Log internal node sequences #518

lphy-base/src/main/java/lphy/base/evolution/tree/TimeTree.java

@@ -131,7 +131,7 @@ private void toNewick(TimeTreeNode node, StringBuilder builder, boolean includeS
             toNewick(node.getChildren().get(0), builder, includeSingleChildNodes);
         } else {
             if (node.isLeaf()) {
-                builder.append(node.id);
+                builder.append(node.getId());
                 // update to handle more than one element in metaData
                 addMetaData(node, builder);
             } else {
@@ -144,6 +144,10 @@ private void toNewick(TimeTreeNode node, StringBuilder builder, boolean includeS
                 }
                 builder.append(")");
             }
+
+            if (!node.isLeaf() && node.getId() != null)
+                builder.append(node.getId());
+
             if (node.isRoot()) {
                 builder.append(":0.0;");
             } else {

lphy-base/src/main/java/lphy/base/function/tree/InternalNodesID.java

@@ -0,0 +1,39 @@
+package lphy.base.function.tree;
+
+import lphy.base.evolution.tree.TimeTree;
+import lphy.base.evolution.tree.TimeTreeNode;
+import lphy.core.model.DeterministicFunction;
+import lphy.core.model.Value;
+import lphy.core.model.annotation.GeneratorCategory;
+import lphy.core.model.annotation.GeneratorInfo;
+import lphy.core.model.annotation.ParameterInfo;
+
+import static lphy.base.evolution.EvolutionConstants.treeParamName;
+
+/**
+ * A function to set internal nodes id given a tree
+ */
+public class InternalNodesID extends DeterministicFunction<TimeTree> {
+
+    public InternalNodesID(@ParameterInfo(name = treeParamName,
+            description = "the tree to set internal nodes id.") Value<TimeTree> tree) {
+        setParam(treeParamName, tree);
+    }
+
+    @GeneratorInfo(name = "setInternalNodesID", category = GeneratorCategory.TREE,
+            description = "set internal nodes id given a tree.")
+    public Value<TimeTree> apply() {
+
+        Value<TimeTree> tree = getParams().get(treeParamName);
+
+        // do deep copy
+        TimeTree newTree = new TimeTree(tree.value());
+
+        for (TimeTreeNode node : newTree.getInternalNodes()) {
+            if (node.getId() == null) // set index as id
+                node.setId(String.valueOf(node.getIndex()));
+        }
+
+        return new Value<>(null, newTree, this);
+    }
+}

lphy-base/src/main/java/lphy/base/spi/LPhyBaseImpl.java

@@ -27,10 +27,7 @@
 import lphy.base.function.datatype.StandardDatatypeFunction;
 import lphy.base.function.io.*;
 import lphy.base.function.taxa.*;
-import lphy.base.function.tree.ExtantTree;
-import lphy.base.function.tree.MigrationCount;
-import lphy.base.function.tree.Newick;
-import lphy.base.function.tree.PruneTree;
+import lphy.base.function.tree.*;
 import lphy.core.model.BasicFunction;
 import lphy.core.model.GenerativeDistribution;
 import lphy.core.spi.LPhyCoreImpl;
@@ -91,8 +88,9 @@ public List<Class<? extends BasicFunction>> declareFunctions() {
                 SelectSitesByMissingFraction.class, RemoveTaxa.class,
                 VariableSites.class, InvariableSites.class, CopySites.class,
                 // Tree
-                LocalBranchRates.class, ExtantTree.class, PruneTree.class, LocalClock.class,
-                SubstituteClade.class, MRCA.class, LabelClade.class,//NodeCount.class, TreeLength.class,
+                LocalBranchRates.class, LocalClock.class,
+                ExtantTree.class, PruneTree.class, InternalNodesID.class,
+                SubstituteClade.class, MRCA.class, LabelClade.class, //NodeCount.class, TreeLength.class,
                 // Matrix
                 BinaryRateMatrix.class, MigrationMatrix.class, MigrationCount.class,
                 // IO