private void writeNode(Tree tree, NodeRef node, boolean attributes, Map<String, Integer> idMap) {
if (tree.isExternal(node)) {
int k = node.getNumber() + 1;
if (idMap != null) k = idMap.get(tree.getTaxonId(k - 1));
out.print(k);
} else {
out.print("(");
writeNode(tree, tree.getChild(node, 0), attributes, idMap);
for (int i = 1; i < tree.getChildCount(node); i++) {
out.print(",");
writeNode(tree, tree.getChild(node, i), attributes, idMap);
}
out.print(")");
}
if (writeAttributesAs == AttributeType.BRANCH_ATTRIBUTES && !tree.isRoot(node)) {
out.print(":");
}
if (attributes) {
Iterator<?> iter = tree.getNodeAttributeNames(node);
if (iter != null) {
boolean first = true;
while (iter.hasNext()) {
if (first) {
out.print("[&");
first = false;
} else {
out.print(",");
}
String name = (String) iter.next();
out.print(name + "=");
Object value = tree.getNodeAttribute(node, name);
printValue(value);
}
out.print("]");
}
}
if (writeAttributesAs == AttributeType.NODE_ATTRIBUTES && !tree.isRoot(node)) {
out.print(":");
}
if (!tree.isRoot(node)) {
double length = tree.getBranchLength(node);
if (formatter != null) {
out.print(formatter.format(length));
} else {
out.print(length);
}
}
}
public Map<String, Integer> writeNexusHeader(Tree tree) {
int taxonCount = tree.getTaxonCount();
List<String> names = new ArrayList<String>();
for (int i = 0; i < tree.getTaxonCount(); i++) {
names.add(tree.getTaxonId(i));
}
if (sorted) Collections.sort(names);
out.println("#NEXUS");
out.println();
out.println("Begin taxa;");
out.println("\tDimensions ntax=" + taxonCount + ";");
out.println("\tTaxlabels");
for (String name : names) {
if (name.matches(SPECIAL_CHARACTERS_REGEX)) {
name = "'" + name + "'";
}
out.println("\t\t" + name);
}
out.println("\t\t;");
out.println("End;");
out.println("");
out.println("Begin trees;");
// This is needed if the trees use numerical taxon labels
out.println("\tTranslate");
Map<String, Integer> idMap = new HashMap<String, Integer>();
int k = 1;
for (String name : names) {
idMap.put(name, k);
if (name.matches(SPECIAL_CHARACTERS_REGEX)) {
name = "'" + name + "'";
}
if (k < names.size()) {
out.println("\t\t" + k + " " + name + ",");
} else {
out.println("\t\t" + k + " " + name);
}
k += 1;
}
return idMap;
}