/**
* Create a tree from the given newick format
*
* @param taxaNames a list of taxa names to use, or null. If null then IsLabelledNewick will be
* set to true
* @param newick the newick of the tree
* @param offset the offset to map node numbers in newick format to indices in taxaNames. so,
* name(node with nodeNumber) = taxaNames[nodeNumber-offset]
* @param adjustTipHeightsWhenMissingDateTraits true if tip heights should be adjusted to zero
* @throws Exception
*/
public TreeParser(
final List<String> taxaNames,
final String newick,
final int offset,
final boolean adjustTipHeightsWhenMissingDateTraits)
throws Exception {
if (taxaNames == null) {
isLabelledNewickInput.setValue(true, this);
} else {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(taxaNames)), this);
}
newickInput.setValue(newick, this);
offsetInput.setValue(offset, this);
adjustTipHeightsInput.setValue(adjustTipHeightsWhenMissingDateTraits, this);
labels = taxaNames;
initAndValidate();
}
/** Ensure the class behaves properly, even when inputs are not specified. */
@Override
public void initAndValidate() throws Exception {
boolean sortNodesAlphabetically = false;
if (dataInput.get() != null) {
labels = dataInput.get().getTaxaNames();
} else if (m_taxonset.get() != null) {
if (labels == null) {
labels = m_taxonset.get().asStringList();
} else { // else labels were set by TreeParser c'tor
sortNodesAlphabetically = true;
}
} else {
if (isLabelledNewickInput.get()) {
if (m_initial.get() != null) {
labels = m_initial.get().getTaxonset().asStringList();
} else {
labels = new ArrayList<>();
createUnrecognizedTaxa = true;
sortNodesAlphabetically = true;
}
} else {
if (m_initial.get() != null) {
// try to pick up taxa from initial tree
final Tree tree = m_initial.get();
if (tree.m_taxonset.get() != null) {
labels = tree.m_taxonset.get().asStringList();
} else {
// m_sLabels = null;
}
} else {
// m_sLabels = null;
}
}
// m_bIsLabelledNewick = false;
}
final String newick = newickInput.get();
if (newick == null || newick.equals("")) {
// can happen while initalising Beauti
final Node dummy = new Node();
setRoot(dummy);
} else {
try {
setRoot(parseNewick(newickInput.get()));
} catch (ParseCancellationException e) {
throw new RuntimeException(
"TreeParser cannot make sense of the Newick string "
+ "provided. It gives the following clue:\n"
+ e.getMessage());
}
}
super.initAndValidate();
if (sortNodesAlphabetically) {
// correct for node ordering: ensure order is alphabetical
for (int i = 0; i < getNodeCount() && i < labels.size(); i++) {
m_nodes[i].setID(labels.get(i));
}
Node[] nodes = new Node[labels.size()];
System.arraycopy(m_nodes, 0, nodes, 0, labels.size());
Arrays.sort(nodes, (o1, o2) -> o1.getID().compareTo(o2.getID()));
for (int i = 0; i < labels.size(); i++) {
m_nodes[i] = nodes[i];
nodes[i].setNr(i);
}
}
if (m_initial.get() != null) processTraits(m_initial.get().m_traitList.get());
else processTraits(m_traitList.get());
if (timeTraitSet != null) {
adjustTreeNodeHeights(root);
} else if (adjustTipHeightsInput.get()) {
double treeLength = TreeUtils.getTreeLength(this, getRoot());
double extraTreeLength = 0.0;
double maxTipHeight = 0.0;
// all nodes should be at zero height if no date-trait is available
for (int i = 0; i < getLeafNodeCount(); i++) {
double height = getNode(i).getHeight();
if (maxTipHeight < height) {
maxTipHeight = height;
}
extraTreeLength += height;
getNode(i).setHeight(0);
}
double scaleFactor = (treeLength + extraTreeLength) / treeLength;
final double SCALE_FACTOR_THRESHOLD = 0.001;
// if the change in total tree length is more than 0.1% then give the user a warning!
if (scaleFactor > 1.0 + SCALE_FACTOR_THRESHOLD) {
DecimalFormat format = new DecimalFormat("#.##");
Log.info.println(
"WARNING: Adjust tip heights attribute set to 'true' in " + getClass().getSimpleName());
Log.info.println(
" has resulted in significant (>"
+ format.format(SCALE_FACTOR_THRESHOLD * 100.0)
+ "%) change in tree length.");
Log.info.println(
" Use "
+ adjustTipHeightsInput.getName()
+ "='false' to override this default.");
Log.info.printf(" original max tip age = %8.3f\n", maxTipHeight);
Log.info.printf(" new max tip age = %8.3f\n", 0.0);
Log.info.printf(" original tree length = %8.3f\n", treeLength);
Log.info.printf(" new tree length = %8.3f\n", treeLength + extraTreeLength);
Log.info.printf(" TL scale factor = %8.3f\n", scaleFactor);
}
}
if (m_taxonset.get() == null && labels != null && isLabelledNewickInput.get()) {
m_taxonset.setValue(new TaxonSet(Taxon.createTaxonList(labels)), this);
}
initStateNodes();
} // init