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;
}
private void setStatusMessage() {
Tree tree = treesPanel.getTree();
if (tree != null) {
String message = "";
message += "Tree loaded, " + tree.getTaxonCount() + " taxa";
TemporalRooting tr = treesPanel.getTemporalRooting();
if (tr.isContemporaneous()) {
message += ", contemporaneous tips";
} else {
NumberFormatter nf = new NumberFormatter(3);
message += ", dated tips with range " + nf.format(tr.getDateRange());
}
statusLabel.setText(message);
}
}