public void initAndValidate() throws Exception {
+    public void initAndValidate() {
     	map = mapInput.get();
     	tree = map.tree;
     	parameter = map.parameterInput.get();

diff --git a/src/beast/evolution/tree/TreeTraitMap.java b/src/beast/evolution/tree/TreeTraitMap.java
@@ -40,7 +40,7 @@ public class TreeTraitMap extends CalculationNode implements TreeTrait<double[]>
 
 	double [] traitvalues;
 	@Override
-	public void initAndValidate() throws Exception {
+	public void initAndValidate() {
 		tree = treeInput.get();
 		int nNodes = tree.getNodeCount();
 		parameter = parameterInput.get();
@@ -111,12 +111,12 @@ public void initAndValidate() throws Exception {
                     }
 		            String[] sStrs = sTrait.split("=");
 		            if (sStrs.length != 2) {
-		                throw new Exception("could not parse trait: " + sTrait);
+		                throw new IllegalArgumentException("could not parse trait: " + sTrait);
 		            }
 		            String sTaxonID = normalize(sStrs[0]);
 		            int iTaxon = sTaxa.indexOf(sTaxonID);
 		            if (iTaxon < 0) {
-		                throw new Exception("Trait (" + sTaxonID + ") is not a known taxon. Spelling error perhaps?");
+		                throw new IllegalArgumentException("Trait (" + sTaxonID + ") is not a known taxon. Spelling error perhaps?");
 		            }
 		            String sTraitValue = normalize(sStrs[1]);
 		            String [] sTraitValues = sTraitValue.split("\\s");
@@ -129,7 +129,7 @@ public void initAndValidate() throws Exception {
 		            	}
 		            }
 		            if (bDone[iTaxon]) {
-		            	throw new Exception("Trait for taxon " + sTaxa.get(iTaxon)+ " defined twice");
+		            	throw new IllegalArgumentException("Trait for taxon " + sTaxa.get(iTaxon)+ " defined twice");
 		            }
 		            bDone[iTaxon] = true;
 		        }

diff --git a/src/beast/evolution/tree/TreeTraitProvider.java b/src/beast/evolution/tree/TreeTraitProvider.java
@@ -133,7 +133,7 @@ public TreeTrait<?> getTreeTrait(String key) {
         private Map<String, TreeTrait<?>> traits = new HashMap<String, TreeTrait<?>>();
 
 		@Override
-		public void initAndValidate() throws Exception {
+		public void initAndValidate() {
 			// nothing to do
 		}
     }