src/beast/base/evolution/TreeWithMetaDataLogger.java

@@ -123,11 +123,15 @@ String toNewick(Node node, List<Function> metadataList, BranchRateModel.Base bra
 		if (someMetaDataNeedsLogging) {
 			buf2.append("[&");
 			if (metadataList.size() > 0) {
+				boolean needsComma = false;
 				for (Function metadata : metadataList) {
 					if (metadata instanceof Parameter<?>) {
 						Parameter<?> p = (Parameter<?>) metadata;
 						int dim = p.getMinorDimension1();
 						if (p.getMinorDimension2() > node.getNr()) {
+							if (needsComma) {
+								buf2.append(",");
+							}
 							buf2.append(((BEASTObject) metadata).getID());
 							buf2.append('=');
 							if (dim > 1) {
@@ -152,19 +156,21 @@ String toNewick(Node node, List<Function> metadataList, BranchRateModel.Base bra
 									buf2.append(metadata.getArrayValue(node.getNr()));
 								}
 							}
+							needsComma = true;
 						} else {
 
 						}
 					} else {
 						if (metadata.getDimension() > node.getNr()) {
+							if (needsComma) {
+								buf2.append(",");
+							}
 							buf2.append(((BEASTObject) metadata).getID());
 							buf2.append('=');
 							buf2.append(metadata.getArrayValue(node.getNr()));
+							needsComma = true;
 						}
 					}
-					if (buf2.length() > 2 && metadataList.indexOf(metadata) < metadataList.size() - 1) {
-						buf2.append(",");
-					}
 				}
 				if (buf2.length() > 2 && branchRateModel != null) {
 					buf2.append(",");

src/beast/base/evolution/alignment/Alignment.java

@@ -24,23 +24,19 @@
 */
 package beast.base.evolution.alignment;
 
-import java.io.PrintStream;
-import java.util.*;
 
-import org.w3c.dom.Node;
+import java.util.*;
 
 import beast.base.core.Description;
 import beast.base.core.Input;
 import beast.base.core.Log;
 import beast.base.core.Input.Validate;
 import beast.base.evolution.datatype.DataType;
-import beast.base.inference.StateNode;
-import beast.base.inference.parameter.Map;
 import beast.pkgmgmt.BEASTClassLoader;
 import beast.pkgmgmt.PackageManager;
 
 @Description("Class representing alignment data")
-public class Alignment extends Map<String> {
+public class Alignment extends TreeTipData {
 
     @Override
 	protected Class<?> mapType() {
@@ -105,12 +101,8 @@ static public DataType getDataTypeByName(String name) {
     final public Input<List<Sequence>> sequenceInput =
             new Input<>("sequence", "sequence and meta data for particular taxon", new ArrayList<>(), Validate.OPTIONAL);
 
-    final public Input<TaxonSet> taxonSetInput =
-            new Input<>("taxa", "An optional taxon-set used only to sort the sequences into the same order as they appear in the taxon-set.", new TaxonSet(), Validate.OPTIONAL);
-
     final public Input<Integer> stateCountInput = new Input<>("statecount", "maximum number of states in all sequences");
     final public Input<String> dataTypeInput = new Input<>("dataType", "data type, one of " + types, NUCLEOTIDE, types.keySet().toArray(new String[0]));
-    final public Input<DataType.Base> userDataTypeInput = new Input<>("userDataType", "non-standard, user specified data type, if specified 'dataType' is ignored");
     final public Input<Boolean> stripInvariantSitesInput = new Input<>("strip", "sets weight to zero for sites that are invariant (e.g. all 1, all A or all unkown)", false);
     final public Input<String> siteWeightsInput = new Input<>("weights", "comma separated list of weights, one for each site in the sequences. If not specified, each site has weight 1");
 
@@ -885,96 +877,6 @@ public String getSequenceAsString(String taxon) {
 	        return freqs;
 	  } // calcFrequencies
 
-	@Override
-	public void init(PrintStream out) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void log(long sample, PrintStream out) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void close(PrintStream out) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public int getDimension() {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public double getArrayValue(int dim) {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	public void setEverythingDirty(boolean isDirty) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public StateNode copy() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public void assignTo(StateNode other) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void assignFrom(StateNode other) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void assignFromFragile(StateNode other) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void fromXML(Node node) {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public String toXML() {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public int scale(double scale) {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-
-	@Override
-	protected void store() {
-		// TODO Auto-generated method stub
-
-	}
-
-	@Override
-	public void restore() {
-		// TODO Auto-generated method stub
-
-	}
-
 
 	@Override
 	public boolean notCloneable() {

src/beast/base/evolution/alignment/TreeTipData.java

@@ -0,0 +1,98 @@
+package beast.base.evolution.alignment;
+
+
+import java.io.PrintStream;
+
+import org.w3c.dom.Node;
+
+import beast.base.core.Description;
+import beast.base.core.Input;
+import beast.base.core.Input.Validate;
+import beast.base.evolution.datatype.DataType;
+import beast.base.inference.StateNode;
+import beast.base.inference.parameter.Map;
+
+@Description("Generic class for associating data to tips of a tree, e.g. an Alignment.")
+public class TreeTipData extends Map<String> {
+
+    final public Input<TaxonSet> taxonSetInput =
+            new Input<>("taxa", "An optional taxon-set used only to sort the sequences into the same order as they appear in the taxon-set.", new TaxonSet(), Validate.OPTIONAL);
+
+    final public Input<DataType.Base> userDataTypeInput = new Input<>("userDataType", "non-standard, user specified data type, if specified 'dataType' is ignored");
+
+	/** Loggable implementation **/
+
+    @Override
+	public void init(PrintStream out) {
+	}
+
+	@Override
+	public void log(long sample, PrintStream out) {
+	}
+
+	@Override
+	public void close(PrintStream out) {
+	}
+
+
+	/** Function implementation **/
+
+	@Override
+	public int getDimension() {
+		return 0;
+	}
+
+	@Override
+	public double getArrayValue(int dim) {
+		return 0;
+	}
+
+	/** Map implementation **/
+
+	@Override
+	protected Class<?> mapType() {
+        return String.class;
+	}
+
+
+	/** StateNode implementation **/
+
+	@Override
+	public void setEverythingDirty(boolean isDirty) {
+	}
+
+	@Override
+	public StateNode copy() {
+		return null;
+	}
+
+	@Override
+	public void assignTo(StateNode other) {
+	}
+
+	@Override
+	public void assignFrom(StateNode other) {
+	}
+
+	@Override
+	public void assignFromFragile(StateNode other) {
+	}
+
+	@Override
+	public void fromXML(Node node) {
+	}
+
+	@Override
+	public int scale(double scale) {
+		return 0;
+	}
+
+	@Override
+	protected void store() {
+	}
+
+	@Override
+	public void restore() {
+	}
+
+}