/**
* Given a map of name translations (string to string), rewrites all leaf ids that match a key in
* the map to the respective value in the matching key/value pair. If current leaf id is null,
* then interpret translation keys as node numbers (origin 1) and set leaf id of node n to
* map.get(n-1).
*
* @param translationMap map of name translations
*/
public void translateLeafIds(final Map<String, String> translationMap) {
for (final Node leaf : getExternalNodes()) {
String id = leaf.getID();
if (id == null || !integerLeafLabels) {
id = Integer.toString(leaf.getNr() + 1);
}
final String newId = translationMap.get(id);
if (newId != null) {
leaf.setID(newId);
}
}
}
@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;
}