@Test
public void testOperator2() throws Exception {
Tree tree;
int taxaSize = 3;
// make a caterpillar
Node left = new ZeroBranchSANode();
left.setNr(0);
left.setHeight(0.0);
for (int i = 1; i < taxaSize; i++) {
Node right = new ZeroBranchSANode();
right.setNr(i);
right.setHeight(i);
Node parent = new ZeroBranchSANode();
parent.setNr(taxaSize + i - 1);
parent.setHeight(i);
left.setParent(parent);
parent.setLeft(left);
right.setParent(parent);
parent.setRight(right);
left = parent;
}
left.setHeight(left.getRight().getHeight() + 2);
tree = new Tree(left);
System.out.println("Tree was = " + tree.getRoot().toShortNewick(false));
TreeDimensionJump operator = new TreeDimensionJump();
operator.initByName("tree", tree);
double logHastingsRatio = operator.proposal();
System.out.println("Proposed tree = " + tree.getRoot().toShortNewick(false));
System.out.println("Log Hastings ratio = " + logHastingsRatio);
}
/**
* Number any nodes in a clade which were not explicitly numbered by the parsed string.
*
* @param node clade parent
*/
private void numberUnnumberedNodes(Node node) {
if (node.isLeaf()) return;
for (Node child : node.getChildren()) {
numberUnnumberedNodes(child);
}
if (node.getNr() < 0) node.setNr(numberedNodeCount);
numberedNodeCount += 1;
}
@Override
public Node visitNode(NewickParser.NodeContext ctx) {
Node node = newNode();
for (NewickParser.NodeContext ctxChild : ctx.node()) {
node.addChild(visit(ctxChild));
}
NewickParser.PostContext postCtx = ctx.post();
// Process metadata
if (postCtx.meta() != null) {
node.metaDataString = "";
for (int i = 0; i < postCtx.meta().attrib().size(); i++) {
if (i > 0) node.metaDataString += ",";
node.metaDataString += postCtx.meta().attrib().get(i).getText();
}
if (!suppressMetadata) {
for (NewickParser.AttribContext attribctx : postCtx.meta().attrib()) {
String key = attribctx.attribKey.getText();
if (attribctx.attribValue().number() != null) {
node.setMetaData(key, Double.parseDouble(attribctx.attribValue().number().getText()));
} else if (attribctx.attribValue().STRING() != null) {
String stringValue = attribctx.attribValue().STRING().getText();
if (stringValue.startsWith("\"") || stringValue.startsWith("\'")) ;
stringValue = stringValue.substring(1, stringValue.length() - 1);
node.setMetaData(key, stringValue);
} else {
// BEAST doesn't do anything with vectors yet.
}
}
}
}
// Process edge length
if (postCtx.length != null) node.setHeight(Double.parseDouble(postCtx.length.getText()));
else node.setHeight(DEFAULT_LENGTH);
// Process label
node.setNr(-1);
if (postCtx.label() != null) {
node.setID(postCtx.label().getText());
if (postCtx.label().number() == null || postCtx.label().number().INT() == null)
integerLeafLabels = false;
// RRB: next line is for debugging only?
@SuppressWarnings("unused")
String postText = postCtx.getText();
// Treat labels as node numbers in certain situations
if (!isLabelledNewickInput.get()
&& postCtx.label().number() != null
&& postCtx.label().number().INT() != null) {
int nodeNr = Integer.parseInt(postCtx.label().getText()) - offsetInput.get();
if (nodeNr < 0)
throw new ParseCancellationException(
"Node number given "
+ "is smaller than current offset ("
+ offsetInput.get()
+ "). Perhaps offset is "
+ "too high?");
node.setNr(nodeNr);
numberedNodeCount += 1;
} else {
if (node.isLeaf()) {
node.setNr(getLabelIndex(postCtx.label().getText()));
numberedNodeCount += 1;
}
}
}
if (node.getChildCount() == 1 && !allowSingleChildInput.get())
throw new ParseCancellationException("Node with single child found.");
if (node.getChildCount() > 2)
throw new ParseCancellationException("Node with two or more children found.");
return node;
}