/**
* Parses Javadoc comment as DetailNode tree.
*
* @param javadocCommentAst DetailAST of Javadoc comment
* @return DetailNode tree of Javadoc comment
*/
public ParseStatus parseJavadocAsDetailNode(DetailAST javadocCommentAst) {
blockCommentLineNumber = javadocCommentAst.getLineNo();
final String javadocComment = JavadocUtils.getJavadocCommentContent(javadocCommentAst);
// Use a new error listener each time to be able to use
// one check instance for multiple files to be checked
// without getting side effects.
errorListener = new DescriptiveErrorListener();
// Log messages should have line number in scope of file,
// not in scope of Javadoc comment.
// Offset is line number of beginning of Javadoc comment.
errorListener.setOffset(javadocCommentAst.getLineNo() - 1);
final ParseStatus result = new ParseStatus();
try {
final ParseTree parseTree = parseJavadocAsParseTree(javadocComment);
final DetailNode tree = convertParseTreeToDetailNode(parseTree);
result.setTree(tree);
} catch (ParseCancellationException ex) {
// If syntax error occurs then message is printed by error listener
// and parser throws this runtime exception to stop parsing.
// Just stop processing current Javadoc comment.
ParseErrorMessage parseErrorMessage = errorListener.getErrorMessage();
// There are cases when antlr error listener does not handle syntax error
if (parseErrorMessage == null) {
parseErrorMessage =
new ParseErrorMessage(
javadocCommentAst.getLineNo(),
MSG_KEY_UNRECOGNIZED_ANTLR_ERROR,
javadocCommentAst.getColumnNo(),
ex.getMessage());
}
result.setParseErrorMessage(parseErrorMessage);
}
return result;
}
/** 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